Biological Opinion for the Long-Term Operation of the CVP and SWP Endangered Species Act Section 7(a)(2) Biological Opinion Reinitiation of Consultation on the Long-Term Operation ofthe Central Valley Project and the State Water Project NMFS Consultation Number: WCR-2019-11484 ESA-Listed Species Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) Central Valley sprmg-run Chinook salmon (0. tshawytscha) California Central Valley steelhead (0. mykiss) Southern Distinct Population Segment of North American green sturgeon (Acipenser medirostris) Southern Resident killer whale ( Orcinus orca) Action Agencies: U.S. BureaU! of Reclamation Af£ect ed Spectes . and NMFS' D etermma . fIOns: Status Is Action Is Action Is Action Likely to Likely To Likely to Adversely Jeopardize Adversely Affect the Species? Affect Species? Critical Habitat? Endangered Yes Yes Yes Is Action Likely To Destroy or Adversely Modify Critical Habitat? Yes Threatened Yes Yes Yes Yes Threatened Yes Yes Yes Yes Threatened Yes No Yes No Endangered Yes Yes NIA NIA Consultation Conducted By: National Marine Fisheries Service, West Coast Region Issued By: Chris Oliver Assistant Administrator for NOAA Fisheries Date: July 1, 2019 1 Biological Opinion for the Long-Term Operation of the CVP and SWP TABLE OF CONTENTS LIST OF ACRONYMS .................................................................................................................6 1. IN'TRODUCTION ..............................................................................................................] 0 1.1 1.2 1.3 1.4 1.5 2 Background ............................................................................................................. 10 Coordinated Operations Agreement ...................................................................... 10 Key Consultation Considerations ......................................................................... .11 1.3.1 Trinity RiverDivision ................................................................................ 11 1.3.2 ESA Consultation on CVP and SWP Hatcheries.......................................! I 1.3 .3 ESA Consultation Linkage to the Operation of Oroville Dam ................. .11 1.3 .4 Individual Contracts except to Sacramento River Settlement Contractors 11 1.3.5 Non-Discretionary Contracts ..................................................................... 12 1.3.6 Peer Review ofNMFS Draft CVP/SWP Operations Opinion ................... 12 1.3. 7 "Not Consulted On" ................................................................................... 13 1.3.8 Without Action Scenario............................................................................ 13 1.3.9 Operations with Shasta Dam Raise ............................................................ 14 1.3.10 Treatment ofCV Spring-Run Chinook Salmon in the San Joaquin River Restoration Program .................................................................................. 14 1.3.11 White House Memorandum on "Promoting the Reliable Supply and Delivery ofWater in the West" ................................................................ .15 1.3.12 Water Infrastructure Improvement for the Nation Act .............................. 15 1.3.13 Term ofthe Opinion ................................................................................... 16 Consultation History .............................................................................................. 16 Proposed Federal Action ........................................................................................20 1.5.1 Interrelated or Interdependent Actions ......................................................23 ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT ........................................................................................................24 2.1 2.2 Analytical Approach ..............................................................................................24 2.1.1 Introduction ................................................................................................24 2.1 .2 Legal and Policy Framework .....................................................................26 2.1.3 Overview of the Approach and Conceptual Models .................................. 30 2.1.4 Evidence Available for the Analysis .......................................................... 51 2.1.5 Integrating the Effects ................................................................................ 55 2.1.6 Presentation of the Analysis in this Opinion ............................................. 56 Range-wide Status of the Species and Critical Habitat ......................................... 57 2.2. 1 Sacramento River Winter-run Chinook Salmon ........................................ 58 2.2.2 Critical Habitat and Physical or Biological Features for Sacramento River Winter-run Chinook Salmon ...................................................................... 60 2 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.2.3 2.2.4 2.3 2.4 2.5 2.6 2.7 Central Valley Spring-run Chinook Salmon .............................................. 61 Critical Habitat and Physical or Biological Features for Central Valley Spring-run Chinook Salmon ...................................................................... 64 2.2.5 California Central Valley Steelhead Distinct Population Segment ........... 64 2.2.6 Critical Habitat and Physical or Biological Features for California Central Valley Steelhead ........................................................................................ 67 2.2.7 Southern Distinct Population Segment ofNorth American Green Sturgeon ...................................................................................................... 67 2.2.8 Critical Habitat Physical or Biological Features for Southern Distinct Population Segment Green Sturgeon ......................................................... 69 2.2.9 Southern Resident Killer Whale Distinct Population Segment ................. 70 Action Area ............................................................................................................. 72 Environmental Baseline ......................................................................................... 72 2.4.1 Landscape Scale Factors Affecting Listed Species in the Central Valley. 73 2.4.2 Other Factors Affecting Listed Fish Species and Critical Habitat in the Action Area ................................................................................................ 83 2.4.3 Sacramento River Winter-run Chinook Salmon ...................................... 101 2.4.4 Central Valley Spring-run Chinook Salmon and California Central Valley Steelhead ................................................................................................... 105 2.4.5 sDPS North American Green Sturgeon ................................................... 112 2.4.6 Importance of the Action Area for the Survival and Recovery of Listed Fish Species ............................................................................................. 116 2.4. 7 Southern Resident Killer Whale .............................................................. 117 Effects of the Action on the Species .................................................................... 127 2.5.1 Stressors and Species Response ............................................................... 129 2.5.2 Upper Sacramento/Shasta Division ......................................................... 155 2.5.3 Trinity River Division (Clear Creek and Spring Creek Debris Dam) ..... 246 2.5.4 American River Division ......................................................................... 288 2.5.5 Bay-Delta Division .................................................................................. 321 2.5.6 Stanislaus River (East Side Division) ...................................................... 537 2.5.7 San Joaquin River (East Side Division) ................................................... 584 2.5.8 Effects of the Action on Southern Resident Killer Whales ..................... 602 2.5.9 LifeCycle Models..................................................................................... 629 2.5.10 Climate Change ........................................................................................ 645 Effects of the Action on Critical Habitat ............................................................. 647 2.6.1 Physical and Biological Features of Listed Central Valley Species ........ 647 2.6.2 Upper Sacramento/Shasta Division ......................................................... 650 2.6.3 Trinity River Division (Clear Creek and Spring Creek Debris Dam) ..... 657 2.6.4 American River Division ......................................................................... 663 2.6.5 Bay-Delta Division .................................................................................. 664 2.6.6 Stanislaus River (East Side Division) ............ .......................................... 682 2.6.7 San Joaquin River (East Side Division) ................................................... 684 Cumulative Effects. .............................................................................................. 685 3 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.7.1 2. 7.2 2.7.3 2.7.4 2.7.5 2.7.6 2.8 2.9 2.1 0 2.1 1 2. 12 2.13 3 DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW ......................................................................................................................... ! 047 3.1 3.2 3.3 4 Unscreened WaterDiversions ..................................................................685 Agriculturall Practices ............................................................................... 686 Wastewater Treatment Plants .................................................................. 686 Increased Urbanization ............................................................................687 Recreational Activities in the Region ...................................................... 688 Changes in Location, Volume, Timing, and Method ofDelivery for NonCVP/SWP Diversions .............................................................................. 688 2.7.7 Activities within the Nearshore Pacific Ocean ........................................ 689 2.7.8 Other Activities ........................................................................................ 689 Integration and Synthesis ..................................................................................... 690 2.8.1 Sacramento River Winter-run Chinook Salmon ......................................691 2.8.2 Sacramento River Winter-run Chinook Salmon Critical Habitat ............ 738 2.8.3 Central Valley Spring-run Chinook Salmon ............................................751 2.8.4 Central Valley Spring-Run Chinook Salmond Critical Habitat............... 795 2.8.5 CCV Steelhead ......................................................................................... 814 2.8.6 CCV Steelhead Critical Habitat.. ............................................................. 869 2.8.7 Green Sturgeon ........................................................................................ 896 2.8.8 Green Sturgeon Critical Habitat.. ............................................................. 927 2.8.9 Southern Resident Killer Whale .............................................................. 935 Conclusion ............................................................................................................940 Reasonable and Prudent Alternatives .................................................................. 941 2.10.1 Organization ofthe RPA ..........................................................................943 2.10.2 RPA Consistency with the Proposed Action ........................................... 956 2.10.3 Consistency with the Scope of the Federal Agency's Legal Authority and Jurisdiction, that is Economically and Technologically Feasible ............ 957 2.10.4 Avoids the Likelihood of Jeopardizing the Continued Existence of Listed Species or Resulting in the Destruction or Adverse Modification of Critical Habitat ......................................................................................... 958 Incidental Take Statement.. .................................................................................. 966 2.11.1 Amount or Extent of Take ....................................................................... 968 2.1 1.2 Effect ofthe Take ........................ ........................................................... 1029 2.11.3 Reasonable and Prudent Measures........................................................ .1 029 2.11.4 Terms and Conditions ............................................................................ 1030 Conservation Recommendations ....................................................................... 1042 Reinitiation of Consultation ............................................................................... 1046 Utility .................................................................................................................. 1047 Integrity ................. ............................................................................................. 1047 Objectivity ........................................................................................................... l047 REFERENCES ...............................................................................................................1048 4 Biological Opinion for the Long-Term Operation of the CVP and SWP 5 APPENDICES ................................................................................................................ 1123 Appendix AI - Reinitiation of Consultation on the Coordinated Long-Term Operation of the Central Valley Project and State Water Project Biological Assessment, Received: February 5, 2019 Appendix A2 - Reinitiation of Consultation on the Coordinated Long-Term Operation of the Central Valley Project and State Water Project Proposed Action, Received: April 30, 2019 Appendix A3 - Reinitiation of Consultation on the Coordinated Long-Term Operation of the Central Valley Project and State Water Project Proposed Action, Received: June 14, 2019 Appendix A4 - Draft Sacramento River Settlement Contractor Resolution and Exhibits Appendix B - Range-wide Status of the Species and Critical Habitat Appendix C- U.S. Fish and Wildlife Service Actions at Federal Fish Hatcheries Appendix D - Delta Passage Model (DPM), Interactive Object-Oriented Simulation (lOS), and SALMOD Model Documentation Appendix E - Reclamation Salmon Mortality Model Documentation Appendix F - Methods for SIT Model Floodplain Habitat Analyses for the Rivers and Bypasses Included in the ROC on LTO Analyses Appendix G- Salvage Density Model Documentation Appendix H - Model Description for the Sacramento River Winter-run Chinook Salmon Life Cycle Model Appendix I - Selected Delta-Related References Relevant to Water Project-Related Effects in the South Delta Appendix J - Delta Performance Metrics: Cumulative and Annual Loss Thresholds Appendix K-New Melones Stepped Release Plan Daily Hydrographs for Critical, Dry, Below Normal, Above Normal and Wet Year Types Appendix L - Estimate of Change in Abundance of Central Valley Chinook Salmon Available to Southern Resident Killer Whales under the Proposed Action Appendix M - Critical Habitat Maps 5 Biological Opinion for the Long-Term Operation of the CVP and SWP LIST OF ACRONYMS ACID AFSP AR4 AR5 ARG BA Bank Banks BMP BSPP CAMT CCC CCF CCR CCV CCWD CDFG CDFW CEQ CESA cfs CHTR CMIP3 CNFH COA cos CRR cv CVP CVPIA CWP CWT 7DADM DAT DCC DDT Delta DIDSON Anderson-Cottonwood Irrigation District Anadromous Fish Screen Program Fourth Assessment Report Fifth Assessment Report American River Group Biological Assessment Liberty Island Conservation Bank Harvey 0. Banks Pumping Plant best management practices Barker Slough Pumping Plant Collaborative Adaptive Management Team Central California Coast Clifton Court Forebay Sacramento River above Clear Creek Gaging Station California Central Valley Contra Costa Water District California Department of Fish and Game California Department of Fish and Wildlife Council on Environmental Quality California Endangered Species Act cubic feet per second Collection, Hauling, Transport, Release Coupled Model Intercomparison Project Coleman National Fish Hatchery Coordinated Operations Agreement Current Operations Scenario cohort replacement rate Central Valley Central Valley Project Central Valley Project Improvement Act Cold Water Pool coded-wire tag 7-day average daily maxima Daily Average Temperature Delta Cross Channel dDchlorodiphenyltrichloroethane Sacramento-San Joaquin Delta Dual-frequency identification sonar 6 Biological Opinion for the Long-Term Operation of the CVP and SWP DO DOl DPM DPS DQA DRERIP DWR DWSC EBMUD EIS EFH EOS EPA ePTM ESA ESU FERC FL FRFH GCID GSI HGMP HORB IGO IPCC lOS ITS JFP JPE KLRC KWK LSNFH LTO LWD LWM M&I MAF mrn MOU Dissolved oxygen Department of Interior Delta Passage Model Distinct population segment Data Quality Act Delta Regional Ecosystem Restoration Implementation Plan California Department of Water Resources Deep Water Ship Channel East Bay Municipal Utility District Environmental Impact Statement Essential Fiish Habitat End of September Environmental Protection Agency enhanced particle tracking model Endangered Species Act Evolutionarily significant unit Federal Energy Regulatory Commission Fork length Feather River Fish Hatchery Glenn Colusa Irrigation District Genetic Stock Information Hatchery Genetic Management Plan Head of Old River Barrier Igo stream gaging station Intergovernmental Panel on Climate Change Interactive Object-Oriented Simulation incidental take statement Joint Federal Project Juvenile production estimate Knights Landing Ridge Cut Keswick Gauge Livingston Stone National Fish Hatchery Long-term operations Large woody debris Large woody material Municipal and Industrial Million acre-feet millimeter Memorandum of Understanding 7 Biological Opinion for the Long-Term Operation of the CVP and SWP MSA Napa County FC&WCD NBA NCO NERC NFH NMFS NMFS 2009 Opinion NTU OHWL OMR Opinjon OTC PA PA component PAHs PBF PCBs PCE PYA PWA RBDD RCP Reclamation RK RM ROC on LTO ROConLTOBA ROD RPA RPM RST RWQCB SAIL SCWD Magnuson-Stevens Fishery Conservation and Management Act Napa County Flood Contral and Water Conservation District North Bay Aqueduct Not Consulted On North American Electric Reliability National Fish Hatchery National Marine Fisheries Service NMFS' June 4, 2009 biological and conference opinion on the Central Valley Project and State Water Project Nephelometric Turbidity Unit Ordinary high water line Old and Middle River Biological Opinion Once Through Cooling Proposed Action An individual element of the Proposed Action polycyclic aromatic hydrocarbons Physical or biological features Polychlorinated biphenyls Primary Constituent Elements Population viability analysis Public Water Agency Red Bluff Diversion Dam Representative Concentration Pathway U.S. Bureau of Reclamation River kilometer River Mile Reinjtiation of Consultation on Long-Term Operations Reclamation's 2019 BA for reinitiation Record of Decision Reasonable and Prudent Alternative Reasonable and Prudent Measures Rotary screw trap Regional Water Quality Control Board Salmon and Sturgeon Assessment of Indicators by Life stage Solano County Water District 8 Biological Opinion for the Long-Term Operation of the CVP and SWP SDFPF sDPS SGMA SI SIT SJRRP SMSCG SONCC SRA SRKW SRTTG SRWTP SWE SWFSC SWP SWRCB SWRI TAF TFCf TCD TCP TRD TRT USFS USFWS VSP WCVI WDR WOA WRLCM WRO WUA YOY Skinner Delta Fish Protection Facility Southern D-istinct Population Segment California Sustainable Groundwater Management Act Sacramento Index Science Integration Team San Joaquin River Restoration Program Suisun Marsh Salinity Control Gates Southern Oregon/Northern California Coast Shaded Riparian Aquatic Southern Resident Killer Whale Sacramento River Temperature Task Group Sacramento Regional Wastewater Treatment Plant Snow Water Equivalents Southwest Fisheries Science Center State Water Project State Water Resources Control Board Surface Water Resources, Inc. Thousand acre-feet Tracy Fish Collection Facility Temperature Control Device Temperature compliance point Trinity River Division Technical Review Team United States Forest Service United States Fish and Wildlife Service Viable salmonid population West Coast Vancouver Island Waste Discharge Requirements Without action Winter-run Chinook Salmon Life Cycle Model Water rights order weighted usable area Young-of-the-year 9 Biological Opinion for the Long-Term Operation of the CVP and SWP 1 INTRODUCTION This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below. 1.1 Background National Oceanic and Atmospheric Administration's (NOAA) National Marine Fisheries Service (NMFS) prepared the biological opinion (Opinion) and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at 50 CFR Part 402. We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act (DQA) (section 515 ofthe Treasury and General Government Appropriations Act for Fiscal Year 2001, Public Law 106-554). 1.2 Coordinated Operations Agreement In November 1986, the United States, through the Bureau of Reclamation (Reclamation), and the California Department of Water Resources (DWR) signed the Coordinated Operations Agreement (COA), which defines the rights and responsibilities ofthe Central Valley Project and State Water Project (CVP/SWP) with respect to in-basin water needs and provides a mechanism to account for those rights and responsibilities. Congress, through Public Law 99-546, authorized and directed the Secretary of the Interior to execute and implement the COA. Under the COA, Reclamation and DWR agree to operate the CVP and SWP, respectively, under balanced conditions in a manner that meets Sacramento Valley and Delta needs while maintaining their respective water supplies, as identified in the COA. "Balanced conditions" are defined as periods when the CVP and SWP agree that releases from upstream reservoirs, plus unregulated flow, approximately equal water supply needed to meet Sacramento Valley in-basin uses and CVP/SWP exports. The COA is the Federal nexus for ESA section 7 consultation on operations of the SWP. In this Reinitiation of Consultation on Long-Term Operations (ROC on LTO), DWR is considered an applicant. In 2018, Reclamation and DWR modified four key elements of the COA to address changes since it was originally signed: (1) im-basin uses; (2) export restrictions; (3) CVP use of Banks Pumping Plant up to 195,000 acre-feet per year; and (4) the periodic review. Full details are provided in the ROC on LTO Biological Assessment (BA), Appendix A, pages A-127 to A-130. COA sharing percentages for meeting Sacramento Valley in-basin uses now vary from 80 percent responsibility of the United States and 20 percent responsibility of the State of California in wet year types to 60 percent responsibility of the United States and 40 percent responsibility of the State of California in critical year types. In a dry or critical year following two dry or critical years, the United States and State will meet to discuss additional changes to the percentage sharing of responsibility to meet in-basin use. When exports are constrained and the Delta is in balanced conditions, Reclamation may pump up to 65 percent of the allowable total exports with DWR pumping the remaining capacity. In excess conditions, these percentages change to 60 percent United States and 40 percent State. 10 Biological Opinion for the Long-Term Operation of the CVP and SWP 1.3 1.3.1 Key Consultation Considerations Trinity River Division Although the Trinity River Division (TRD) is part of the Central Valley Project, in its April30, 2019, revised BA (Appendix A2), Reclamation removed all action components associated with the Trinity River portion of the TRD. The remaining PA components of the TRD are associated with transbasin diversions into Whiskeytown Reservoir. As a result, NMFS did not analyze any aspects of the proposed action on the Trinity and Klamath rivers, or their associated listed species (i.e., Pacific eulachon, Southern Oregon/Northern California Coast coho salmon) and designated critical habitats. Neither was production of currently-unlisted Upper Klamath-Trinity River Chinook salmon evaluated as it pertains to Chinook salmon availability as prey for Southern Resident killer whales (SRKW). 1.3.2 ESA Consultation on CV!P and SWP Hatcheries CVP and SWP hatcheries within the Central Valley include the Livingston Stone National Fish Hatchery (LSNFH), Coleman National Fish Hatchery (CNFH), Feather River Fish Hatchery (FRFH), and Nimbus Fish Hatchery. Since production from these hatcheries are to mitigate lost habitat from the construction of CVP and SWP dams, which are components ofthe environmental baseliine, the production from these hatcheries is also included in the environmental baseline. There is one exception to the abov,e consultation consideration on CVP hatcheries. Reclamation included in its PA that it will complete a Hatchery Genetic Management Plan (HGMP) for steelhead and a hatchery management plan for fall-run Chinook salmon for Nimbus Fish Hatchery. Completing an IIGMP is a process that will begin when a draft is sent to NMFS for review and to begin consultation. In this Opinion, we consider the effects from the HGMP at the Framework-level. 1.3.3 ESA Consultation Linkage to the Operation of Oroville Dam The Oroville Complex (Oroville Dam and related facilities, including the FRFH) is part of the SWP. DWR has been operating the Oroville Complex under a Federal Energy Regulatory Commission (FERC) license and is currently undergoing a relicensing process with FERC (FERC Project No. 2100-134). The FERC license expired in January 2007, and until a new license is issued, DWR operates to the existing FERC license. On December 5, 2016, NMFS completed the section 7 consultation and issued a biological opinion to FERC regarding the effects of relicensing the Oroville Complex for 50 years. That biological opinion analyzes the effects of the proposed relicensing of the Oroville Facilities in the Feather River and the effects of FRFH salmonid strays in the Sacramento River watershed. Because the effects of the Oroville Complex were considered in the biological opinion to FERC, the effects of operation of Oroville Dam on listed fish within the Feather River are considered in the environmental baseline for this consultation. 1.3.4 Individual Contracts except to Sacramento River Settlement Contractors This consultation addresses the long-term operations of the CVP and SWP, and does not satisfy Reclamation's ESA section 7(a)(2) obligations for issuance of individual water supply contracts, 11 Biological Opinion for the Long-Term Operation of the CVP and SWP except to the Sacramento River Settlement Contractors. Reclamation should consult with NMFS separately on their issuance of individual contracts. The analysis of effects of the proposed action, however, assumes water deliveries under the contracts, as described and modeled in the BA. NMFS requests that by June 17, 2020, Reclamation provide written notification to NMFS and the State Water Resources Control Board (SWRCB) of any contract that it believes creates a nondiscretionary obligation to deliver water, including the basis for this determination and the quantity of nondiscretionary water delivery required by the contract. Any incidental take due to delivery of water to such a contractor (except Sacramento River Settlement Contractors) is not exempt from the ESA section 9 take prohibition in this Opinion. 1.3.5 Non-Discretionary Contracts Reclamation proposes to operate the CVP (and DWR for the SWP) to deliver water under the terms of all existing contracts (but not execute any new contracts or amend any existing contracts as part ofthis consultation) up to full contract amounts, which includes the impacts of maximum water deliveries and diversions under the terms of existing contracts and agreements, including timing and allocation (see ROC on LTO BA Section 4.4 CVP Water Contracts). The contracts include water service and water repayment contracts, as well as settlement, exchange, and refuge contracts. In addition, it includes water delivery through temporary, not to exceed 1 year, "Section 215 Contracts," when there are surplus flood flows, and the conveyance of non-CVP (which includes SWP) water when there is excess capacity available in CVP facilities (pursuant to the Warren Act). Finally, Reclamation proposes to operate the CVP to meet its obligations to deliver water to senior water right holders who receivedl water prior to construction of the CVP, to wildlife refuge areas identified in the CVPIA, and to water service contractors. 1.3.6 Peer Review of NMFS Draft CVP/SWP Operations Opinion NMFS sought peer reviews of its draft ROC on LTO Opinion through a contract with Anchor QEA. Three reviewers, Dr. Dave Hankin (Professor Emeritus, Humboldt State University, Dr. Kenneth Rose (Professor, University of Maryland Center for Environmental Science), and Dr. John Skalski (Professor, School of Aquatic and Fishery Sciences, University of Washington), were selected from a pool of 33 potential reviewers, based on availability, knowledge, and experience. The panel reviewed the Analytical Approach through Effects sections ofthe draft opinion for all ESA-listed species and their critical habitats. The reviewers received relevant background information and supplemental materials to consider in their reviews. NMFS was available for a conference call during the review period to respond to questions or address clarification needs during the reviews. Reviewers were expected to convene at least one conference call to discuss major findings and identify and attempt to rectify any conflicting guidance. As a result of the Opinion deadline extension to July I , 2019 (see Section 1.4.10) and the resulting revised/delayed period of performance, and the daunting amount of materials to be reviewed in the short review period, on June 9, 2019, Dr. Hankin informed Anchor QEA that he would not be able to continue on with the review. On June 14,2019, the peer reviewers issued their individual reports and findings to Anchor QEA and NMFS, according to the format provided by the hiring contractor. Each of the peer review 12 Biological Opinion for the Long-Term Operation of the CVP and SWP reports had constructive recommendations towards the development of a more scientifically robust final Opinion. However, in general, all of the peer reviewers and their reports acknowledged the incredibly complex proposed action, and that NMFS applied the best available information in its development of the draft Opinion. This Opinion, and its supporting administrative record, considered and/or incorporated all of the substantive peer review recommendations, as appropriate. 1.3.7 "Not Consulted On" Table 4-6 of the ROC on LTO BA identifies each of the components of the proposed action for the subject consultation. Reclamation characterized completed consultations with existing biological opinions that address the effects of long-term operations and do not trigger reinitiation under this consultation are identified by "NCO" (Not Consulted On). Therefore, all components that are characterized as NCO were not considered as part of the proposed action nor effects of the action in this consultation. 1.3.8 Without Action Scenario The ROC on LTO BA, Environmental Baseline Section 3.3, describes a "without-action" (WOA) scenario that does not include any past or current CVP or SWP operations. Reclamation provided this WOA scenario that includes the existence of the dams and south Delta facilities, but does not include description of past or current operations ofthese facilities. This WOA scenario is a useful analytical tool to separate some of the effects related to the existence of CVP and SWP facilities and provides context for how these facilities have shaped the habitat conditions for species and critical habitat in the action area. The WOA scenario also provides a useful context for understanding that Reclamation and DWR exercise a broad range of discretion over the operations of the CVP and SWP. Specifically, the ROC on LTO BA describes the WOA scenano as: " ... in a consultation on an ongoing action, the without-action scenario cannot be defined by simply projecting the status quo into the future, because doing so would improperly include in the baseline the continued effects ofthe action under consultation. Instead, in a consultation on an ongoing action, such as operation ofthe CVP and SWP, the baseline analysis must project a future condition without the action. This allows for isolation of the effects ofthe action from the without-action scenario and, in turn, a determination of whether the action is likely to jeopardize listed species and/or destroy or adversely modify critical habitat. Thus, to provide a snapshot ofthe species' survival and recovery prospects without the proposed action, Reclamation is analyzing a without-action scenario. The without-action scenario entails no future operations of the CVP and SWP: in other words, no discretionary regulation offlows through the system, including, for example, storing and releasing water from reservoirs and delivering water otherwise required by contract. " In addition, through modeling, the ROC on LTO BA, Section 5.5 Effects ofthe Action, uses the WOA scenario in order to compare the effects of the PA against the WOA scenario. 13 Biological Opinion for the Long-Term Operation of the CVP and SWP As described in Section 2.4, of this Opinion, the environmental baseline includes the past and present impacts of all federal, state, or private actions and other human activities in the action area, the anticipated impacts of all proposed federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of state or private actions which are contemporaneous with the consultation in process (50 CFR 402.02 2007). In this Opinion, the effects ofpast CVP/SWP operations are also part of the environmental baseline. Effects of those actions have been analyzed through past consultation and contributed to the current condition of the species and critical habitat in the action area. Other past, present, and ongoing impacts of human and natural factors (including proposed Federal projects that have already undergone section 7 consultation) contributing to the current condition of the species and critical habitat in the action area are also included in the environmental baseline. It is important to note that for ESA section 7, each time the operations of the CVP and SWP are consulted on (e.g., 2004 and 2008/2009), the impacts of past and present operations of the CVP and SWP become part of the environmental baseline for subsequent consultations. The operations of the CVP and SWP over time is not one continuous Federal action in the context of ESA compliance. Rather, the CVP and SWP action described and analyzed in the 2004 biological opinion was discrete from the CVP and SWP action described and analyzed in 2008/2009, which again, is discrete from the proposed CVP and SWP action analyzed in this Opinion. In other words, each PA had specific components and operating criteria, and were therefore separate Federal actions requiring separate ESA section 7 consultations and analyses. 1.3.9 Operations with Shasta Dam Raise Reclamation has proposed to operate the CVP and Shasta Reservoir after the Shasta Dam raise construction has been completed (current estimate is 10 years for construction). Operations with the Shasta Dam raise was not modeled nor included in the ROC on LTO BA. However, Reclamation has stated that operations with Shasta Dam raise will not change from the modeling of operations without the Shasta Dam raise. Therefore, NMFS will also make the assumption in the effects of the action, that operations will not change with the Shasta Dam raise. One of the conditions of reinitiation of consultation in the interagency cooperation governing section 7 consultations (50 CFR 402.16) is '"If new information reveals effects of the action that may affect listed species or critical habitat in a manner or to an extent not previously considered." Therefore, NMFS has provided a specific reinitiation of consultation trigger in section 2.13 to address the potential that operations with the Shasta Dam raise result in effects to the listed species or critical habitat in a manner or to an extent not considered in this Opinion. 1.3.10 Treatment of CV Spring-Run Chinook Salmon in the San Joaquin River Restoration Program In 2013, NMFS designated a non-essential experimental population ofCV spring-run Chinook salmon for reintroduction to the San Joaquin River in accordance with section 1OG) of the ESA (78 FR 79622 2013). This designation allows for the release of listed CV spring-run Chinook salmon outside their current range as an experimental population; given that, the non-essential population is geographically separate from the threatened population ofthe same species and if lost, will not significantly impact the status of that speciies. In addition, ESA section 4(d) provides protective regulations including ESA section 9 take exceptions for activities preformed during otherwise lawful activities within the experimental population area. Any activities that 14 Biological Opinion for the Long-Term Operation of the CVP and SWP result in direct intentional take, harm, or activities that are illegal in nature are still subject to ESA section 9 provisions. The lOU) rule has allowed the San Joaquin River Restoration Program (SJRRP) to begin reintroduction efforts in the restoration area while still meeting the San Joaquin River Restoration Settlement Act's (Settlement Act) requirement of no more than de minimus water supply impacts to third parties. The Settlement Act states in section 10011(c)(3) that the reintroduction ofCV spring-run Chinook by the SJRRP w111 not impose more than de minimus water supply reductions, additional water storage releases, or bypass flows on unwilling third parties due to the reintroduction. Outside of the reintroduction area, CV spring-run Chinook salmon in the San Joaquin River or its tributaries downstream to Mossdale County Park in San Joaquin County will continue to be cover,e d by the same take prohibitions and exceptions applicable to nonexperimental populations, except when potential regulatory measures to address take would affect the de minimus conditions of the Settlement Act. Section 10011 (c) of the Settlement Act includes the Central Valley Project contractors outside of the Friant Unit and State Water Project in the definition of "third parties," and NMFS develops an annual technical memorandum to describe the accounting of any experimental non-essential CV spring-mn Chinook salmon during the operations of these facilities. That report can be found on the NMFS San Joaquin River Restoration website. 1.3.11 White House Memorandum on "Promoting the Reliable Supply and Delivery of Water in the West" On October 19, 2018, the White House issued a memorandum titled, "Promoting the Reliable Supply and Delivery of Water in the West". The key excerpts pertaining to this ROC on LTO consultation include: "Section 2(c)(ii): The Secretary of the Interior shall issue fmal biological assessments for the long-term coordinated operations of the Central Valley Project and the California State Water Project not later than January 31 , 2019. Section 2(c)(iii): The Secretary of the Interior and the Secretary of Commerce shall ensure the issuance of their respective final biological opinions for the long-term coordinated operations of the Central Valley Project and the California State Water Project within 135 days of the deadline provided in section 2(c)(ii) of this memorandum. To the extent practicable and consistent with law, these shall be joint opinions." The Council on Environmental Quality (CEQ) granted NMFS a 2-week extension to July 1, 2019, to issue a final Opinion. 1.3.12 Water Infrastructure Improvement for the Nation Act Section 4004 of the Water Infrastructure Improvement for the Nation Act of2016 requires the Secretary of Commerce to ensure "that any public water agency that contracts for the delivery of water from the Central Valley Project or the State Water Project that so requests shall "receive a copy of any draft biological opinion and have the opportunity to review that document and provide comment to the consulting agency through the action agency, which comments will be afforded due consideration during the consultation." The Analytical Approach through Effects sections were shared with the public water agencies (PWAs) through Reclamation on June 3, 15 Biological Opinion for the Long-Term Operation of the CVP and SWP 201 9. The PW As provided written comments on the draft biological opinion on June 14, 20 19, through Reclamation, which were afforded due consideration during the consultation. 1.3.13 Term of the Opinion This Opinion is effective through D ecember 31, 2030, and is subject to the reinitiation of consultation triggers in Section 2.13 and at 50 CFR 402. 16. However, if conditions past 2030 are similar to the analysis period, this opinion can remain in effect. 1.4 Consultation History On October 22, 2004, NMFS issued its Opinion on the proposed CVP/SWP operations (National Marine Fisheries Service 2004). On June 4, 2009, NMFS issued its Op inion and conference opinion on the proposed CVP/SWP operations (NMFS 2009 Opinion)(National Marine Fisheries Service 2009b), that superseded the 2004 opinion. Within the NMFS 2004 Opinion and the NMFS 2009 Opinion were consultation histories ranging from February 1991 to June 2004 and April2006 to January 2009, respectively, which are incorporated here by reference. Table 1.4-1 [Section 1.4 of ROC on LTO BA (Reclamation 2019)], provides a summary ofthe consultation history from February 1992 through January 2019. Table 1.4-1. Consult.ation History tabulated in ROC on LTO BA (Reclamation 2019) Da te Issuer Document Rationale for Consultation Su bject/ Species Finding February 1992 USSR Interim Central Valley Project Operations Criteria and Plan June 1993 NMFS. so Winter-Run listed in 1991 Winter-Run Chinook Salmon Jeopardy March 1995 USFWS BO Delta Smelt listed in March 1993; Splittail proposed in 1994 Delta Smelt and Splittail Non-Jeopardy June 2004 USSR SA Combined ESA species consultation in one assessment Winter-Run Chinook Salmon, Spring-Run Chinook Salmon, Steelhead, Coho Salmon, Delta Smelt Likely to Adversely Affect: Winter-run, Spring-run, CV Steelhead; May Affect/Not Likely to Adversely Affect: Coho, Delta Smelt July 2004 USFWS so Coordinate with combined NMFS ESA species consultation Delta Smelt Non-Jeopardy October 2004 NMFS. 80 Combined ESA species consultation Winter-Run Chinook Salmon, Spring-Run Chinook Salmon, Steelhead, Coho Salmon Non-Jeopardy May 2008 USSR SA Green Sturgeon was listed in 2006; Pelagic Organism Decline Winter-Run Chinook Salmon, Spring-Run Chinook Salmon, Adversely Affect: Delta Smelt; LAA: CV steelhead, Winter-run, Spring- OCAP 16 Biological Opinion for the Long-Term Operation of the CVP and SWP Date Issuer Document Rationale for Consultation Subject/ Species Finding Steelhead, Green Sturgeon, Coho Salmon, Delta Smelt run; Green Sturgeon; NLAA: Coho Salmon December 2008 USFWS BO Pelagic Organism Decline; conflicts with Sturgeon Delta Smelt Jeopardy June 2009 NMFS. BOand Conference Opinion Green Sturgeon listed in 2006 Winter-Run Chinook Salmon, Spring-Run Chinook Salmon, Steelhead, Green Sturgeon* Jeopardy and Adverse Mod January 20 19 USSR BA Drought; New Science; Declining status Winter-Run Chinook Salmon, Spring-Run Chinook Salmon, Steelhead, Green Sturgeon, Coho, Delta Smelt* See Effects Dete rmination in theBA *Southern Resident killer whales were also part of the consultations, but their critical habitat is not in the action area. On August 2, 2016, the Reclamation requested ESA section 7 reinitiation of consultation on the CVP/SWP, ROC on LTO based on new information related to multiple years of drought, recent data demonstrating extremely low listed-salmonid population levels for the endangered winterrun Chinook salmon, and new information available and expected to become available as a result of ongoing work through collaborative science processes. On August 17, 2016, NMFS responded, indicating that this type of operations consu]tation is most efficiently done with participation of multiple agencies, including Reclamation, DWR, California Department ofFish and Wildlife (CDFW), and the U.S. Fish and Wildlife Service (USFWS), along with NMFS (collectively "five agencies"). In addition, NMFS indicated staff resource constraints and inability to begin work on the ROC on LTO until the California WaterFix Opinion and the Shasta Reasonable and Prudent Alternative (RPA) adjustment efforts were completed. NMFS issued the California WaterFix Opinion to Reclamation and DWR on June 16, 2017, and issued a draft proposed Shasta RPA amendment to Reclamation on January 19, 2017. From February 2017 through June 2018, Reclamation convened a five agencies ROC on LTO Core Team, with biweekly meetings to work through various issues associated with the ROC on LTO, for example, duration ofthe proposed action, environmental baseline, and inclusion (or not) of operations associated with California WaterFix. The five agencies Core Team also developed background and process materials in preparation for brainstorming meetings. From June 2017 through January 2018, Reclamation led five-agency (plus watershed tribes and Western Area Power Administration representatives) brainstorming workshops within each CVP-controlled stream geographic area to help Reclamation develop National Environmental Protection Act alternatives for the reinitiation. 17 Biological Opinion for the Long-Term Operation of the CVP and SWP In November 2017, Reclamation advised the ROC on LTO Core Team of the Department of the Interior's (DOI) direction to pursue 3 tracks to completing the reinitiated consultation. In the fall of 2018, Reclamation acknowledged that the actions proposed in Track 1 had substantial controversy, likely would not result in "not likely to adversely affect" determinations, and ESA compliance likely would not be completed within calendar year 2018. Reclamation, therefore, did not pursue Track 1 for ESA consultation and compliance. Because of a substantial effort towards Track 1, not much effort was spent on Track 2. Reclamation subsequently decided that Tracks 2 and 3 would be combined into the ROC on LTO. On October 19,2018, the White House issued a memorandum titled, "Promoting the Reliable Supply and Delivery of Water in the West". The key excerpts pertaining to the CVP/ SWP operations consultation include: "Section 2(c)(ii): The Secretary ofthe Interior shall issue.final biological assessments for the long-term coordinated operations ofthe Central Valley Project and the California State Water Project not later than January 31, 2019. Section 2(c)(iii): The Secretary ofthe Interior and the Secretary of Commerce shall ensure the issuance oftheir respective final biological opinions for the long-term coordinated operations ofthe Central Valley Project and the California State Water Project within 135 days ofthe deadline provided in section 2(c)(ii) of this memorandum. To the extent practicable and consistent with law, these shall be joint opinions. " Throughout November and December, 2018, NMFS provided Reclamation with technical assistance towards their development of a BA for the ROC on LTO. NMFS was affected by the partial Federal government shutdown from December 22, 2018, through January 25, 2019, precluding any further technical assistance from NMFS staff, including the opportunity to review much of the draft BA effects analyses prior to finalization on January 31,2019. On January 31,2019, Reclamation submitted a letter, transmitting an enclosed BA to NMFS, requesting the ROC on LTO and its effects on: • • • • Sacramento River winter-run Chinook salmon (Oncorhy nchus tshawytscha) and their designated critical habitat, Central Valley spring-run Chinook salmon (0. tshawytscha) and their designated critical habitat, California Central Valley (CCV) steelhead (0. mykiss) and their designated critical habitat, Southern Distinct Population Segment (sDPS) of North American green sturgeon (Acipenser medirostris) and their designated critical habitat, • Southern Oregon/Northern California Coast (SONCC) coho salmon (0. kisutch) and their designated critical habitat, • Southern DPS of eulachon (Thaleichthys pacificus) and their designated critical habitat, and, 18 Biological Opinion for the Long-Term Operation of the CVP and SWP • Southern Resident killer whales (SRKW) (Orcinus orca). Reclamation made "no effect" determinations on Central California Coast (CCC) steelhead ( 0. my kiss) and their designated critical habitat. Therefore, is not requesting initiation of section 7 consultation for CCC steelhead or their designated critical habitat. In addition, Reclamation made the following effect determinations for essential fish habitats (EFH): • Would adversely affect o o • Pacific Coast Salmon Pacific Coast Groundfish Not likely to adversely affect: o Coastal Pelagic Species Therefore, Reclamation also requested EFH consultation pursuant to the Magnuson-Stevens Fishery Conservation and Management Act of 1976. On February 5, 2019, Reclamation informed DWR, CDFW, USFWS, and NMFS that a final version of the CVP/SWP Operations BA had been posted to Reclamation's website. From February 5 to F ebruary 21 , 2019, NMFS completed its initial rev iew ofthe final BA. On February 22, 2019, NMFS sent to the five agencies a list ofthe most important comments associated with the proposed action and effects ofthe action. On February 22,2019, the five agencies convened an all-day meeting to discuss the most important issues in the BA associated with Shasta Reservoir and Delta operations, in particular. Follow-up meetings for the Trinity River, Clear Creek, Feather River, American River, the Delta, and the Stanislaus River were scheduled for the week of February 27, 2019. Follow-up meetings for storage management and allocations, and seas onal temperature management modeling, were scheduled for March 5 and March 12, 2019, respectively. NMFS requested and Reclamation provided results for the following: ( 1) Additional DSM2HYDRO analyses, (2) CalSimll model, (3) HEC-5Q temperature model, (4) RBM-10 temperature model, (5) Sacramento River egg mortality models (both Anderson and Martin), (6) Delta Passage Model, (7) lOS model, (8) Central Valley Project Improvement Act (CVPIA) Science Integration Team (SIT) survival relationships, (9) Salvage-Density Method, (10) SALMOD, (11) Weighted usable area analyses, (12) Trinity Stream Salmonid Simulator model, and (13) Coho salmon habitat modeling. Reclamation submitted to NMFS the last of the model results on April 5, 2019. On March 25, 2019, Reclamation withdrew all actions associated with the Trinity River from their proposed action (e.g., seasonal operations, Grass Valley Creek, and lower Klamath fall flow augmentation). The only components remaining within the Trinity River Division in the proposed action were operations associated with Whiskeytown Reservoir and Clear Creek, and the Spring Creek Debris Dam. On April 1, 2019, in preparation for a water user forum meeting, Reclamation distributed via email a revised PA that included track changes compared to the February 5, 2019, version. On April19, 2019, Reclamation informed NMFS that the ROC on LTO BA and Appendix E was 19 Biological Opinion for the Long-Term Operation of the CVP and SWP updated on Reclamation's website. NMFS requested a track changes version of the BA, as we did not have time to compare the two documents to identify the changes. On April 30, 2019, Reclamation sent NMFS an e-mail, transmitting the April19, 2019, revised PAin track changes, compared to the February 5, 2019, version of the PA (Appendix A2). Revisions include inclusion (or removal) of P A components (e.g., revised PA Table 4-6), clarification of P A components (e.g., 4 .1 0.1.4 Fall and Winter Refill and Redd Maintenance), and more complete description of PA components (e.g., Section 4.10.5.8 Clifton Court Aquatic Weed and Algal Bloom Management). On May 16,2019, CEQ granted NMFS a 2-week extension to July 1, 2019, to issue a final biological opinion. In the interest of meeting expectations within the White House's October 19, 2018, memorandum on "Promoting the Reliable Supply and Delivery of Water in the West," from May 9 to May 23, NMFS distributed various sections of the draft biological opinion to NOAA General Counsel and the Department of the Interior's (DOl) Solicitors, including the Status of the Species and Critical Habitats, Environmental Baseline, effects of the action on listed species and designated critical habitats, and integration and synthesis. From May 14 through May 24, DOl Solicitors provided comments back on the sections. On May 21, 22, and 24, NMFS, Reclamation, and the USFWS met to talk through Reclamation's main comments, especially those that pertained to its PA. Reclamation offered clarifications during the meetings, that were later reflected in the deconstructed action sections within each division in the effects section. In addition, on May 29, 2019, NMFS received a more detailed description of the PA component Spring Creek Debris Dam. Meetings continued through June 11 to work through performance measures for the Shasta Division, with the objective to develop and manage toward tier-based temperature-dependent egg mortality and total egg-to-fry survival levels with periodic independent reviews; performance measures for the Delta Division, with the objective to bound the loss of salmon and steelhead at the export facilities to not exceed loss levels over the past 10 years with periodic independent reviews; and other issues, including consideration of systemwide drought management plan to confer on actions necessary to minimize effects. Multiple drafts of sections of the Opinion were shared with the Department of the Interior from May 29 through June 21,2019. A final PA was issued to NMFS on June 14, 2019. 1.5 Proposed Federal Action "Action" means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02 2007). In this case, Reclamation, with DWR, have requested ROC on LTO of the CVP and SWP to maximize water supply delivery and optimize power generation consistent with applicable laws, contractual obligations, and agreements. It is also Reclamation's stated goal to increase operational flexibility by focusing on non-operational measures to avoid significant adverse effects, based on the conditions estimated to occur through 2030. The PA for this consultation is a "mixed programmatic" action as defined by 80 FR 26832 (20 15) because it includes some action components for which no additional authorization will be necessary, and others that are considered at a "framework-level". The components that require no additional authorization are analyzed in this Opinion, and exemption from take prohibitions is provided in the ITS of this Opinion. The other action components that are considered at a 20 Biological Opinion for the Long-Term Operation of the CVP and SWP framework-level are also analyzed in this Opinion, but with a broader scale of examination of the components' potential impacts on listed species and critical habitat. Exemption from take prohibitions for these components is not provided in the ITS of this Opinion. Once frameworklevel action components are further developed to provide sufficient detail for take determination, they will require additional ESA section 7 consultation before implementation; and this subsequent consultation will include an ITS for those components. Regardless of the timing ofthe individual action components, the operation ofthe CVP is coordinated with the SWP to achieve the intended project purposes according to CVPIA [Pub. L. No. 102-575, 106 Stat. 4706 (1992)]. The CVP and SWP are two major inter-basin water storage and delivery systems that capture, retain, release, and divert water primarily from the northern portion of the state for export south of the Sacramento-San Joaquin Delta (Delta). The CVP's major storage facilities are Shasta, Trinity, Folsom and New Melones reservoirs, while the SWP primarily relies on Lake Oroville. These upstream reservoirs are operated to provide water for the Delta, which can then be exported, either by the CVP through the Jones Pumping Plant, or by the SWP through the Harvey 0. Banks Pumping Plant (Banks), to be stored in the joint San Luis Reservoir. In addition, exported water can be delivered via either the Delta Mendota Canal (part ofCVP), or the California Aqueduct (part ofSWP). The continued, coordinated LTO of the CVP and SWP facilities (the PA subject of this Opinion) is described in detail in Chapter 4 ofthe ROC on LTO BA, as transmitted on January 31,2019, and uploaded onto Reclamation 's BayDelta Office website on February 5, 2019. Additional clarifications to the PA were provided by Reclamation and are included in the revised/supplemental PA transmitted to NMFS on April 30, 2019 (Appendix A2). Reclamation proposed a number of site-specific and programmatic components, which include three proposed implementation approaches: Core, Scheduling, and Collaborative Planning. "Core" actions are part of the Core Water Operations of the CVP and SWP. With "Scheduling" actions, agencies and water users provide recommendations to Reclamation on scheduling and shaping specific flow actions. With "Collaborative Planning" actions, agencies and water users work collaboratively to define, plan, and implement an action. Each component is organized according to watershed or river basin, but implemented in concert to achieve the comprehensive project goals. The PA consisted of the following components, which included a number of discrete action components over which Reclamation lacks discretionary authority or for which there is an existing biological opinion that covers the action. In subsequent sections, especially the effects of the action sections, NMFS describes the disposition of those PA components. • CVP/SWP-Wide: o o • Divert and store water consistent with obligations under water rights and decisions by the State Water Resources Control Board Shasta Critical Determinations and Allocations to Water Service and Water Repayment Contractors Upper Sacramento: o o o o Seasonal Operations Spring Pulse Flows Shasta Cold Water Pool Management Fall and Winter Refill and Redd Maintenance 21 Biological Opinion for the Long-Term Operation of the CVP and SWP o Operation of a Shasta Dam Raise o Rice Decomposition Smoothing o Spring Management of Spawning Locations o Cold Water Management Tools (e.g., Battle Creek Restoration, Intake Lowering near Wilkins Slough Shasta TCD Improvements) o Spawning and Rearing Habitat Restoration o Small Screen Program o Winter-run Conservation Hatchery Production o Adult Rescue o Juvenile Trap and Haul • Trinity/Clear Creek o Seasonal Operations o Whiskeytown Reservoir Operations o Clear Creek Minimum Flows o Clear Creek Geomorphic and Spring Attraction Pulse Flows o Spring Creek Debris Dam • American: o Seasonal Operations o 2017 Flow Management Standard Releases and "Planning Minimum" o American River Pulse Flows o Spawning and Rearing Habitat Restoration o Drought Temperature Facility Improvements • Stanislaus River: o o o o Seasonal Operations Stanislaus River Stepped Release Plan Stanislaus River Pulse Flows Alteration of Stanislaus DO Requirement o Spawning and Rearing Habitat Restoration o Temperature Management Study • San Joaquin o Lower San Joaquin River Habitat • Bay-Delta: o o o o o o o o o Seasonal Operations Minimum Export Rate Delta. Cross Channel Operations Agricultural Barriers Contra Costa Water District (CCWD) Rock Slough Operations North Bay Aqueduct (NBA) Water Transfers Clifton Court Aquatic Weed Removal Old and Middle River (OMR) Management 22 Biological Opinion for the Long-Term Operation of the CVP and SWP o Tracy Fish Collection Facility Operations o Skinner Fish Facility Operations o Delta. Smelt Habitat o Clifton Court Predator Management o San Joaquin Basin Steelhead Telemetry Study o Sacramento Deepwater Ship Channel Food Study o North Delta Food Subsidies/Colusa Basin Drain Study o Suisun Marsh Roaring River Distribution System Food Subsidies Study o Tidal Habitat Restoration (Complete 8,000 acres from 2008 biological opinion) o Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project o Predator Hot Spot Removal o Delta Cross Channel Gate Improvements o Tracy Fish Facility Improvements o Skinner Fish Facility Improvements o Small Screen Program During consultation, the Sacramento River Settlement Contractors drafted for vote A Resolution Regarding Salmon Recovery Projects in the Sacramento River Watershed, Actions Related to Shasta Reservoir Annual Operations, and Engagement in the Ongoing Collaborative Sacramento River Science Partnership Effort (Appendix A4). The Sacramento River Settlement Contractors, a California nonprofit mutual benefit corporation, consists of individuals and entities (collectively, SRS Contractors) that individually hold settlement agreements (the SRS Contracts) with the United States Bureau of Reclamation (Reclamation). The SRS Contractors consist of 31 members with an annual water supply of 1,974,324 acre feet. Reclamation operates Shasta Dam and Keswick Dam as part of the Central Valley Project and in accordance with the terms of the SRS Contracts. The draft SRS Contractors resolution includes three key actions that are integrated into the description of the proposed action in this opinion: 1. The SRS Contractors intend to meet and confer with Reclamation, NMFS, and other appropriate agencies in connection with Reclamation's operational decision-making for Shasta Reservoir annual operations during drier water years with operational conditions as described in the Tier 3 and Tier 4 scenarios. 2. The SRS Contractors intend to continue to participate in, and act as project champions for, similar types of future Recovery Program projects, subject to the availability of funding, regulatory approvals, acceptable regulatory assurances. 3. The SRS Contractors are committed to continue their active engagement and leadership in the ongoing collaborative Sacramento River Science Partnership effort. 1.5.1 Interrelated or Interdependent Actions "Interrelated actions" are those that are part of a larger action and depend on the larger action for their justification. "Interdependent actions" are those that have no independent utility apart from the action under consideration (50 CFR 402.02 2007). There are no interdependent or interrelated activities associated with the proposed Federal action. 23 Biological Opinion for the Long-Term Operation of the CVP and SWP 2 ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT The ESA establishes a national program for conserving threatened and endangered species of fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a)(2) of the ESA, each Federal agency must ensure that its actions arc not likely to jeopardize the continued existence of endangered or threatened species, or adversely modify or destroy their designated critical habitat. Per the requirements of the ESA, Federal action agencies consult with NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides an opinion stating how the agency's actions would affect listed species and their critical habitats. If incidental take is reasonably certain to occur, section 7(b)(4) requires NMFS to provide an ITS that specifies the impact of any incidental taking and includes non-discretionary reasonable and prudent measures (RPMs) and terms and conditions to minimize such impacts. 2.1 2.1.1 Analytical Approach Introduction This section describes the analytical approach used by NMFS to evaluate the likely effects of the PA on listed species under NMFS jurisdiction and critical habitat designated for those species. The approach is intended to ensure that NMFS comports with the requirements of the statute and regulations when conducting and presenting the analysis. This includes using the best scientific and commercial data available in formulating the Opinion. ESA section 7(a)(2) requires that the action agency "insure" that a PA "is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of [designated critical] habitat. ... " This Opinion includes both a jeopardy analysis and an adverse modification analysis. The jeopardy analysis relies upon the regulatory definition of"to jeopardize the continued existence of' a listed species, which is "to engage in an action that would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species" (50 CFR 402.02 2007). Therefore, the jeopardy analysis considers both survival and recovery of the species. This Opinion also relies on the regulatory defmition of" destruction or adverse modification," which means "a direct or indirect alteration that appreciably diminishes the value of critical habitat for the conservation of a listed species. Such alterations may include, but are not limited to, those that alter the physical or biological features essential to the conservation of a species or that preclude or significantly delay development of such features" (81 FR 7214 2016, 81 FR 7414 2016). The designations of critical habitat for some of the listed fish included in this consultation use the term "primary constituent elements" (PCE) or "essential features." The revised critical habitat regulations (81 FR 7414 2016) replace this term with physical or biological features (PBFs). The shift in terminology does not change the approach used in conducting a "destruction or adverse modification" analysis, which is the same regardless of whether the original designation identified PCEs, PBFs, or essential features. In this Opinion, NMFS uses the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat. 24 Biological Opinion for the Long-Term Operation of the CVP and SWP NMFS uses the following approach to determine whether a PA is likely to jeopardiz,e listed species or destroy, or adversely modify, critical habitat: • • • • • • • Identify the range-wide status of the species and critical habitat likely to be adversely affected by the P A. Describe the environmental baseline in the action area as defmed in the ESA implementing regulations (50 CFR 402.02). Analyze the effects of the P A on both species and their habitat using an "exposureresponse-risk" approach. Describe any cumulative effects in the action area. Integrate and synthesize the above factors as follows: (1) review the status of the species and critical habitat; and (2) add the effects of the action, the environmental baseline, and cumulative effects to assess the risk that the PA poses to species and critical habitat. Reach a conclusion about whether the PA is likely to jeopardize the continue existence of a listed species or result in the destruction or adverse modification of critical habitat. If necessary, suggest a reasonable and prudent alternative to the PA. The subsections of Section 2.1 outline the specific conceptual framework, key steps, assumptions, and professional judgment NMFS used to assess the effects of the action on listed species and critical habitat. Wherever possible, these subsections apply to all five listed species and associated designated critical habitats occurring in the action area. The listed species and critical habitat include the following: • • • • • Endangered Sacramento River winter-run Chinook salmon evolutionarily significant unit (ESU) (Oncorhynchus tshawytscha) and its designated critical habitat Threatened Central Valley (CV) spring-run Chinook salmon ESU (0. tshawytscha) and its designated critical habitat Threatened California Central Valley (CCV) steelhead distinct population segment (DPS) (0. mykiss) and its designated critical habitat Threatened sDPS ofNorth American green sturgeon (Acipenser medirostris) and its designated critical habitat Endangered Southern Resident killer whale DPS (Orcinus orca). The subsections of the analytical approach are as follows: • • • Section 2.1.2 describes some aspects ofthe legal and policy framework provided by the ESA, implementing regulations, case law, and policy guidance related to section 7 consultations that informs and/or directs our analytical approach. Section 2.1.3 gives a general overview ofhow NMFS conducts its section 7 analysis. It includes various conceptual models ofthe overa11 approach and specific features of the approach. It also includes information on tools that NMFS used in the analysis specific to this consultation. The section first describes the 1isted species analysis as it pertains to individual fish species and the physical, chemical, and biotic changes to the ecosystem caused by the PA. It then describes the critical habitat analysis. Section 2.1.4 discusses the evidence available for the analysis and related uncertainties. We also describe the assumptions made using the best available data together with professional ,expertise and judgment to bridge data gaps, which contributes to the analyses. 25 Biological Opinion for the Long-Term Operation of the CVP and SWP • • Section 2.1.5 diagrams the overall conceptual approach in the assessment to address integration of all available information and decision frameworks to support tihe assessment ofthe effects ofthe PA. Section 2.1.6 discusses the presentation of all analyses within this Opinion as a guide to locating results of specific analytical steps. NMFS has evaluated the PA for this consultation as a "mixed programmatic" action as defined by 50 CPR 402.02 because it includes some action components for which no additional authorization will be necessary and others that are considered at a framework-level. Components that require no additional authorization are analyzed in this Opinion and exemptions from take prohibitions provided in the incidental take statement of this Opinion. Action components that are considered at a framework-level are also analyzed in this Opinion, but with a broader scale of examination of the components' potential impacts on listed species and critical habitat. Exemption from take prohibitions are not provided for these components in the incidental take statement of this Opinion. Once framework-level action components are further developed and provide sufficient detail for take determination, they will require additional ESA section 7 consultation before implementation; this subsequent consultation will include an incidental take statement for those components. For components ofthe PA that lacked the specificity in description required to analyze a particular effect in detail, NMFS took a reasonably conservative approach to analyzing the range of effects that could result. This approach, paired with NMFS' identification of framework-level action components and the inclusion of additional analytical methods not used in the BA, could result in NMFS drawing different conclusions from our analaysis than the action agency's conclusions in the biological assessment. We identify the lines of evidence to support NMFS' conclusions in the Effects Analyses and Integration and Synthesis sections of this Opinion. 2.1.2 Legal and Policy Framework The ESA and its implementing regulations require NMFS to use the best scientific and commercial data available to complete formal consultations. However, NMFS is "'not required to support its finding that a significant risk exists with anything approaching scientific certainty"' San Luis & Delta-Mendota Water Auth. v. Jewell, 747 F.3d 581, 592 (9th Cir. 2014) (citations omitted). The final determination of whether or not the JPA is likely to jeopardize the species' continued existence or destroy or adversely modify its critical habitat will be the product of a multi-layered analytical approach in which many of the intermediate results have associated degrees of uncertainty. When considering the uncertainty of the data, analytical methods, and results, NMFS takes into account the underlying purposes of Section 7 of the ESA and employs the precautionary principle where appropriate. Consultations designed to allow Federal agencies to fulfill the requirements of section 7 of the ESA conclude with issuing a biological opinion or a concurrence letter. For biological opinions, section 7 of the ESA, implementing regulations (50 CPR 402.14), and associated guidance documents (USFWS and NMFS 1998 ESA Consultation Handbook) result in biological opinions to present the following: • • A description of the proposed Federal action A summary of the status of the affected species and its critical habitat 26 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • A summary of the environmental baseline within the action area as defmed in the ESA implementing regulations (50 CFR 402.02 ). A detailed analysis of the effects of the PA on the affected species and critical habitat A description of cumulative effects A conclusion as to whether it is reasonable to expect that the P A is not likely to appreciably reduce the species' likelihood ofboth surviving and recovering in the wild by reducing its reproduction, numbers, or distribution or result in the destruction or adverse modification ofthe species' designated critical habitat The purpose of the jeopardy analysis is to determine whether appreciable reductions in the likelihood of both the survival and recovery of the species in the wild are reasonably expected, but not to precisely quantify the amount of those reductions. As a result, this assessment often focuses on whether an appreciable reduction is expected or not; it does not focus on detailed analyses designed to quantify the absolute amount of reduction or the resulting population characteristics (absolute abundance, for example) that could occur as a result ofPA implementation. For Pacific salmon, steelhead, and certain other species, we commonly use four "viable salmonid population" (VSP) parameters (McElhany et al. 2000) to assess the viability of the populations that, together, constitute the species. When these parameters are collectively at an appropriate level, they maintain a population's capacity to adapt to various envirorunental conditions and allow it to sustain itself in the natural environment. A designation of "a high risk of extinction" or "low likelihood of becoming viable" indicates that the species faces significant risks from internal and external processes that can drive it to extinction. The status assessment considers and diagnoses both internal and external processes affecting a species' extinction risk. As identified in McElhany et al. (2000), the four VSP parameters for salmonids are important to consider because they are predictors of extinction risk. The parameters reflect general biological and ecological processes that are critical to the survival and recovery of the listed salmonid species (McElhany et al. 2000). The VSP parameters of productivity, abundance, and population spatial structure are consistent with the "reproduction, numbers, or distribution" referenced within the regulatory definition of "jeopardize the continued existence of' (50 CFR 402.02 2007) and are used as surrogates for "reproduction, numbers, or distribution." The VSP parameter of diversjty relates to all three. For example, reproduction, numbers, and distribution are all affected when genetic or life history variability is lost or constrained, resulting in reduced population resilience to environmental variation at local or landscape levels. McElhany et al. (2000) highlight that the VSP framework will include "a degree of uncertainty in much of the relevant information," and that "because of this uncertainty, management applications ofVSP should employ both a precautionary approach and adaptive management." The PA does not include an explicit approach to adaptive management ofthe project components. While the February 5, 2019, version of the BA included project components that Reclamation labeled as "Adaptive Management" in Table 4-6, those items were relabled as "Scheduling" components in the revised proposed action posted by Reclamation on April 22, 2019. NMFS encourages the development of an adaptive management program to address uncertainties associated with the effectiveness of management actions taken to avoid jeopardy to federally listed species and destruction or adverse modification of critical habitat. A robust adaptive management component that would address the uncertainty identified by McElhany et 27 Biological Opinion for the Long-Term Operation of the CVP and SWP al. (2000) is expected to focus heavily on filling critical data and information gaps, enhancing the existing monitoring network, and improving quantitative modeling capability. NMFS notes the regulatory definition of "jeopardize the continued existence of' includes the term '"recovery" (50 CFR 402.02). NMFS finalized recovery plans for the listed Central Valley salmon and steelhead species in 2014 (National Marine Fisheries Service 2014b) and for the listed sDPS of green sturgeon in 2018 (National Marine Fisheries Service 2018g) These recovery plans, which include recovery objectives and criteria, also identify stressors or threats to the recovery ofthe species throughout their life cycles. This consultation uses the primary stressor and threat categories from the recovery plans as the basis for identification of potential stressors that could result from the proposed action and therefore could not only reduce appreciably the likelihood of survival of the species but also the likelihood of recovery of the species. The information from recovery plans and the 2015/2016 Five-Year Status Reviews for each species represent the best scientific and commercial data available describing their respective current status, and were, therefore, incorporated into this Opinion. A technical recovery team (TRT) that assisted in the Central Valley salmonids recovery planning effort produced a "Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin" (Lindley et al. 2007). Along with assessing the current viability of the listed Central Valley salmon and steelhead species, Lindley et al. (2007) made recommendations for recovering those species. The framework was used to inform the current status of the listed Central Valley salmon and steelhead species within this Opinion. The recovery plans, status reviews, and Lindley et al. (2007) were used as the foundation to determine whether the PA reasonably would be expected to "reduce appreciably the likelihood of both the survival and recovery of a listed species ... ". NMFS has also applied this framework in analyzing likely effects to recovering the sDPS of green sturgeon, a population represented by a single spawning population, much like the Sacramento River winter-run Chinook salmon population. Additional requirements for the analysis of the effects of an action are described in regulations (50 CFR §402). The conclusions related to "jeopardize the continued existence of' and "destruction or adverse modification" require an expansive evaluation of direct and indirect consequences of the PA, interrelated and interdependent actions, and the overall context of the impacts to the species and habitat from past, present, and future actions as well as the condition of the affected species and critical habitat (for example, see the definitions of"cumulative effects" and "effects of the action" in 50 CFR §402.02 and the requirements of 50 CFR §402.14(g)). Recent court cases have reinforced the requirements provided in the ESA section 7 implementing regulations that NMFS must evaluate the effects of a P A within the context of the current condition of the species and critical habitat, including other factors affecting the survival and recovery of the species and the functions and value of critical habitat for the conservation of the species. In addition, our risk assessments must consider the effects of climate change on the species and critical habitat and our analysis of the future impacts of a proposed action. NMFS acknowledges that the effects of climate change could have notable impacts on listed species while also recognizing the challenge in quantifying those effects. Conservation of protected resources becomes more difficult when considering a changing climate, especially when accounting for the relative uncertainty of the rate and magnitude of climate-related changes and 28 Biological Opinion for the Long-Term Operation of the CVP and SWP the response of organisms to those changes. Accordingly, NMFS issued general policy guidance for treatment of climate change in ESA decisions (Sobeck 2016). This guidance aligns with case law, noting the need to consider climate change in determinations and decisions despite the challenges of climate change uncertainty, and it provides policy considerations related to climate change that NMFS should use in ESA decision making, including ESA section 7 consultations. In addition to Sobeck (2016), NMFS regional guidance (Thorn 2016) further recommends use of the Representative Concentration Pathway (RCP) 8.5 scenario from the Fifth Assessment Report (AR5). Sobeck (2016) notes that "when data specific to (the RCP 8.5) pathway are not available, (NMFS) will use the best available science that is as consistent as possible with RCP 8.5." Climate change is incorporated into this analysis implicitly to an extent by the modeling results provided in the BA and additionally by qualitative evaluations that reflect more recent climate predictions applied in the Opinion. The modeling of the P A as provided in the biological assessment characterizes a 2030 scenario of climate conditions, water demands, and build-out. In doing so, the PA uses a multi-model ensemble-informed approach to identify a best estimate of the consensus of climate projections from the third phase of the Coupled Model lntercomparison Project (CMIP3), which informed the Intergovernmental Panel on Climate Change's (IPCC) Fourth Assessment Report (AR4). These results are downscaled to a spatial resolution of approximately 12 km. This assessment report and approach results in an anticipated temperature change of +0.7 to + 1.4 °C (representing the 25th to 75 1h quartile) and a precipitation change of -6 percent to +6 percent. Additionally, the approach used in for the PA characterizes 2030 sea level rise an 15 em. However, based on results from the application ofRCP 4.5 and RCP 8.5 in California's Fourth Climate Change Assessment (He et al. 2018, Pierce et al. 2018), NMFS expects that climate conditions will follow a more extreme trajectory of higher temperatures and shifted precipitation into 2030 and beyond. As provided! by the assessment, NMFS assumes that temperatures would increase up to 1.9 °C between 2020-2059 and precipitation changes would range from -6 percent to +24 percent in the same period (He et al. 2018). Sea level rise is expected to range up to 15 em in 2030 and 10-38 em in 2050 (Pierce et al. 20 18). The October 29, 2018, Presidential Memorandum on Promoting the Reliable Supply and Delivery ofWater in the West directed NMFS to complete this biological opinion within 135 days of receiving the biological assessment, and modeling for the proposed operations that uses data specific to RCP 8.5 is currently unavailable. Therefore this consultation assumes that the provided modeling represents a best-case scenario regarding climate conditions for 2030 and, to account for the differential in increased temperature, shifted precipitation, and projected sea level rise between the CMIP3 and California's Fourth Climate Change Assessment, NMFS will layer qualitative evaluations of increased climate effects onto the provided modeled data. This is consistent with guidance that "NMFS does not need to know with precision the magnitude of change over the relevant time period if the best available information allows NMFS to reasonably predict the directionality of climate change and overall extent of effects to species or its habitat" (Sobeck 2016) Longer-term responses to climate uncertainty can be incorporated into a reinitiation trigger focused on regular assessments of adherence to the climate assumptions used in the analysis of this Opinion. To address shorter-term deviation from the current predictions, NMFS expects to be able to incorporate climate uncertainty into science plans by including monitoring of climate change effects and projections; taking management actions; and adjusting water operations, research, and monitoring in response as needed. Such responses may include, for instance, 29 Biological Opinion for the Long-Term Operation of the CVP and SWP identifying alternative locations for implementing restoration or habitat protection actions to increase habitat availability and suitability, increasing productivity of the food web, better managing predators and invasive species, or allowing species movement across environmental gradients. Adjustments to water operations associated with inflow, outflow, and exports are another example of potential responses to approaching reintiation triggers. 2.1.3 Overview of the Approach and Conceptual Models NMFS uses a series of sequential activities and analyses to assess the effects ofFederal actions on endangered and threatened species and designated critical habitat. These sequential activities and analyses are illustrated in Figure 2.1.3-1 for listed species and Figure 2.1.3-2 for critical habitat. The final step in the series integrates the conclusions drawn from these activities, summarizing analyses in table format with consistent terms to facilitate the review of effects. In order for us to analyze the PA, it was first separated into components (deconstructed) for each division (as described in the BA). The first analysis uses the identified action components and interrelated and interdependent actions that resulted from the deconstruction of the action to identify environmental stressors. Specifically, the physical, chemical, or biotic aspects of the PA that are likely to have individual, interactive, or additive direct and indirect effects on the environment. As part of this step, NMFS identifies the spatial and temporal extent of both the action components and any potential stressors, recognizing that the spatial extent of the stressors may change with time. NMFS notes that the spatial extent of potential stressors may extend beyond the geographic area included in the project description (i.e., a project description of in-Delta operations may have effects that extend upstream; the spatial extent of those effects is traced as part of this analysis). The next step in the series of analyses starts by identifying the threatened or endangered species or designated critical habitat that are likely to be exposed to (occur in the same space and at the same time as) the potential stressors and their spatial extent. We estimate the nature of cooccurrence of individuals and effect to represent the individual exposure assessment. In this step, we identify the proportion of a population (or number of individuals when available) and age (or life stage) that are likely to be exposed to an action's effects, and the specific areas and PBFs of critical habitat that are likely to be affected. We then assess the severity of an effect based on expected impact to the individual and its continued fitness or the expected impact to PBFs and value for conservation of critical habitat. Finally, we consider the incidence of exposure based on the activities in the description of the proposed action. 30 Biological Opinion for the Long-Term Operation of t he CVP and SWP 0 Action Characterization • Effects Analysis 0 0 Reference Condition Jeopardy Determination ASSESS RISK TO INDIVIDUALS (EFFECTS ON FITNESS) Assess Environment al Baseline and Status of t he Species INTEGRATION AND SYNTHESIS: ASSESS RISK TO SPECIES Assess R1sk to Populations (To Survival and Recovery) Effects from Interrelated and Interdependent Actions Jeopardy or No Jeopardy Opinion Determination Figure 2 .1.3-1. General Conceptual Model for Conducting Section 7 Analyses as Applied to Listed Species. 31 Biological Opinion for the Long-Term Operation of the CVP and SWP Descri be the Proposed Action Deconstruct the Action Describe Env:ironmental Baseline Action Characterization - Effects Analysis 0 0 Identify Action Component s Describe Status of Critical Habitat 0 Reference Condition Determination Identify Environmental Stressors (Temporal and Spatial Extent) Define the Action Area ASSESS EFFECT TO PBF (CHANGE IN VALUE FOR CONSERVATION) Assess Environmental Baseline and Status of Critical Habitat Exposure Assessment (PBFs) Response Analysis INTEGRATION AND SYNTHESIS: ASSESS RISK TO CRITICAL HABITAT (CHANGE IN VALUE FOR CONSERVATION) Assess Risk to Critical Hab itat Effects from Interrelated and Interdependent Actions Cumulative Effects Adverse Modification or No Adverse Modification Determination Figure 2.1.3-2. General Conceptual Model for Conducting Section 7 Analyses as Applied to C ritical Habitat. Once we identify which listed resources (i.e., endangered and threatened species and designated critical habitat) are likely to be exposed to potential stressors associated with an action and the nature of the exposure, we examine the best scientific and commercial data available to determine whether and how those listed resources are likely to respond given their exposure. This represents the individual response analysis. The final steps of our series of analyses establish the risks those responses pose to listed resources, with recognition that responses of individuals may differ within and lbetween (subwatershed) populations and among species. These steps represent our risk analysis. They are different for listed species and designated critical habitat and are discussed in the following sections. 2.1.3.1 Application of the Approach to Listed Species Analyses Our jeopardy determinations must be based on an action's effects on the likelihood of survival and recovery of threatened or endangered species as listed (e.g., as true biological species, subspecies, or distinct population segments of vertebrate species). Because the continued existence of listed species depends on the fate of the populations that comprise them, the 32 Biological Opinion for the Long-Term Operation of the CVP and SWP probability of extinction or probability of persistence of listed species depends on the probabilities of extinction and persistence of the populations that comprise the species. Similarly, the continued existence of a population is determined by the fate of the individuals that comprise it; populations grow or decline as the individuals that comprise the population live, die, grow, mature, migrate, and reproduce (or fail to do so). The approach for specific species are included below in Section 2.1.3.1.1 for salmonids and sturgeon and Section 2.1.3.1.2 for Southern Resident killer whale. 2.1.3.1.1 The Viable Salmonid Populations Framework Approach for Listed Salmonids and Southern Distinct Population Segment of Green Sturgeon Although McElhany et al. (2000) specifically addresses viable populations of salmonids, NMFS believes that the concepts and viability parameters in McElhany et al. (2000) can also be applied to the Southern DPS of green sturgeon due to the general similarity in life cycle and freshwater/ocean use. Therefore, in this Opinion, NMFS applies McElhany et al. (2000) and the viability parameters in its characterization of the status of the species, environmental baseline, and analysis of effects of the action to the Southern DPS of green sturgeon. Our analyses reflect these relationships. We identify the risks that actions pose to listed individuals that are likely to be exposed to effects of the actions. Our analyses then integrate the individuals' risks to identify consequences to the proportion of populations represented by the individuals ( Figure 2.1.3-1 ). Our analyses conclude by determining the consequences of those populationlevel risks to the species that the populations comprise. To measure risks to listed individuals, we use changes in the individual's "fitness" as a metric. "Fitness" can be characterized as an individual's growth rate, survival probability, annual reproductive success, or lifetime reproductive success. In particular, during the individual response analysis, we examine the best scientific and commercial data available to determine if an individual's response to the effect of an action on the environment is likely to have consequences for the individual's fitness. When individuals are expected to experience reduced fitness, we expect those reductions to also reduce the population abundance or rates of reproduction or growth rates (or to increase the variance in these rates) (Stearns 1992). Reduction in one or more of these variables is a necessary condition for decreases in a population's viability, which is a necessary condition for decreases in a species' viability. If we conclude listed individuals are likely to experience reductions in their fitness, we evaluate whether those fitness reductions are likely to decrease the viability of the populations those individuals represent, or to reduce the likelihood of survival and recovery of those populations. This can be measured using changes in population abundance, reproduction rate, diversity, spatial structure and connectivity, growth rate, or variances in these metrics. In this step of our analysis, we use the population's baseline condition (established in the Status of the Species section of this Opinion) as our point of reference because the baseline condition is a measure of how close a species is to extinction. An important tool in this step of the assessment is a consideration of the life cycle of the species. The consequences on a population's probability of extinction as a result of impacts to different 33 Biological Opinion for the Long-Term Operation of the CVP and SWP life stages are assessed within the framework of this life cycle and our current know ledge of the transition rates between life stages, the sensitivity of population growth to changes in those rates, and the uncertainty in the available estimates or information. An example of a Pacific salmonid life cycle is provided in Figure 2.1.3-3, which shows the cycle ofthe upstream freshwater spawning, juvenile smoltification and outmigration, ocean residence, and upstream spawning migration. Though not identical, the life history of green sturgeon is similar (i.e., spawning in upstream freshwater locations, juv·enile outmigration through the riverine and estuarine areas, long ocean residence before returning to upstream spawning areas), and we take a similar approach in analyzing effects to both salmonids and sturgeon. Various sets of data and modeling efforts are useful to consider when evaluating the transition rates between life stages and consequences on population growth as a result of variations in those rates. These data are not available for all species considered in this Opinion; however, data from surrogate species may be available for inference. Where available, information on transition rates, sensitivity of population growth rate to changes in these rates, and the relative importance of impacts to different life stages is used to inform the translation of individual effects to population-level effects. Oceali Figure 2.1.3-3. Conceptual Diagram of the Life Cycle of a Paeific Salmonid (NMFS 2016). In addition, we recognize that populations may be vulnerable to small changes in life stage transition rates. Small reductions across multiple life stages can be sufficient to cause the extirpation of a population. This is. illustrated in Figure 2.1.3-4 for two hypothetical scenarios with different transition rates (numbers included are for explanatory purposes only and do not reflect either observed or expected survival or production rates). For two adult salmon (a spawning pair) that produce 2,000 eggs that then experience a 20 percent survival rate to the juvenile stage, a 10 percent survival to smoltification, and a 5 percent survival over several years 34 Biological Opinion for the Long-Term Operation of the CVP and SWP at sea, two adult salmon will return to spawn again. However, if the survivorship is reduced to 18 percent at the juvenile stage, 8 percent at the smolt stage, and 4 percent at the sea stage, then only one adult salmon will return, leading to eventual extirpation if the trend continues. Cumulative effects 2 adults / 4% 40 smolts .!... 1000 Ill eggs extinction , . . . 2000 eggs ¥ 8% dt 1t 400 juveniles Figure 2.1.3-4. Illustration of Population Vulnerability to Small Changes in Transition Rates (Naiman and Turner 2000). The section 7 consultation process requires assessment of the effects of several stressors to the species. The effects of these stressors require conceptual understanding of both the species' use of the area and the effects of the stressors on the species. NMFS closely considered the conceptual models of the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP) (Williams 2010) and the Salmon and Sturgeon Assessment of Indicators by Life stage (SAIL) (Reub lein et al. 2017, Johnson et al. 2017, Windell et al. 20 17) when identifying and evaluating the effects of activities associated with the PA. These models identify the effects of stressors such as increased temperature, toxins, changes in flow, minor and major diversions, the site of action, and the life stage affected. These stressors and their effects are reflected in the structure and evaluations of the effects analysis. Our assessment next determines if changes in population viability are likely to be sufficient to reduce the viability of the species the population comprises. In this assessment, we use the species' status (established in the Status of the Species section of this Opinion) as our point of reference. We also use our knowledge ofthe population structure ofthe species (e.g., from the relevant recovery plan) to assess the consequences of the increase in extinction risk to one or more of those populations. Our Status of the Species section discusses the available information on the structure and diversity of the populations that comprise the listed species and any 35 Biological Opinion for the Long-Term Operation of the CVP and SWP available guidance on the role of those populations in the recovery of the species, noting that an action that is helping to implement recovery actions or strategies is less likely to jeopardize the continued existence of the species. We consider that recovery objectives and strategies are described in recovery plans and inform our analyses on likelihood of the proposed action to reduce appreciably the likelihood of species recovery. An example of structure and diversity information used in this assessment is provided in Figure 2. 1.3-5 for CV spring-run Chinook salmon. This figure illustrates the historic distribution and structure of the species and notes those populations that have been extirpated. This information provides a sense of existing and lost diversity and structure within the species, which are important considerations wlhen evaluating the recovery consequences of extinction risk or effects to current or potential habitat. 36 Biological Opinion for the Long-Term Operation of the CVP and SWP Central Valley Spriing-run Chinook Salmon Current and Historical Distribution - - Cwrmt s pe... -lr:dcptndr:nt PopulaliOfl - - Omre, Sac San upgrade) Environmental Variations ai d Climate Change PAST Date of consultation 50 FUTURE Biological Opinion for the Long-Term Operation of the CVP and SWP Figure 2.1.3-8 illustrates that the integrated analysis will include the effects to listed species and critical habitat from past actions governed by components of the 2009 NMFS Opinion along with effects of the P A. 2.1.4 Evidence Available for the Analysis The primary source of initial project-related information was the biological assessment for the ROC on LTO of the CVP and SWP, multi-agency meetings with the action agency to discuss project details and clarifications, and supplemental notes and data files provided through April of 2019. However, to conduct the consultation analyses, NMFS considered current literature and published information to provide a foundation for the analysis and represent evidence or absence of adverse consequences. In addition to a thorough review of up-to-date literature and publications reflected in the references cited in individual sections, the following provides a list of resources that we considered in the development of our analyses: • • • • • • • • • • • • • • • • • Final rules listing the species in this Opinion as threatened or endangered Final rules designating critical habitat for the CV salmon and steelhead species and sDPS of green sturgeon Final rule describing the use of surrogates in ITSs (80 FR 26832 20 15) Final rule defining destruction or adverse modification of critical habitat (81 FR 7214 2016) Final rule defining physical and biological features as replacements for primary constituent elements (81 FR 7414 2016) 2016 5-year Status Review: Summary and Evaluation of Sacramento River Winter-run Chinook Salmon ESU 2016 5-year Status Review: Summary and Evaluation ofCV Spring-run Chinook SalmonESU 2016 5-year Status Review: Summary and Evaluation of CCV Steelhead DPS 2015 5-year Status Review: Summary and Evaluation ofsDPS Green Sturgeon 2016 5-year Status Review: Summary and Evaluation ofSoutlhern Resident Killer Whale NMFS 2009 biological opinion on CVP and SWP operations and 2011 amendments to the reasonable and prudent alternative 2014 NMFS Recovery Plan for CV salmonids 2018 NMFS Recovery Plan for sDPS of green sturgeon 2008 NMFS Recovery Plan for Southern Resident killer whale Past independent reviews (i.e., CVP and SWP biological opinions, CVP/SWP operations biological opinion annual reviews) Information included in Collaborative Science and Adaptive Management Program processes NMFS Selected Science Review for the Reinitiation Effort (Byrne 20 18) 2.1.4.1 Primary Analytical Models The ROC on LTO BA includes a suite of models used in the analysis of the effects of the operations of the P A. NMFS used these model results along with results from additional 51 Biological Opinion for the Long-Term Operation of the CVP and SWP analytical methods listed below, with an asterisk(*) denoting models specific to the Opinion. The models specific to the Opinion were not included in the BA submission but were provided to NMFS by Reclamation at NMFS' request. NMFS did not develop new scenarios for analysis; that is, the BA included modeling of two scenarios (a proposed action and a current operations scenario), and NMFS analyzed the results ofthese scenarios. Not all tools were used in all divisions, as some are only applicable to certain rivers or geographic areas. Fundamental models used in the Opinion include the following: • • • • • • • • • • • • CalSimii: A hydrological planning scenario tool that provides monthly average flows for the entire SWP and CVP system based on an 82-year record (1922-2003). DSM2-HYDRO: One-dimensional hydraulic model used to predict flow rate, stage, and water velocity in the Delta and Suisun Marsh and used to support routing and hydrodynamic analyses. HEC-5Q: Uses CalSimJI fl ow and climatic model output to predict monthly water temperature on the Trinity, Feather, American, and Stanislaus River basins and upstream reservmrs. Reclamation Egg Mortality Model*/SacSalMort*: Temperature-exposure mortality criteria for three life stages (pre-spawned eggs, fertilized eggs, and pre-emergent fry) are used along with the spawnilng distribution data and output from the river temperature models to compute percentage of salmon spawning losses; used in fall-run and late fallrun Chinook salmon analysis in evaluation of SRKW prey base. SALMOD*: Predicts effects of flows on habitat suitability and quantity for all races of Chinook salmon in the Sacramento River. DPM*: Simulates migration and mortality of Chinook salmon smolts entering the Delta from the Sacramento, Mokelumne, and San Joaquin rivers through a simplified Delta channel network, and provides quantitative estimates of relative Chinook salmon smolt survival through the Delta to Chipps Island. IOS*: A stochastic life cycle model for winter-run Chinook salmon the Sacramento River. Salvage-Density Analysis*: A model of entrainment into the south Delta facilities as a function of flow based on historical salvage data. NMFS-Southwest Fisheries Science Center Temperature Dependent Egg Mortality Model (Martin et at. 2017): A temperature-dependent mortality model for Chinook salmon embryos that accounts for the effect of flow and dissolved oxygen on the thermal tolerance of developing eggs. Sacramento River Winter-run Chinook Salmon Life Cycle Model*: A state-space and spatially explicit life cycle model of eggs, fry, smolts, juveniles in the ocean,. and mature adults that includes density-dependent movement among habitats. Anderson Egg Mortality Model: Models for managing the Sacramento River temperature during the incubation of winter-run Chinook salmon which characterize temperature-and density-dependent mortality from egg through fry survival. Weighted Usable Area*: A computation of the surface area of physical habitat available weighted by its suitability according to studies assessing suitability of physical and (at times) chemical factors such as substrate particle size, water depth, flow velocity, and dissolved oxygen. 52 Biological Opinion for the Long-Term Operation of the CVP and SWP • • Floodplain Inundation*: Analysis of flow results to determine suitable area based on floodplain hydraulic modeling studies that informed relationships between floodplain flow and suitable area. STARS Model (Perry et al. 2019): Survival, Travel Time, and Routing Simulation model developed by USGS. A stochastic, individual based simulation model designed to predict survival of a cohort of a fish that experiences variable daily river flows as they migrate through the Delta. H)ldrologic Scenario Planning • CaiSimll Flow, Storage Delta H)ldrod)lnamics • DSM2-HYDRO Velocity, Depth ------ Flow, Storage Biological Reseonse • SacSal Mort/Reel a mation Egg Morta Iity Model • SALMOD • Delta Passage Model • Interactive Object-Oriented Simulation • Sacramento Winter-Run Chinook Life Cycle Model • Martinet al. Temperature Dependent Egg Mortality Model • Anderson Temperature Dependent Egg Mortality Model • USGS STARS Model • Floodplain Inundation • Weighted Usable Area Temeerature • HEC-SQ Temperature Figure 2.1.4-1. Main Models Used in the Analysis of Operations in the Biological Opinion and T heir Information Flow with Respect to Each Other. Figure 2.1.4-1 provides a schematic of how the models relate to each other in terms of information flow. Because the CalSimll modeling characterized a projected 2030 climate scenario, that climate condition was represented in all "downstream" modeling that used the CalSimii results. NMFS notes that several of these models have not been updated to be recalibrated to recent data, especially that of the recent drought. This does introduce an additional component of uncertainty to their application. However, the tools still represent the best options available to NMFS for use in this analysis. Given the approach of applying them to an 82-year sample set of hydrologies, we believe that the tools capture the effects ofthe majority of years, but we do encourage the developers to capitalize upon the recent extreme conditions to strengthen the application base for these models. Though salmon life cycle modeling was not used in the previous biological opinion on systemwide water project operations in the Central Valley (i.e., NMFS 2009 Opinion), NMFS has recognized the need to better integrate life cycle models: into their assessments of the effects of water operations on the listed anadromous fish species. Peer reviews (Cummins et al. 2008, Anderson et al. 2009, National Research Council 2010) recommended increased use oflife cycle 53 Biological Opinion for the Long-Term Operation of the CVP and SWP modeling as part of the consultation analyses and provided general recommendations on how NMFS should proceed with further incorporating life cycle modeling into ongoing analyses (Rose et al. 2011 ). In response, NMFS has developed a life cycle modeling framework for CV Chinook salmon that is used in this Opinion to allow better evaluation of how complex and interacting management actions affect salmon populations. Specifically, the analyses include results from a model framework developed by the NMFS Southwest Fisheries Science Center to describe salmon population dynamics given water management, habitat restoration, and climate change scenarios (Hendrix et al. 2014, Hendrix et al. 2017). The framework relies upon standard Central Valley physical (i.e., CalSimll, DSM2, HEC-RAS) and chemical (i.e., temperature models, DSM2QUAL) models to provide a characterization of abiotic conditions for a given scenario. A stagestructured population dynamics model of Chinook salmon links the habitat information to density-dependent stage transitions. These transitions describe the movement, survival, and reproduction that drive the dynamites of salmon populations. The physical models applied in the BA and relied upon in this Opinion are generalized and simplified representations of a complex water resources system. The models are not predictive models of actual operations, and, therefore, the results cannot be considered as absolute and within a quantifiable confidence interval. For instance, CalSimll is a monthly planning model; it is not calibrated and cannot be used in a real-time predictive manner. CaiSimii results are intended to be used in a comparative manner, which allows for assessing the changes in the CVP and SWP system operations and resulting incremental effects between two scenarios. This and any subsequent models that use CalSimll results require caution when used to characterize absolute conditions or conditions on a sub-monthly time step. Similarly, each of the analytical model s have limitations to their application and interpretation, and we discuss these limitations in effects analysis sections where they are applied and incorporated into evulation of effects. Given the nature of modeling outputs and historical data, throughout this Opinion we often analyze effects in a comparative analysis between two scenarios or in relation to baseline conditions to place the difference in context given conditions and operations in the last decade. And although the results of the analytical tools require a more comparative analysis, the analysis for section 7 consultation requires that the effects of the project be evaluated in the aggregate. Our analysis culminates in an aggregate assessment with baseline effects in Sections 2.8 and 2.9 Integration and Synthesis to draw conclusions according to the ESA. Therefore, NMFS used the results of the analysis in the exposure-risk-response framework along with knowledge of the species status and environmental baseline to evaluate the overall conditions that fish experience. The quantitative results of the analytical methods are used to inform this evaluation as much as possible, though, given the limitations of many of the models to comparative analyses, this assessment does rely on a qualitative analysis and application of results. 2.1.4.2 Critical Assumptions in the Analysis To address the uncertainties identified above related to the PA and the analysis provided in the BA, NMFS used its professional judgement to establish a set of reasonable key assumptions required to address existing data gaps in the BA that are critical to our analysis of effects. General assumptions that were made in filling those data gaps include the following: 54 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • • Species presence data are an accurate description of when and where a proportion of a particular species can be expected to occur in a particular area. While real-time monitoring in any given year may provide an opportunity to fine-tune short-term presence information, the available data that characterize both the bulk of presence and the tails (that is, smaller proportion) of presence are considered the best information for informing exposure and risk. The characterization offuture conditions incorporated into the PA and Opinion analysis is applicable throughout operations until a subsequent consultation on the CVP and SWP is completed. The PA and Opinion analyses characterize climate conditions, water demands, and build-out as predicted for approximately 2030. The project, as characterized in the modeling provided by the BA, does not simulate short-term real-time operations, especially those that are dependent on biological triggers. Because the modeling analysis is based on comparative long-term scenario planning tools, it is not able to emulate the daily operations that would be implemented to manage to biological, water quality, and other constraints. NMFS has analyzed the effects of the project as characterized by an initial approach to operations as identified by the operational criteria of the PA and completed auxiliary analyses when possible to evaluate the effects of real-time operations that are within the operational criteria identified in the PA. Results that include confidence intervals to characterize uncertainty are viewed in totality, considering the range of results over the intervals and not simply mean or median values. Exposure of a few individuals to a stressor, as indicated by the species presence, does not result in no adverse effect. Exposure of a small number of individuals may still result in incidental take of those individuals, however few, and this incidental take should not be ignored. If the magnitude of effect to those individuals is low, it will be stated as such. Many of the methods described above focus the analyses on particular aspects of the action or affected species. Key to the overall assessment, however, is an integration ofthe effects of the PA with each other and with the baseline set of stressors to which the species and critical habitat are also exposed. In addition, the final steps of the analysis require a consideration of the effects of the action within the context of the baseline condition of the species and critical habitat. That is, following the hierarchical approaches outlined above, NMFS combines the effects of the action to determine whether the action is likely to appreciably reduce the likelihood of both the survival and recovery of the species or likely to result in the destruction or adverse modification of critical habitat. Because not all components of the P A were presented with the specificity required to analyze a particular outcome of effect, NMFS' determination is based on a collection of site-specific and framework-level action components. This can explain and result in differenet conclusions in the BA compared to the Opinion. 2.1.5 Integrating the Effects The preceding discussions describe the various quantitative and qualitative models, decision frameworks, and ecological foundations for the analyses presented in this Opinion. The purpose of these various methods and tools is to provide a transparent and repeatable mechanism for conducting analyses to determine whether the PA is likely to jeopardize the continued existence 55 Biological Opinion for the Long-Term Operation of the CVP and SWP of the listed species or result in the destruction or adverse modification of designated critical habitat. Many methods described above focus the analyses on particular aspects of the action or affected species. Key to the overall assessment, however, is integration and synthesis which consists of: (1) Reviewing the status of the species and critical habitat; and (2) adding the effects ofthe action, the environmental baseline, and cumulative effects to assess the risk that the proposed action poses to species and critical habitat ( Figure 2.1.3-1 and Figure 2.1.3-2). That is, following the hierarchical approaches outlined above, NMFS integrates the effects of the action with the baseline condition as the foundation to determine whether the action is reasonably expected to appreciably reduce the likelihood of both the survival and recovery of listed species in the wild and whether the action is likely to appreciably diminish the value of designated critical habitat for the conservation of the species. 2.1.6 Presentation of the Analysis in this Opinion Opinions are constructed around several basic sections that in many cases represent specific requirements placed on the analysis by the ESA and implementing regulations. These sections contain different portions of the overall analytical approach described here. This section is intended as a basic guide to the other sections of this Opinion and the analyses that can be found in each section. Every step of the analytical approach described above is presented in this Opinion in either detail or summary form. Description of the Proposed Action-This section summarizes the proposed Federal action and any interrelated or interdependent actions. This description is the first step in the analysis where we consider the various elements of the action and determine the stressors expected to result from those elements. The nature, timing, duration, and location of those stressors defme the action area and provide the basis for our exposure analyses. Range-wide Status of the Species and Critical Habitat-This section provides the baseline condition for the species and critical habitat at the listing and designation scale. For example, NMFS evaluates the current viability of each salmonid ESU/DPS given its exposure to human activities and natural phenomena such as variations in c1imate and ocean conditions, throughout its geographic distribution. These reference conditions form the basis for determining whether the PAis likely to jeopardize the continued existence of the species or result in the destruction or adverse modification of critical habitat. Other key analyses presented jn this section include critical information on the biological and ecological requirements of the species and critical habitat and the impacts to species and critical habitat from existing stressors. Environmental Baseline-This section provides the baseline condition for the species and critical habitat within the action area. By regulation, the environmental baseline includes the past and present impacts of all Federal, state, or private actions and other human activities in the action area; the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation; and the impact of state or private actions, which are contemporaneous with the consultation in process on the species and critical habitat. This section will also include anticipated effects of climate change on the species and critical habitat within the action area. In this Opinion, some analysis may be contained within the Status of the Species and Critical Habitat section, due to the large size of the action area (which 56 Biological Opinion for the Long-Term Operation of the CVP and SWP entirely or almost entirely encompasses the freshwater geographic ranges of some listed fish species). This section also summarizes the impacts from stressors that will be ongoing in the same areas and times as the effects of the PA. This information forms part of the foundation of our exposure, response, and risk analyses. Effects of the Proposed Action-This section details the results of the exposure, response, and risk analyses NMFS conducted for effects of the PA on individuals and proportion of the listed species population and PBFs and value for the conservation of the species of critical habitat within the action area. This will include the direct and indirect effects of an action on the species or critical habitat, together with the effects of other activities that are interrelated or interdependent with that action, that will be added to the environmental baseline (50 CFR 402.02 2007). Indirect effects are those that are caused by the PA and are later in time, but still are reasonably certain to occur. Discussion of results will include identification ofuncertainties associated with analytical methods or interpretation and will highlight instances of application of the precautionary principle. In the case of the PA, climate change effects as modeled for a 2030 climate scenario will be incorporated into the analysis by explicit modeling and additional qualitative evaluations to better incorporate more recent climate projections. Cumulative Effects-This section summarizes the impacts of future non-Federal actions reasonably certain to occur within the action area, as required by regulation. Similar to the rest of the analysis, if cumulative effects are expected, NMFS determines the exposure, response, and risk posed to individuals of the species and features of critical habitat. Future Federal actions that are unrelated to the PA are not considered in this section because they require separate consultation pursuant to section 7 of the ESA. Integration and Synthesis of Effects-Section 2. 7, Integration and Synthesis, is the final step in our assessment of the risk posed to species and critical habitat as a result of implementing the PA. In this section, we add the effects of the action to the environmental baseline and the cumulative effects, taking into account the status of the species and critical habitat, to formulate NMFS' Opinion as to whether the PA is likely to: (I) reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing its reproduction, numbers, or distribution; or (2) appreciably diminish the value of designated critical habitat for the conservation of the species. Discussion will include identification ofuncertainties associated with the integration of effects and will highlight instances of application of the precautionary principle. 2.2 Range-wide Status of the Species and Critical Habitat This section provides a summary of the status of each species that would be adversely affected by the PA. The status is determined by the level of extinction risk that the listed species face, based on parameters considered in documents such as recovery plans, status reviews, and listing decisions. This informs the description of the species' likelihood of both survival and recovery. This species status section also helps to inform the description of the species' current "reproduction, numbers, or distribution" as described in 50 CFR §402.02. This section also provides a summary of the condition of critical habitat throughout the designated area, evaluates the value of the various watersheds and coastal and marine environments that make up the designated area, and discusses the current function of the essential PBFs that help to form that 57 Biological Opinion for the Long-Term Operation of the CVP and SWP value for the conservation of the species. A more detailed description of the status of the species and designated critical habitats is provided in Appendix B and in the Environmental Baseline. 2.2.1 • • • Sacramento River Winter-run Chinook Salmon First listed as threatened (54 FR 32085; August 4 , 1989) Reclassified as endangered (59 FR 440; January 4, 1994); reaffirmed as endangered (70 FR 37160; June 28, 2005) Designated critical habitat (58 FR 33212; June 16, 1993) The federally listed ESU of Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) and designated critical habitat occurs in the action area and may be affected by the PA. Detailed information regarding ESU listing and critical habitat designation history, designated critical habitat, ESU life history, and VSP parameters can be found in Appendix B: Rangewide Status of the Species and Critical Habitat. Historically, winter-run Chinook salmon population estimates were as high as 120,000 fish in the 1960s, but declined to less than 200 fish by the 1990s (National Marine Fisheries Service 20llc). In recent years, since carcass surveys began in 2001, the highest adult escapement occurred in 2005 and 2006 with 15,839 and 17,296, respectively (California Department of Fish and Wildlife 2016c). However, from 2007 to 2017, the population has shown a precipitous decline, averaging 2,733 during this period, with a low of 827 adults in 2011 (California Department ofFish and Wildlife 20 18b) This recent declining trend is likely due to a combination of factors such as poor ocean productivity (Lindley et al. 2009), drought conditions from 2007 to 2009, low in-river survival (National Marine Fisheries Service 2011c), and extreme drought conditions in 2012 to 2016 (National Marine Fisheries Service 2016c). In 2015, the population was 3,015 adults, slightly above the 2007 to 2012 average, but below the high (17,296) for the last 10 years (California Departm,ent ofFish and Wildlife 2016c). The year 2014 was the third year of a drought that resulted in increased water temperatures in the upper Sacramento River, and egg-to-fry survival to the Red Bluff Diversion Dam (RBDD) was approximately 5 percent (National Marine Fisheries Service 2016c). Due to the anticipated lower than average survival in 2014, hatchery production from LSNFH was tripled (i.e., 612,056 released) to offset the impact of the drought (CVP and SWP Drought Contingency Plan 2014). In 2014, hatchery production represented 83 percent of the total in-river juvenile production. In 2015, egg-to-fry survival was the lowest on record (approximately 4 percent) due to the inability to release cold water from Shasta Dam in the fourth year of the drought. Winter-run Chinook salmon returns in 2016 to 2018 were low, as expected, due to poor in-river conditions for juveniles from brood year 2013 to 2015 during drought years. The 2018 adult winter-run return (2,458) improved from 2017 (1 ,155), though was similarly dominated by hatchery-origin fish. Although impacts from hatchery :fish (i.e., reduced fitness, weaker genetics, smaller size, less ability to avoid predators) are often cited as having deleterious impacts on natural in-river populations (Matala et al. 2012), the winter-run Chinook salmon conservation program at LSNFH is strictly controlled by the USFWS to reduce such impacts. The average annual hatchery production at LSNFH is approximately 216,015 per year (200 1 to 2018 average) compared to the estimated natural production that passes RBDD, which is 2.9 million per year based on the 2002 to 2018 average (Poytress and Carrillo 2011, U.S. Fish and Wildlife Service 2018a). Therefore, hatchery production typically represents approximately 7 percent of the total 58 Biological Opinion for the Long-Term Operation of the CVP and SWP in-river juvenile production in any given year. This percentage of hatchery origin emigrants results in a higher percentage of hatchery-origin spawners, with an average of21 percent hatchery-origin spawners over the last 18 years (about six generations), putting the population at a moderate risk of extinction (National Marine Fisheries Service 20 I 6c). The distribution ofwinter-run Chinook salmon spawning and initial rearing historically included the upper Sacramento River (upstr·e am of Shasta Dam), McCloud River, Pitt River, and Battle Creek, where springs provided cold water throughout the summer, allowing for spawning, egg incubation, and rearing during the mid-summer period (Yoshiyama et al. 1998). The construction of Shasta Dam in 1943 blocked access to all these waters except Battle Creek, which also had its own impediments to upstream migration (i.e., a number of small hydroelectric dams situated upstream of the CNFH weir). As of2019, implementation of the Battle Creek Salmon and Steelhead Restoration Project has completed construction ofphase 1 (of2), which included removal of one fish passage barrier (dam), and construction ofNMFS-approved fish screens and ladders at the two remaining dams on North Fork Battle Creek. Phase 2 of the project has completed planning, and is currently in design phase. Additionally, beginning in 2018, winterrun Chinook salmon juveniles produced at LSNFH have been released into North Fork Battle Creek in an effort to jump-start the reintroduction efforts described in the plan (ICF International 20 I 6, U.S. Fish and Wildlife Service 20 18b). Approximately 299 miles of former tributary spawning habitat above Shasta Dam is inaccessible to winter-run Chinook salmon. Yoshiyama et al. (2001) estimated that in 1938, the upper Sacramento River had a "potential spawning capacity" of approximately 14,000 redds equal to 28,000 spawners. Since 2001, the majority ofwinter-run Chinook salmon redds have occurred in the first 10 miles downstream of Keswick Dam. Most components of the winter-run Chinook salmon life history (e.g., spawning, incubation, freshwater rearing) have been compromised by the construction of Shasta Dam (National Marine Fisheries Service 20 14b). The greatest risk factor for winter-run Chinook salmon lies within its spatial structure (National Marine Fisheries Service 2011c). The winter-run Chinook salmon ESU comprises only one population that spawns below Keswick Dam. The remnant and remaining population cannot access 95 percent of their historical spawning habitat and must, therefore, be artificially maintained in the Sacramento River by spawning gravel augmentation, hatchery supplementation, and regulation of the finite cold water pool behind Shasta Dam to reduce water temperatures. Winter-run Chinook salmon require cold water temperatures in the summer that simulate their upper basin habitat, and they are more likely to be exposed to the impacts of drought in a lower basin environment. Battle Creek is currently the most feasible opportunity for the ESU to expand its spatial structure. The Central Valley Salmon and Steelhead Recovery Plan (National Marine Fisheries Service 20 14b) includes criteria for recovering the winter-run Chinook salmon ESU, including re-establishing a population into historical habitats in Battle Creek as well as upstream of Shasta Dam (National Marine Fisheries Service 2014b). As mentioned above, in 2017 and 20I 8 action was taken to initiate the reintroduction of winter-run Chinook salmon to Battle Creek using the progeny of captive broodstock from LSNFH(U.S. Fislh and Wildlife Service 20 I 8b). This decision to spawn captive broodstock and u se their progeny to initiate reintroduction of Sacramento River winter-run Chinook salmon into historic spawning habitats of Battle Creek was called the winter Chinook salmon "Jumpstart" Project (U.S. Fish and 59 Biological Opinion for the Long-Term Operation of the CVP and SWP Wildlife Service 20 18b). In March and early April of 2018, progeny of the winter-run Chinook salmon captive broodstock were released into the North Fork Battle Creek. Currently, the plan is for this Jumpstart Project to continue until a "Transition Plan" is developed to merge the Jumpstart Project with the Reinitiation Plan (U.S. Fish and Wildlife Service 2018b). Winter-run Chinook salmon embryonic and larval life stages that are most vulnerable to warmer water temperatures occur during the summer, so this run is particularly at risk from climate warming. The only remaining population of winter-run Chinook salmon relies on the cold water pool in Shasta Reservoir, which buffers the effects of warm temperatures in most years. The exception occurs during drought years, which are predicted to occur more often with climate change (Yates et al. 2008). The long-term projection of how the CVP and SWP will operate incorporates the effects of potential climate change in three possible forms: less total precipitation; a shift to more precipitation in the form of rain rather than snow; or earlier spring snow melt (U.S. Bureau of Reclamation 2008). Additionally, air temperature appears to be increasing at a greater rate than what was previously analyzed (Lindley 2008, Beechie et al. 2012, Dimacali 2013). These factors will compromise the quantity and/or quality of winter-run Chinook salmon habitat available downstream of Keswick Dam. It is imperative for additional populations of winter-run Chinook salmon to be re-established into historical habitat in Battle Creek and above Shasta Dam for long-term viability ofthe ESU (National Marine Fisheries Service 2014b). 2.2.1.1 Summary of the Sacramento River Winter-run Chinook Salmon Evolutionarily Significant Unit Viability There are several criteria that would qualify the winter-run Chinook salmon population at moderate risk of extinction (continued low abundance, a negative growth rate over two complete generations, significant rate of decline since 2006, increased hatchery influence on the population, and increased risk of catastrophe), and because there is still only one population that spawns below Keswick Dam, the winter-run Chinook salmon ESU is at high risk of extinction in the long term (Lindley et al. 2007). The extinction risk for the winter-run Chinook salmon ESU has increased from moderate risk to high risk of extinction since 2005, and several listing factors have contributed to the recent decline, including drought and poor ocean conditions (National Marine Fisheries Service 2016c). Thus, large-scale fish passage and habitat restoration actions are necessary for improving the winter-run Chinook salmon ESU viability (National Marine Fisheries Service 20 16c). 2.2.2 Critical Habitat and Physical or Biological Features for Sacramento River Winterrun Chinook Salmon The critical habitat designation for Sacramento River winter-run Chinook salmon lists the PBFs (58 FR 33212; June 16, 1993), which are described in Appendix B. This designation includes the following waterways, bottom and water of the waterways, and adjacent riparian zones: the Sacramento River from Keswick Dam (river mile [RM] 302) to Chipps Island (RM 0) at the westward margin of the Delta; all waters from Chipps Island westward to the Carquinez Bridge, including Honker Bay, Grizzly Bay, Suisun Bay, and the Carquinez Strait; all waters of San Pablo Bay westward ofthe Carquinez Bridge; and all waters of San Francisco Bay north ofthe San Francisco-Oakland Bay Bridge from San Pablo Bay to the Golden Gate Bridge (58 FR 33212; June 16, 1993). NMFS clarified that "adjacent riparian zones" are limited to only those 60 Biological Opinion for the Long-Term Operation of the CVP and SWP areas above a stream bank that provide cover and shade to the nearshore aquatic areas (58 FR 33212; June 16, 1993). Although the bypasses (e.g., Yolo, Sutter, and Colusa) are not currently designated critical habitat for winter-run Chinook salmon, NMFS recognizes that they may be utilized when inundated with Sacramento River flood flows, and are important rearing habitats for juvenile winter-run. Also, juvenile winter-run Chinook salmon may use tributaries of the Sacramento River for non-natal rearing (Maslin et al. 1997, Pacific States Marine Fisheries Commission 2014, Phillis et al. 20 18). 2.2.2.1 Summary of Winter-run Chinook Salmon Critical Habitat Currently, many of these PBFs are degraded and provide limited high quality habitat. Factors that lessen the quality ofthe migratory corridor for juveniles include unscreened diversions, altered flows in the Delta, Sacramento River and its tributaries, and the lack of floodplain habitat. In addition, water operations that limit the extent of cold water below Shasta Dam have reduced the available spawning habitat and degraded juvenile rearing and outmigration habitat (based on water temperature). Although the critical habitat for winter-run Chinook salmon has been highly degraded, the importance of the reduced spawning habitat, migratory corridors, and rearing habitat that remains is of high value for the conservation of the species. 2.2.3 • • Central Valley Spring-run Chinook Salmon Listed as threatened (64 FR 50394; September 16, 1999); reaffirmed as threatened (70 FR 37160; June 28, 2005) Designated critical habitat (70 FR 52488; September 2, 2005) The federally listed ESU of CV spring-run Chinook salmon and designated critical habitat occur in the action area and may be affected by the PA. Detailed information regarding ESU listing and critical habitat designation history, designated critical habitat, ESU life history, and VSP parameters can be found in Appendix B. Historically, spring-run Chinook salmon were the second most abundant salmon run in the Central Valley and one of the largest on the west coast (California Department ofFish and Game 1990). These fish occupied the upper and middle elevation reaches (1,000 to 6,000 feet) ofthe San Joaquin, American, Yuba, Feather, Sacramento, McCloud, and Pit rivers, with smaller populations in most tributaries with sufficient habitat for over-summering adults (Stone 1872, Rutter 1908, Clark 1929). The Central Valley drainage as a whole is estimated to have supported spring-run Chinook salmon runs as large as 600,000 fish between the late 1880s and 1940s (California Department ofFish and Game 1998). The San Joaquin River historically supported a large run of spring-run Chinook salmon, suggested to be one of the largest runs of any Chinook salmon on the West Coast with estimates averaging 200,000 to 500,000 adults returning annually (California Departm,e nt ofFish and Game 1990). Currently, CV spring-run Chinook salmon are extirpated from the San Joaquin River due to habitat loss (National Marine Fisheries Service 2016a). Monitoring the Sacramento River mainstem during spring-run Chinook salmon spawning timing indicates that some spawning occurs in the river. Genetic introgression between fall-run and spring-run CV Chinook salmon populations has likely occurred due to lack of physical separation, temporal overlap, and hatchery practices (California Department of Water Resources 2001). Sacramento River tributary populations in Mill, Deer, and Butte creeks are likely the best 61 Biological Opinion for the Long-Term Operation of the CVP and SWP trend indicators for the CV spring-run Chinook salmon ESU. Generally, these streams have shown a positive escapement trend since 1991, displaying broad fluctuations in adult abundance (Table B-3 in Appendix B). The FRFH spring-run Chinook salmon population represents the only remaining evolutionary legacy of the spring-run Chinook salmon populations that once spawned above Oroville Dam, and has been included in the ESU based on its genetic linkage to the natural spawning population and the potential development of a conservation strategy for the hatchery program (70 FR 37160; June 28, 2005). Hatchery-produced CV spring-run Chinook salmon may affect ESU diversity through (1) introgression with CV fall-run Chinook salmon due to overlap in spawn timing; (2) straying ofFRFH spring-run into natural-origin CV spring-run spawning habitat; and (3) disproportionately high levels of returning spawners in comparison to natural-origin fish (National Marine Fisheries Service 2016a). The Central Valley TRT estimated that historically there were 18 or 19 independent populations of CV spring-run Chinook salmon, along with a number of dependent populations, all within four distinct geographic regions, or diversity groups (Lindley et at. 2004). Of these populations, only three independent populations currently exist (Mill, Deer, and Butte creeks, tributary to the upper Sacramento River), and they represent only the northern Sierra Nevada diversity group (National Marine Fisheries Service 2014b). Additionally, smaller, dependent, populations in Antelope and Big Chico creeks and the Feather and Yuba rivers in the northern Sierra Nevada diversjty group (California Department ofFish and Game 1998). The northwestern California diversjty group contains two small persisting populations, in Clear and Beegum creeks. In the basalt and porous lava diversity group, in addition to a potential returning population to the Sacramento River, downstream of Keswick Dam, a small population in Battle Creek is currently persisting. In the San Joaquin River basin, the southern Sierra Nevada diversity group, observations in the last decade suggest that spring-running populations may currently occur in the Stanislaus and Tuolumne rivers (Franks 2014). Restoration efforts in the Stanislaus, Tuolumne, and Merced rivers and reintroduction of CV spring-run Chinook salmon in the San Joaquin River are beneficial to the spatial structure and genetic diversity of the ESU will benefit (National Marine Fisheries Service 2016a). The CV spring-run Chinook salmon ESU comprises two known genetic complexes. Analysis of natural and hatchery spring-run Chinook salmon stocks in the Central Valley indicates that the northern Sierra Nevada diversity group spring-run Chinook salmon populations in Mill, Deer, and Butte creeks retain genetic integrity as opposed to the genetic integrity of the Feather River population, which has been somewhat compromised by introgression with the fall-run ESU (Good et al. 2005, Garza et al. 2008, Cavallo et al. 2011 ). Because the populations in Butte, Deer and Mill creeks are the best trend indicators for ESU viability, we can evaluate risk of extinction based on VSP parameters in these watersheds. Over the long term, these three remaining populations are considered to be vulnerable to anthropomorphic and naturally occurring catastrophic events. The viability assessment of CV spring-run Chinook salmon conducted during NMFS' 2010 status review (National Marine Fisheries Service 20 11a) found that the biological status of the ESU had worsened since the last status review (2005). In 2012 and 2013, most tributary populations increased in returning adults, averaging over 13,000. However, 2014 returns were lower again, just over 5,000 fish, indicating the ESU remains highly fluctuating. The most recent status review, conducted in 2015 (National Marine Fisheries Service 2016a), looked at promising increasing populations in 2012 to 2014. However, CDFW has documented critically low spring-run Chinook salmon adult returns to Mill 62 Biological Opinion for the Long-Term Operation of the CVP and SWP and Deer creeks for the fourth consecutive year, due in part, to one of California's most severe and prolonged droughts on record (December 2011 to March 2017). From 2015 through 2018, both Mill and Deer creeks spring-run Chinook salmon populations had adult returns below 500. The final 2018 escapement estimates for Mill and Deer creeks were 152 and 159 CV spring-run Chinook salmon, respectively (California Department ofFish and Wildlife 2019). These estimates are among the lowest number of adults returning to Mill and Deer Creeks since records began in 1960. Mill and Deer Creeks spring-run Chinook salmon represent two of only three extant independent Chinook salmon populations in California's Central Valley, and therefore are vital to the health of the CV spring-run Chinook salmon ESU. In response to the recent reduction in adult escapement, NMFS and CDFW are jointly developing an Emergency Spring-run Action Plan, which aims to identify and outline the implementation of immediate, targeted efforts that are vital for stabilizing the populations that are most at risk (Mill, Deer, and Butte creeks). Immediate management actions under consideration include efforts to increase flows, possible implementation of a supplementation program (utilizing hatchery-origin CV spring-run Chinook salmon), and completion of fish passage improvement projects. CV spring-run Chinook salmon adults are vulnerable to climate change because they oversummer in freshwater streams before spawning in autumn (Thompson et al. 2011 ). CV springrun Chinook salmon spawn primarily in the tributaries to the Sacramento River, and those tributaries without cold water refugia (usually input from springs) will be more susceptible to impacts of climate change. Even in tributaries with cool water springs, in years of extended drought and warming water temperatures, unsuitable conditions may occur. Additionally, juveniles often rear in the natal stream for one to two summers prior to emigrating, and would be susceptible to warming water temperatures (National Marine Fisheries Service 2016a). In Butte Creek, fish are limited to low elevation habitat that is currently thermally marginal, as demonstrated by high summer mortality of adults in 2002 and 2003, and will become intolerable within decades if the climate warms as expected. Ceasing water diversion for power production from the summer holding reach in Butte Creek resulted in cooler water temperatures, more adults surviving to spawn, and extended population survival time (Mosser et al. 2013). 2.2.3.1 Summary of the Central Valley Spring-run Chinook Salmon Evolutionarily Significant Unit Viability In summary, the extinction risk for the CV spring-run Chinook salmon ESU remains at moderate risk of extinction (National Marine Fisheries Service 2016a). However, based on the severity of the drought and the low escapements, as well as increased pre-spawn mortality in Butte, Mill, and Deer creeks in 2015, there is concern that these CV spring-run Chinook salmon strongholds will deteriorate into high extinction risk in the coming years based on the population size or rate of dec1ine criteria (National Marine Fisheries Service 2016a). This predicted trend has been validated in recent y,ears through escapement data collected by CDFW for Mill and Deer creeks (California Department ofFish and Wildlife 2019). With adult returns below 500 individuals for the fourth consecutive year (20 15-20 18), these populations are at an increased risk of extinction (Lindley et al. 2007) . In response to these alarming trends, CDFW and NMFS intend to implement the suite of actions described in the draft Emergency Spring-run Action Plan as soon as possible upon finalizing the plan. 63 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.2.4 Critical Habitat and Physical or Biological Features for Central Valley Spring-run Chinook Salmon The critical habitat designation for CV spring-run Chinook salmon lists the PBFs (70 FR 52488; September 2, 2005), which are described in Appendix B. In summary, the PBFs for CV springrun Chinook salmon critical habitat include freshwater spawning sites, freshwater migratory habitat, freshwater rearing sites, and estuarine habitat. The geographical range of designated critical habitat includes stream reaches of the Feather, Yuba, and American rivers; Big Chico, Butte, Deer, Mill, Battle, Antelope, and Clear creeks; and the Sacramento River downstream to the Delta, as well as portions of the northern Delta (70 FR 52488; September 2, 2005). 2.2.4.1 Summary of Central Valley Spring-run Chinook Salmon Critical Habitat Currently, many of the PBFs of CV spring-run Chinook salmon critical habitat are degraded and provide limited high-quality habitat. Factors that lessen the quality of migratory corridors for juveniles include unscreened or inadequately screened diversions, altered flows in the Delta and mainstem Sacramento River, scarcity of complex in-river cover, in-river predation, degraded water quality, suboptimal water temperatures, and the lack of floodplain habitat. Altlhough the current conditions of CV spring-run Chinook salmon critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain are considered to have high intrinsic value for the conservation of the species. 2.2.5 • • California Central Valley Steelhead Distinct Population Segment Originally listed as threatened (63 FR 13347; March 19, 1998), reaffirmed as threatened (71 FR 834; January 5, 2006) Designated critical habitat (70 FR 52488; September 2, 2005) The federally listed DPS of CCV steelhead and designated critical habitat occur in the action area and may be affected by the P A. Detailed information regarding DPS listing and critical habitat designation history, designated critical habitat, DPS life history, and VSP parameters can be found in Appendix B. Historic CCV steelhead run sizes are difficult to estimate given the paucity of data, but may have approached one to two million adults annually (McEwan 2001). By the early 1960s, the CCV steelhead run size had declined to about 40,000 adults (McEwan 2001). Current abundance data are limited to returns to hatcheries and redd surveys conducted on a few rivers. The lhatchery data are the most reliable, as redd surveys for CCV steelhead are often made difficult by high flows and turbid water usually present during the winter-spring spawning period. CCV steelhead returns to CNFH increased from 2011 to 2015 (see Appendix B for further information). After reaching a low of only 790 fish in 201 0, the years 2013 to 2015 averaged 2,854 fish. Natural-origin adults counted at the hatchery each year represent a small fraction of overall returns, but their numbers have remained relatively steady, typically 200 to 300 fish each year, ranging from 252 to 610 from 2010 to 2017, respectively (Figure B-8 in Appendix B). Redd counts are conducted in the American River and in Clear Creek (Shasta County). An average of approximately 123 redds have been counted on the American River from 2002 to 2018 (Figure B-9 in Appendix B; data from (Cramer Fish Sciences 2016, American River Group 2017, 20 18)). An average of 183 redds have been counted in Clear Creek from 2001 to 201 7 64 Biological Opinion for the Long-Term Operation of the CVP and SWP following the removal of Saeltzer Dam, which allowed steelhead access to additional spawning habitat. The Clear Creek redd count data estimated a range from 100 to 1,023 spawning adult steelhead on average each year, indicating an upward trend in abundance since 2006 (U.S. Fish and Wildlife Service 2015a). An estimated 100,000 to 300,000 naturally-produced juvenile steelhead leave the Central Valley annua[ly, based on rough calculations from sporadic catches in trawl gear (Good et al. 2005). Nobriga and Cadrett (2001) used the ratio of adipose fin-clipped (hatchery) to unclipped (natural-origin) steelhead smolt catch ratios in the Chipps Island trawl from 1998 through 2000 to estimate that about 400,000 to 700,000 steelhead smolts are produced naturally each year in the Central Valley. Updated through 2017, the trawl data indicate that the level of natural production of steelhead has remained very low since the 2011 status review (National Marine Fisheries Service 2011 b), suggesting a decline in natural production based on consistent hatchery releases. Catches of steelhead at the fish collection facilities in the southern Delta are another source of information on the relative abundance of the CCV steelhead DPS as well as the production of natural-origin steelhead relative to hatchery steelhead (California Department of Fish and Wildlife 20 17b). The overall catch of steelhead has declined dramatically since the early 2000s, with an overall average of 2,795 from 2004 to 2017, as measured by expanded salvage. The percentage of natural-origin (unclipped) fish in salvage has fluctuated, but has leveled off to an average of 34 percent since a high of 93 percent in 1999. About 80 percent of the historical spawning and rearing habitat once used by anadromous steelhead in the Central Valley is now upstream of impassible dams (Lindley et al. 2006). Many historical populations of CCV steelhead are entirely above impassable barriers and may persist as resident or adfluvial rainbow trout, although they are presently not considered part ofthe DPS. Steelhead are well-distributed throughout the Central Valley below the major rim dams (Good et al. 2005, National Marine Fisheries Service 20 16b). Most ofthe steelhead populations in the Central Valley have a high hatchery-origin component, including those from Battle Creek (adults intercepted at the Coleman NFH weir), American River, Feather River, and Mokelumne River. The continued decline of CCV steelhead abundance and population growth rates is largely the result of a significant reduction in the amount and diversity of habitats available to these populations (Lindley et al. 2006), and is likely influenced by changes to the underlying genetic and environmental factors that support the anadromous phenotype of this species (Kendall et al. 2014). Past research has emphasized that genetic makeup (Pearse et al. 2014), growth and survival in freshwater, survival during migration and at sea, and asymptotic sizes achievable in freshwater are likely key factors in determining life-history expression and adaptation (e.g., Satterthwaite et al. 2009, Satterthwaite et al. 2010). However, despite decades of research on this topic, reviewed by Kendall et al. (2014), considerable uncertainty remains regarding the factors that drive the expression of anadromy in 0. Myldss. Though genetic analyses conducted over the last twenty years illustrate that there is still significant genetic population structure among steelhead populations within the California Central Valley, they also provide evidence of recent reduction in population size for steelhead throughout the Central Valley (Nielson et al. 2005). Additionally, historical hatchery practices have had a profound influence on the genetic makeup of CCV steelhead. Garza et al. (2008) analyzed the genetic relationships among CCV steelhead populations and found that unlike the situation in coastal California watersheds, fish below barriers in the Central Valley were often more closely 65 Biological Opinion for the Long-Term Operation of the CVP and SWP related to below barrier fish from other watersheds than to steelhead above barriers in the same watershed. This pattern suggests the ancestral genetic structure is still relatively intact above barriers, but may have been altered below barriers by stock transfers. The genetic diversity of CCV steelhead is also compromised by hatchery-origin fish, which likely comprise the majority of the annual spawning runs, placing the natural-origin population at a high risk of extinction (Lindley et al. 2007). Steelhead in the Central Valley historically consisted ofboth summer-run and winterrun Chinook salmon migratory forms. Only winter-run (ocean-maturing) steelhead are currently found in Central Valley rivers and streams, as summer-run steelliead have been extirpated (McEwan and Jackson 1996, Moyle 2002). Although CCV steelhead will experience similar effects of climate change to Chinook salmon, as they are also blocked from the vast majority of their historic spawning and rearing habitat, the effects may be even greater in some cases, as juvenile CCV steelhead need to rear in the stream for one to two summers prior to emigrating as smolts. In the Central Valley, summer and fall temperatures below the dams in many streams already exceed the recommended temperatures for optimal growth of juvenile steelhead, which range from 57°F to 66°F (14°C to l9°C). However, one study did find that juvenile steelhead could achieve average growth rates exceeding 1mm/day in the American River even when summer water temperatures regularly exceed 20°C (Sogard et al. 2012). It is unknown if this observation is applicable to steelhead in other Central Valley rivers, but such results from Sogard et al. (2012), and other salmonid-focused studies (Manhard et al. 2018), highlight the interactive role of water temperature and food availability in modulating growth in salmonids. Several studies have found that steelhead require colder water temperatures for spawning and embryo incubation than salmon (McCullough et al. 2001). In fact, McCullough et al. (2001) recommended an optimal incubation temperature at or below 52°F to 55°F (11 oc to 13°C). Successful smoltification in steelhead may be impaired by temperatures above 54°F (l2°C), as reported in Richter and Kolmes (2005). As stream temperatures warm due to climate change, the growth rates of juvenile steelhead could increase in some systems that are currently relatively cold, but potentially at the expense of decreased survival due to higher metabolic demands and greater presence and activity of predators. Stream temperatures that are currently marginal for spawning and rearing may become too warm to support natural-origin steelhead populations. 2.2.5.1 Summary of California Central Valley Steelhead Distinct Population Segment Viability All indications are that natural-origin CCV steelhead have continued to decrease in abundance and in the proportion of natural-origin to hatchery-origin fish over the past 25 years (Good et al. 2005, National Marine Fisheries Service 2016b); the long-term trend remains negative. Hatchery-origin production and returns are dominant over natural-origin fish. Most naturalorigin CCV steelhead populations are very small and may lack the resiliency to persist for protracted periods if subjected to additional stressors, particularly widespread stressors such as climate change. The genetic diversity of CCV steelhead has likely been impacted by low population sizes and high numbers of hatchery-origin fish relative to natural-origin fish. In summary, the 5-year status review of the CCV steelhead DPS (National Marine Fisheries Service 2016b) found that the status ofthe DPS appears to have remained unchanged since the 2011 status review (National Marine Fisheries Service 2011b), and the DPS is likely to become endangered within the foreseeable future throughout all or a significant portion of its range. 66 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.2.6 Critical Habitat and Physical or Biological Features for California Central Valley Steelhead The critical habitat for CCV steelhead lists the PBFs (70 FR 52488; September 2, 2005), which are described in Appendix B. In summary, the PBFs include freshwater spawning sites, freshwater rearing sites, freshwater migration corridors, and estuarine areas. The geographical extent of designated critical habitat includes, but is not limited to, the following: Sacramento, Feather, and Yuba rivers; Clear, Deer, Mill, Battle, and Antelope creelks in the Sacramento River basin; the San Joaquin River, including its tributaries; and the waterways of the Delta. 2.2.6.1 Summary of California Central Valley Steelhead Critical Habitat Many ofthe PBFs of CCV steelhead critical habitat are degraded and provide limited high quality habitat. Passage to historical spawning and juvenile rearing habitat has been largely reduced due to dam construction throughout the Central Valley. Levee construction has also degraded the freshwater rearing and migration habitat and estuarine areas as riparian vegetation has been removed, reducing habitat complexity and food resources and resulting in many other ecological effects. Contaminant loading and poor water quality (including warm water temperatures) in central California waterways pose a tlrreat to CCV steelhead, their habitat, and food resources. Additionally, due to reduced access to historical habitat, genetic introgression is occurring because natural-origin fish are interacting with hatchery-origin fish, providing the potential to reduce the long-term fitness and survival of this species. Although the current conditions of CCV steelhead critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain in the Sacramento-San Joaquin River watershed and the Delta are considered to have high intrinsic value for the conservation of the species as they are critical to ongoing recovery efforts. 2.2.7 • • Southern Distinct Population Segment of North American Green Sturgeon Listed as threatened (71 FR 17757; April 7, 2006) Designated critical habitat (74 FR 52300; October 9, 2009) The federally listed sDPS ofNorth American green sturgeon and its designated critical habitat occur in the action area and may be affected by the PA. Detailed information regarding DPS listing and critical habitat designation history, designated crucial habitat, DPS life history, and VSP parameters can be found in Appendix B. Although McElhany et al. (2000) specifically addresses viable populations of salmonids, NMFS believes that the concepts and viability parameters in McElhany et al. (2000) can be applied to sDPS green sturgeon (see Analytical Approach section 2-1). Green sturgeon are known to range from Baja California to the Bering Sea along the North American continental shelf. During late summer and early fall, subadults and non-spawning adult green sturgeon can frequently be found aggregating in estuaries along the Pacific coast (Emmett et al. 1991, Moser and Lindley 2007). Using polyploid microsatellite data, Israel et al. (2009) found that green sturgeon within the Central Valley of California belong to the sDPS. Additionally, acoustic tagging studies have found that green sturgeon found spawning within the Sacramento River are exclusively sDPS green sturgeon (Lindley et al. 2011 ). In waters inland from the Golden Gate Bridge in California, sDPS green sturgeon are known to range through the 67 Biological Opinion for the Long-Term Operation of the CVP and SWP estuary and Delta and up the Sacramento, Feather, and Yuba rivers (Israel et al. 2009, S.P. Cramer & Associates 2011, Seesholtz et al. 20 14). It is unlikely that green sturgeon utilize areas of the San Joaquin River upriver of the Delta with regularity, and spawning events are thought to be limited to the upper Sacramento River and its tributaries. There is no known modem usage of the upper San Joaquin River, and adult green sturgeon spawning has not been documented (Jackson and Van Eenennaarn 2013). However, there was a sighting of an adult green sturgeon in the Stanislaus River in October 2017. Recent research indicates that the sDPS is composed of a single, independent population, which principally spawns in the mainstem Sacramento River (Israel et al. 2009), and also spawns opportunistically in the Feather River and possibly even the Yuba River (S.P. Cramer & Associates 2011, Seesholtz et al. 2014). Concentration of adults into a very few select spawning locations makes the species highly vulnerable to poaching and catastrophic events. The apparent, but unconfirmed, extirpation of spawning populations from the San Joaquin River narrows the available habitat within their range, offering fewer habitat alternatives. Whether sDPS green sturgeon display diverse phenotypic traits, such as ocean behavior, age at maturity, and fecundity, or ifthere is sufficient diversity to buffer against long-term extinction risk is not wellunderstood. It is likely that the diversity of sDPS green sturgeon is low, given recent abundance estimates (National Marine Fisheries Service 2015a). Trends in abundance of sDPS green sturgeon have been estimated from two long-term data sources: (1) salvage numbers at the State and Federal pumping facilities (Figure B-16 in Appendix B), and (2) incidental catch of green sturgeon by the CDFW's white sturgeon sampling/tagging program. Historical estimates from these sources are expected to be unreliable, as sDPS green sturgeon were likely not taken into account in incidental catch data, and salvage does not capture range-wide abundance in all water year types. Recently, more rigorous scientific inquiry has been undertaken to generate abundance estimates (Israel and May 2010, Mora et al. 2015). A decrease in sDPS green sturgeon abundance has been inferred from the amount of take observed at the south Delta pumping facilities: the Skinner Delta Fish Protection Facility (SDFPF) and the Tracy Fish Collection Facility (TFCF). These data should be interpreted with some caution; operations and practices at the facilities have changed over the decades, which may affect the salvage data shown in Figure B-16 of Appendix B. The salvage data likely indicate a high production year versus a low production year qualitatively, but cannot be used to rigorously quantify abundance. Since 2010, more robust estimates of sDPS green sturgeon have been generated. As part of a doctoral thesis at U.C. Davis, Ethan Mora has been using acoustic telemetry as well as Dualfrequency identification sonar (DIDSON) to locate green sturgeon in the Sacramento River and to derive an adult spawner abundance estimate (Mora et al. 2015). Results of these surveys estimate an average annual spawnmg run of223 (DIDSON) and 236 (telemetry) fish. These estimates do not include the number of spawning adults in the lower Feather or Yuba rivers, where green sturgeon spawning was recently confirmed (Seesholtz et al. 2014). The parameters of green sturgeon population growth rate and carrying capacity in the Sacramento Basin are poorly understood. Larval count data show enormous variance among years. In general, sDPS green sturgeon year class strength appears to be highly variable with overall abundance dependent upon a few successful spawning events (National Marine Fisheries 68 Biological Opinion for the Long-Term Operation of the CVP and SWP Service 2010). Other indicators of productivity, such as data for cohort replacement ratios and spawner abundance trends, are not currently available for sDPS green sturgeon. The sDPS green sturgeon spawn primarily in the Sacramento River in the spring and summer. The Anderson-Cottonwood Irrigation District Diversion Dam (ACID) is considered the upriver extent ofsDPS green sturgeon migration in the Sacramento River (71 FR 17757; April 7, 2006). The upriver extent of sDPS green sturgeon spawning, however, is approximately 30 kilometers downriver of ACID because water temperatures in this section of the river are too cold for spawning. Thus, if water temperatures increase with climate change, temperatures adjacent to ACID may remain within tolerable levels for the embryonic and larval life stages of green sturgeon, but temperatures at spawning locations lower in the river may be more affected. It is uncertain, however, if green sturgeon spawning habitat exists closer to ACID, which could allow spawning to shift upstream in response to climate change effects. Successful spawning of sDPS green sturgeon in other accessible habitats in the Central Valley (i.e., the Feather River) is limited, in part, by late spring and summer water temperatures (National Marine Fisheries Service 2015a). Similar to salmonids in the Central Valley, sDPS green sturgeon spawning in tributaries to the Sacramento River is likely to be further limited if water temperatures increase and higher elevation habitats remain inaccessible. 2.2.7.1 Summary of Green Sturgeon Southern Distinct Population Segment Viability The viability of sDPS green sturgeon is constrained by factors including a small population size, lack of multiple populations, and concentration of spawning sites into few locations. The risk of extinction is believed to be moderate (National Marine Fisheries Service 2010). Although threats due to habitat alteration are thought to be high and indirect evidence suggests a decline in abundance, there is much uncertainty regarding the scope of threats and the viability of population abundance indices (National Marine Fisheries Service 201 0). Lindley et al. (2008), in discussing winter-run Chinook salmon, states that an ESU represented by a single population at moderate risk of extinction is at high risk of extinction over a large timescale; this would apply to green sturgeon. The most recent 5-year status review for sDPS green sturgeon found that some threats to the species have been eliminated, such as take from commercial fisheries and removal of some passage barriers (NationaE Marine Fisheries Service 20 15a). Since many of the threats cited in the original listing still exist, the threatened status ofthe DPS is still applicable (National Marine Fisheries Service 2015a). 2.2.8 Critical Habitat Physical or Biological Features for Southern Distinct Population Segment Green Sturgeon The designated critical habitat for sDPS green sturgeon lists the PBFs (74 FR 52300; October 9, 2009), which are described in Appendix B. In summary, the PBFs include the following for both freshwater riverine systems and estuarine habitats: food resources, water flow, water quality, migratory corridor, depth, and sediment quality, as well as substrate type or size for just freshwater riverine systems. In addition, the PBFs include migratory corridor, water quality, and food resources in nearshore coastal marine areas. The geographical range of designated critical habitat includes the following: • In freshwater, the geographic range includes: 69 Biological Opinion for the Long-Term Operation of the CVP and SWP o o o o • The Sacramento River from the Sacramento !-Street Bridge to Keswick Dam, including the Sutter and Yolo bypasses and the lower American River from the confluence with the mainstem Sacramento River upstream to the highway 160 bridge The Feather River from its confluence with the Sacramento River upstream to the Fish Barrier Darn The Yuba River from the confluence with the Feather River upstream to Daguerre Point Dam The Sacramento-San Joaquin Delta (as defined by California Water Code section 12220, except for listed excluded areas) In coastal bays and estuaries, the geographical range includes: o o o o San Francisco, San Pablo, Suisun, and Humboldt bays in California Coos, Winchester, Yaquina, and Nehalem bays in Oregon Willapa Bay and Grays Harbor in Washington The lower Columbia River estuary from the mouth to river kilometer (RK) 74 In coastal marine waters, the geographic range includes all United States coastal marine waters out to the 60-fathom-depth bathymetry line, from Monterey Bay, California, north and east to include the Strait of Juan de Fuca, Washington. 2.2.8.1 Summary of Southern Distinct Population Segment Green Sturgeon Critical Habitat Currently, many of the PBFs of sDPS green sturgeon are degraded and provide limited high quality habitat. Factors that lessen the quality of migratory corridors for juveniles include unscreened or inadequately screen diversions, altered flows in the Delta, and presence of contaminants in sediment. Although the current conditions of green sturgeon critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain in both the Sacramento-San Joaquin River watersheds, the Delta, and nearshore coastal areas are considered to have high intrinsic value for the conservation of the species. 2.2.9 • • Southern Resident Killer Whale Distinct Population Segment Listed as endangered (70 FR 69903; November 18, 2005) Designated critical habitat (71 FR 69054; November 29, 2006) The Federally listed DPS of Southern Resident Killer Whale (SRKW) occurs in the action area and may be affected by the PA. Designated critical habitat for SRKW does not occur within the action area of the PA. SRKW occur throughout the coastal waters off Washington, Oregon, and Vancouver Island and are known to travel as far south as central California and as far north as Southeast Alaska (National Marine Fisheries Service 2008b, Hanson et al. 2013, Carretta et al. 2017). Three podsJ, K, and L- make up the SRKW population. During the spring, summer, and fall months, the whales spend a substantial amount of time in the inland waterways of the Strait of Georgia, Strait of Juan de Fuca, and Puget Sound (Bigg 1982, Ford et al. 2000, Krahn et al. 2002, Hauser et al. 2007). In general, the three pods are increasingly present in May and June and spend a considerable amount of time in inland waters through September. Sightings in late fall decline as 70 Biological Opinion for the Long-Term Operation of the CVP and SWP the whales shift to the outer coastal waters. Satellite-linked tag deployments have also provided more data on the SRKW movements in the winter indicating that K and L pods use the coastal waters along Washington, Oregon, and California during non-summer months. The limited range of the sightings or acoustic detections of J pod in coastal waters, the lack of coincident occurrence during the K and L pod sightings, and the results from satellite tagging in 2012 to 2016 (NWFSC unpublished data) indicate J pod's limited occurrence along the outer coast and extensive occurrence in inland waters. At present, the SRKW population has declined to the lowest levels seen in over thirty years. During an international science panel review of the effects of salmon fisheries (Hilborn et al. 2012), the panel stated that during 1974 to 2011, the population experienced a realized growth rate of0.71 percent, from 67 individuals to 87 individuals. However, as of December 2018, the population has decreased to only 74 whales, a historical low in the last 30 years with a current realized growth rate (from 1974 to 20 17) at half of the previous estimate described in the science panel report; 0.29 percent. There is representation in all three pods, with 22 whales in J pod, 18 whales in K pod and 34 whales in L pod. Seasonal mortality rates among SRKW may be highest during the winter and early spring, based on the numbers of animals missing from pods returning to inland waters each spring:. Olesiuk et al. (2005) identified high neonate mortality that occurred outside of the summer season. Additionally, stranding rates are higher in winter and spring for all killer whale forms in Washington and Oregon (Norman et al. 2004). Recent updates to population viability analyses suggest a downward trend in population growth projected over the next 50 years (National Marine Fisheries Service 2016e). This downward trend is in part due to the changing age and sex structure of the population, but also related to the relatively low fecundity rate observed over the period from 2011 to 2016 (National Marine Fisheries Service 20 16e). To explore potential demographic projections, Lacy et al. (20 17) constructed a population viability assessment that considered sublethal effects and the cumulative impacts of threats (contaminants, acoustic disturbance, and prey abundance). They found that over the range of scenarios tested, the effects of prey abundance on fecundity and survival had the largest impact on the population growth rate. Furthermore, they suggested in order for the population to reach the recovery target of2.3 percent growth rate, the acoustic disturbance would need to be reduced in half and the Chinook abundance would need to be increased by 15 percent (Lacy et al. 20 17). Several factors identified in the final recovery plan for SRKW may be limiting recovery. These are quantity and quality of prey, toxic chemicals that accumulate in top predators, and disturbance from sound and vessels. When prey is scarce, SRKW likely spend more time foraging than when prey is plentiful. Increased energy expenditure and prey limitation can cause poor body condition and nutritional stress. Nutritional stress is the condition of being unable to acquire adequate energy and nutrients from prey resources and as a chronic condition, can lead to reduced body size of individuals and to lower reproductive and survival rates of a population (Trites and Donnelly 2003). Oil spills are also a risk factor. It is likely that multiple threats are acting together to impact the whales. Modeling exercises have attempted to identify which threats are most significant to survival and recovery (Lacy et al. 2017) and available data suggests that all of the threats are potential limiting factors (National Marine Fisheries Service 2008b). 71 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.2.9.1 Summary of Southern Resident Killer Whale DPS Viability In summary, the SRKW DPS is at risk of extinction primarily from low abundance and impaired survival and fecundity, especially in recent years. Major threats to this species include limitations in available preferred prey (Chinook salmon), vessel and sound impacts, contaminants, and climate change. SRKW would benefit from the recovery of Chinook salmon populations and increased access to prey, as well as protections to reduce the impacts of vessels and sound, as well as reduced exposure to contaminants in prey items and in the marine environment. 2.3 Action Area "Action area" means all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action (50 CFR 402.02). There are two action areas identified in this biological opinion. Generally, for listed anadromous fish, the action area encompasses the following reservoirs, rivers, and the land between the levees adjacent to the rivers: (1) Shasta and Keswick reservoirs, and the Sacramento River from Keswick Reservoir downstream to and including the Sacramento-San Joaquin Delta; (2) Whiskeytown Reservoir, and Clear Creek from Whiskeytown Reservoir to its confluence with the Sacramento River; (3) Folsom Reservoir, Lake Natoma, and the American River from Lake Natoma downstream to its confluence with the Sacramento River; (4) New Melones Reservoir, and the Stanislaus River from New Melones Reservoir to its confluence with the San Joaquin River; (5) San Joaquin River from the confl.uence of the Stanislaus River downstream to and including the SacramentoSan Joaquin Delta; and (6) San Francisco Bay and Suisun Marsh. For purposes of the SRKW DPS only, the action area includes nearshore coastal areas in California, Oregon, and Washington, not including Puget Sound. Additionally, the areas affected by the PA include Shasta, Whiskeytown, Folsom, and New Melones dams and reservoirs because they are influenced by the operation ofCVP and SWP. Starting in 2016, Friant Dam and the Upper San Joaquin River have been hydrologically reconnected to the Delta through the release of San Joaquin River Restoration Program flows. However, operations ofFriant Dam are not included in the PA. Therefore, the action area within the mainstem San Joaquin River is limited to the section from the confluence of the Stanislaus River downstream to, and including, the Sacramento-San Joaquin Delta. The CVP and SWP affects the abundance of Central Valley Chinook salmon originating from the Sacramento and San Joaquin rivers . Central Valley Chinook salmon is a prey species for SRKW. The action area for SRKWs is the area of co-occurrence of Central Valley Chinook salmon and SRKWs in the nearshore coastal waters of California, Oregon, and Washington, excluding Puget Sound. 2.4 Environmental Baseline This section describes the past and ongoing factors leading to the status ofESA-listed species and the condition of their critical habitat within the action area. As defined by ESA regulations, the environmental baseline includes the past and present impacts of all federal, state, or private actions and other human activities in the action area, the anticipated impacts of all proposed federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of state or private actions which are contemporaneous with the 72 Biological Opinion for the Long-Term Operation of the CVP and SWP consultation in process (50 CFR 402.14 1986). The key purpose of the Environmental Baseline is to describe the condition of the listed species/critical habitat in the Action Area. Per this regulatory definition, past and present CVP/SWP operations are federal actions in the action area, and thus the impacts associated with those federal actions previously consulted on become part of the environmental !baseline for subsequent consultations. It is important to note that for ESA section 7, each time the operations ofthe CVP/SWP are consulted on (e.g., 2004 and 2008/2009), the impacts of past and present operations of the CVP/SWP become part of the environmental baseline for subsequent consultations. The operations of the CVP/SWP over time is not one continuous Federal Action in the context ofESA compliance. Rather, the CVP/SWP action described and analyzed in the 2004 Opinion was discrete from the CVP/SWP action described and analyzed in 2008/2009, which again, is discrete from the proposed CVP/SWP action analyzed in this Opinion. Each proposed action had specific components and operating criteria, and is therefore considered separate federal actions requiring separate ESA section 7 consultations and analyses. Reclamation established a WOA scenario as part of the BA's Environmental Baseline to isolate and define potential effects of the PA apart from effects of non-proposed actions. The model run representing this scenario does not include CVP and SWP operations, but does include the operations of non-CVP and non-SWP facilities, such as operation of public and private reservoirs on the Yuba, Tuolumne, and Merced rivers. NMFS considers the without-action scenario to represent effects related to the existence of CVP and SWP facilities. The without-action scenario provides context for how these facilities have shaped the habitat conditions for species and critical habitat in the action area. The environmental baseline section in Reclamation's BA includes a WOA scenario and also the past, present, and ongoing impacts of human and natural factors, including the present and ongoing effects of current operations that were considered in prior consultations. The NMFS analysis recognizes that the PA is not simply an ongoing action that projects the status quo into the future, but a new operational approach with a different suite of operational criteria and associated effects that must be distinguished and analyzed on their own. NMFS' analysis traces and evaluates the proposed action. With respect to dams, NMFS treats the existence of dams and some past operations in the baseline with respect to future effects on the status of the species and habitat conditions. NMFS considers in the effects analysis how future daily, monthly and seasonal operational decisions to store or release water from CVP/SWP reservoirs can have effects downstream and through the Delta, in various timescales. Depending on the flow and quality (e.g., temperature) of the water released, the timing and location, and life stage and species affected, these effects can be both beneficial or adverse. 2.4.1 Landscape Scale Factors Affecting Listed Species in the Central Valley Since settlement of the Central Valley in the rnid-1800s, populations of native Chinook salmon, steelhead, and green sturgeon have declined dramatically, largely due to factors that completely reshaped the aquatic ecosystem such as dam construction, water management, hydropower facilities, levee construction, and before those, gold mining. These land use changes eliminated important habitats, or blocked access to them, and reduced the abundance, productivity, and distribution of Central Valley salmonids and sturgeon. Habitat simplification, fishing, hatchery impacts, and other stressors led to the loss of genetic and phenotypic (life history, morphological, 73 Biological Opinion for the Long-Term Operation of the CVP and SWP behavioral, and physiological) diversity in Central Valley salmonids, which has reduced their capacity to cope with a variable and changing climate (Herbold et al. 2018). Given tlhe reliance of SRKW on Chinook salmon prey resources that include Central Valley Chinook salmon (described further in Section 2.4.7.4 Factors Affecting the Prey ofSouthern Residents in the Action Area), these factors have also been, and continue to, affect the available prey base of SRKWs. Land use changes to support and protect California's rapidly increasing human population combined with substantial and widespread water development, including the construction and operation of the CVP/SWP, have been accompanied by significant declines in nearly all species of native fish (State Water Resources Control Board 20 17b). Recent evidence from a study that used a novel combination of tagging technologies suggests that the freshwater and estuarine environment has been so dramatically altered by habitat loss and water management that the anadromous life history strategy may no longer be sustainable for Central Valley salmon (Michel 20 18). Dams, levees, water management, and gold mining are the main landscape-scale factors that have shaped the Central Valley environment to what it is today, with climate change providing additional impacts. These landscape-scale factors and their impact on Central Valley listed species and critical habitat are discussed below, followed by a section on more localized, but also important factors affecting listed species in the Central Valley. Included is a description of the status of each Central Valley anadromous fish species and their critical habitat in the action area. The Environmental Baseline chapter wraps up with a discussion on the status of Southern Resident killer whales and an overview of the factors affecting their prey. 2.4.1.1 Dams The construction of dams around the Central Valley has blocked anadromous salmonids and sturgeon from most of their historic spawning and initial rearing habitat, eradicating most historic populations of winter-run Chinook salmon, spring-run Chinook salmon, steelhead, and green sturgeon. Between 72 to 90 percent of the origina1 Chinook salmon spawning and holding habitat in the Central Valley drainage is no longer accessible due to dam construction (Figure 2.4.1-1) (Yoshiyama et al. 2001 );(Cummins et al. 2008). Winter-run Chinook salmon lost three of its four historic spawning populations with the construction of Keswick and Shasta Dams. Perhaps 15 of the 18 or 19 historical populations ofCV spring-run Chinook salmon are extirpated, with their entire historical spawning habitats upstream from impassable dams (Lindley et al. 2007). Currently, impassable dams block access to 80 percent of historically available habitat, and block access to all historical spawning habitat for about 38 percent of the historical populations of steelhead (Lindley et al. 2006). Impassable barriers are considered to be the main threat to sDPS green sturgeon as migration corridors are blocked and migration cues (water flow) are altered (National Marine Fisheries Service 2018g). The existence of these impassable barriers have significant adverse effects on species in the past, present and future. 74 Biological Opinion for the Long-Term Operation of the CVP and SWP Figure 2.4.1-1 Historical habitat accessible to salmonids (A, in blue) and lost upstream habitat (B, in black) from construction of impassible dams (black squares). Remaining anadromous habitat for multiple life stages of salmon is largely confined to the valley floor (B, in blue). 2.4.1.2 Levees The construction of levees throughout the Sacramento and San Joaquin River watersheds has resulted in a landscape in which less than 5 percent of the native wetland, riparian, and floodplain habitats remain (Whipple et al. 2012). Ninety-three percent of historic floodplain rearing habitat is no longer accessible due to levee construction (Figure 2.4.1-2) (Herbold et al. 2018). Those dynamic shallow water habitats that historically provided food rich areas for rearing salmon ids have been almost entirely replaced by urban and agricultural landscapes (Herbold et al. 20 18). Given that juvenile salmon grow faster when they have access to inundated floodplain habitat than in adjacent river channels (Sommer et al. 200lb, Jeffres et al. 2008), it is likely that overall salmonid productivity has been diminished with the majority of Sacramento and San Joaquin rivers now confined by levees in all but the wettest years. Central Valley salmonids evolved with access to a diverse suite of shallow water habitats, promoting resilience against a variable climate. Now adaptations to earlier conditions are mismatched with the current simplified river systems. Important sources of habitat diversity for juvenile salmonids in the current system are Yolo and Sutter flood bypasses, where salmonids can access food rich floodplain habitat under high flows. Still, with so little freshwater habitat now available in the Central Valley, habitat heterogeneity has decreased, and we expect salmonid population diversity and resilience has decreased (Figure 2.4.1-3), and vulnerability to climate variability and change has increased (Herbold et al. 2018). 75 Biological Opinion for the Long-Term Operation of the CVP and SWP ·-. ._. .- .·- Historical Floodplain & Wetlands 1.2 Million hectares Current Agricultural, Fallow, & Urban Areas 1 million hectares Current Floodplain Remnants 76,000 hectares (-7% of Historic) + 31,000 hectares of Open Water Figure 2.4.1-2 Historical floodplain and Delta wetlands habitat ; (B) remnant floodplain and wetland habitat currently in agricultural lands, fallow lands, or urban areas; and (C) floodplain and wetland remnants (Herbold et al. 2018). 76 Biological Opinion for the Long-Term Operation of the CVP and SWP Trait Diversity Figure 2.4.1-3 Conceptual model of how habitat heterogeneity creates trait and phenotypic diversity to promote population resilience (Herbold et al. 2018) 2.4.1.3 Water Management Large amounts of water have historically been and currently are exported from throughout the Central Valley watershed to support agricultural, industrial, and urban demands. Upstream water diversions combined with water exports in the Delta have reduced January to June outflows by an estimated 56 percent (average), and annual outflow by an estimated 52 percent (average). In the driest condition, in certain months outflows are reduced by more than 80 percent, January to June flows are reduced by more than 70 percent and annual flows are reduced by more than 65 percent (State Water Resources Control Board 2017b). To help put the Central Valley outflow reductions in context it is helpful to look at how other aquatic ecosystems have responded to water extractions. (Richter et al. 2012) concluded that flow modifications greater than 20 percent likely result in moderate to major changes in natural structure and ecosystem function, with greater risk associated with greater levels of alteration. Based on published studies of European and Asian rivers, Rozengurt et al. (1987) concluded that when successive spring and annual water withdrawals exceeded 30 percent and more than 40-50 percent of the normal unimpaired flow respectively, water quality and fishery resources in the river and estuary ecosystems deteriorated to levels which overrode the ability of the system to restore itself. In the context of Richter et al. (20 12) and Rozengurt et al. (1987), it is not surprising that native fish and wildlife in the Bay-Delta watershed have been significantly impacted by removing over half of the water. Water diversions and the corresponding reduction in flows are not the only factor contributing to Central Valley anadromous fish species declines, but they are a significant one (State Water Resources Control Board 2017b). The CVP/SWP is one of the world's largest water storage and conveyance systems with both the federal and the state portions of the projects capable of storing and exporting millions of acre77 Biological Opinion for the Long-Term Operation of the CVP and SWP feet of water away from the Delta each year (Figure 2.4.1-4). The large volumes being exported combined with the location of the pumps in the south Delta result in significantly modified hydrologic (Figure 2.4.1-5) and biological systems (Cummins et al. 2008). The Delta also has been physically modified with development of the CVP/SWP. The Public Policy Institute of California summarized the changes and resultant impact on native fish as follows: "After the SWP began operations in the late 1960s, the combined effects of CVP and SWP impoundments and diversions-along with those of hundreds of other water users-became clearly apparent. River flows and water quality declined, threatening both economic and environmental uses; and the ecological balance of the Delta became disastrous to native fish species (Lund et al. 2007, Moyle and Bennett 2008, Lund et at. 20 10). The conversion of the 700,000-acre tidal freshwater marsh to a network of rock-lined channels had severely limited available habitat for fish, and dramatic reductions in the quantity and quality of Delta inflows further degraded that habitat. As the SWP increased its exports in the 1980s-almost doubling direct extractions from the Delta-conditions reached a crisis point (Figure 1.4)" (Figure 2.4.1-6) (Hanak et al. 2011). 78 Biological Opinion for the Long-Term Operation of the CVP and SWP - Million Acre Feet 9 8 7 Other Diversions including Contra Costa Water District and the North Bay Aqueduct D D State Water Project diversions from the south Delta D Surface water diversion for In-Delta use .... "" Central Valley Project diversion from the Delta "" 6 5 4 3 2 p. 0 1930 I 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 Figure 2-4.1-4 Annual Water Diversions from within the Delta (California Department of Water Resources 2013). 79 Biological Opinion for the Long-Term Operation of the CVP and SWP Figure 2.4.1-5 Flow direction in the South Delta. The left panel depicts the tidally averaged flow direction in the absence of export pumping. The right panel depicts reversal of tidally averaged flows that occurs during times of high exports (pumping) and low inflows to the Delta (Delta Stewardship Council 2013). 80 Biological Opinion for the Long-Term Operation of the CVP a nd SWP 7 • CVP - Winter-run Chinook salmon • SWP - - Delta smelt 400 6 -.;_ ' +- ro 450 350 5 300 0"1 c ·a. 4 250 :::l ro 200 3 :::l c c <( c.(1) E a. x - (1)0 -cO 2 I I 150 I II (1) ro ro c :::l ro -a'..OIIl roo ..c:." lllOI ·- .-- 100 50 0 ,"Jso ,"Jrd>< ,"Jo?:> ,"J11. ,q1o ,"J?:>r>. ,"J?:>?:> ,q"J'1- ,"J"Jo SOURCES: For Delta exports, California Department of Water Resources Dayflow dat a; for fish populations, California Department of Fish and Game survey data. NOTES: Both the CVP and t he SWP pump water from the southwestern Delta. CVP exports include pumping from the Contra Costa Water District, w hich draws from the Contra Costa Canal in t he western Delta (roughly 120,000 acre-feet [af]l in the 2000s), and SWP exports include pumping from the North Bay Aqueduct, which draws from the northern Delta to supply Solano and Napa Counties (roughly 50,000 af in the 2000s). Series for salmon and adult delta smelt are not available before the years shown. Figure 2.4.1 -6 Native Delta fish populations declined as exports increased (Hanak et al. 2011). Past and current operations of the CVP/SWP, including flow releases and water temperatures, have reduced survival of juvenile salmonids outmigrating through the Delta. Prior to the protections established by the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), mortality of winter-run juveniles entering the interior of the Delta (through DCC or Georgiana Slough) was estimated to be approximately 66 percent, with a range of 35-90 percent mortality (Burau et al. 2007, Perry and Skalski 2008, Vogel 2008). Studies indicate overall mortality through the Delta for late fall-run Chinook salmon releases near Sacramento from 2006 through 2010 ranged from 46 to 83 percent (Perry et al. 20 16). The available studies are consistent in that mortality is considerably higher through the central and south Delta than if the juveniles stayed within the mainstem Sacramento River. The operation of the Delta Cross Channel gates can negatively impact migration of sDPS green sturgeon as well by providing false migration cues for juvenile and adult sturgeon to move from the lower Sacramento River to the central Delta rather than their intended destination of the western Delta and San Francisco Bay (National Marine Fisheries Service 2018g). Green sturgeon are also highly vulnerable to entrainment in the diversions of the Sacramento River and Delta; 81 Biological Opinion for the Long-Term Operation of the CVP and SWP flow and pipe configuration affects entrainment rates (Mussen et al. 2014a, Poletto et al. 2014). Efforts to salvage gr,een sturgeon at the CVP/SWP have been conducted for decades; the number of green sturgeon observed in these facilities is typically low with a few individuals per year (National Marine Fisheries Service 2018g). Flow fluctuations from past and current Sacramento River operations management of the CVP have resulted in stranding ofjuvenile salmon ids, Chinook salmon redd dewatering and redd scour in the Sacramento River. High flows have also resulted in CCV steelhead redd scour on the American River but the frequency of redd scouring flows are expected to be slightly lower with completion of the Folsom Dam and Lake Water Control Manuel (National Marine Fisheries Service 201 8e). 2.4.1.4 Gold Mining The first major anthropogenic impact on the Central Valley watersheds came from hydraulic mining in the years shortly after the California gold rush began in 1848. By 1859, an estimated 5,000 miles of mining flumes and canals diverted streams used by salmonids and sturgeon for spawning and nursery habitat. Habitat alteration and destruction also resulted from tlhe use of hydraulic cannons, and from hydraulic and gravel mining, which leveled hillsides and sluiced an estimated 1.5 billion cubic yards of debris into the streams and rivers of the Central Valley (Lufkin 1991 ). Mining practices profoundly altered landscape form and process: streams were dammed, diverted or drained; soil and vegetation was stripped over large areas; piles of coarse mine tailings reduced floodplain inundation; and excessive sediment loading massively aggraded and armored stream channels. Many of these impacts persist today, with severe and enduring effects on critical habitat for salmon species (National Marine Fisheries Service 2014b), and for green sturgeon (National Marine Fisheries Service 2018g). 2.4.1.5 Climate Change One major factor affecting the range-wide status of the threatened and endangered anadromous fish in the Central Valley and aquatic habitat at large is climate change. From 2012 to 2016, California experienced the most extreme drought since instrumental records began in 1895. A growing body of evidence suggests that climate change has increased the likelihood of extreme droughts in California (Department of Water Resources 2018). Warmer temperatures associated with climate change reduce snowpack and alter the seasonality and volume of seasonal hydrograph patterns (Cohen et al. 2000). Central California bas shown trends toward warmer winters since the 1940s (Dettinger and Cayan 1995). An altered seasonality results in runoff events occurring earlier in the year due to a shift in precipitation falling as rain rather than snow (Roos 1991, Dettinger et al. 2004). Specifically, the Sacramento River basin annual runoff amount for April-July has been decreasing since about 1950 (Roos 1987, Roos 1991 ). Increased temperatures influence the timing and magnitude patterns of the hydrograph, and strain the ability of reservoir water managers to provide cold water releases for salmonids. The magnitude of snowpack reductions is subject to annual variability in precipitation and air temperature. Large spring snow water equivalent (SWE) percentage changes, late in the snow season, are due to a variety of factors including reduction in winter precipitation and temperature 82 Biological Opinion for the Long-Term Operation of the CVP and SWP increases that rapidly melt spring snowpack (Vanrheenen et al. 2004). Factors modeled by Vanrheenen et al. (2004) show that the melt season shifts to earlier in the year, leading to a large percent reduction of spring SWE (up to 100 percent in shallow snowpack areas). Additionally, an air temperature increase of 2.1 oc (3 .8°F) is expected to result in a loss of about half of the average April snowpack storage (Vanrheenen et al. 2004). The decrease in spring SWE (as a percentage) would be greatest in the region of the Sacramento River watershed, at the north end of the Central Valley, where snowpack is shallower than in the San Joaquin River watersheds to the south. Warming attributed to climate change is expected to affect Central Valley anadromous salmonids and green sturgeon more than it already has. Because the Central Valley salmon, steelhead, and green sturgeon runs are restricted to low elevations as a result of impassable dams, if climate warms by soc (9°F), it is questionable whether any Central Valley Chinook salmon, and green sturgeon populations can persist (Williams 2006, National Marine Fislheries Service 20 18g). Based on an analysis of an ensemble of climate models and emission scenarios and a reference temperature from 19S1-1980, the most plausible projection for warming over Northern California is 2.S°C (4.S°F) by 20SO and soc by 2100, with a modest decrease in precipitation (Dettinger 200S). Chinook salmon in the Central Valley are at the southern limit of their range, and warming will shorten the period in which the low elevation habitats can support salmonid life stages. Projected 33 percent salinity increases in the Sacramento River Basin in the 21st century due to climate change may result in declining habitat quality and food web productivity; climate change will alter the salinity and prey base in green sturgeon juvenile rearing habitat and adult migration corridors (CH2M IDLL 2014, National Marine Fisheries Service 2018g). 2.4.2 Other Factors Affecting Listed Fish Species and Critical Habitat in the Action Area 2.4.2.1 Hatcheries Hatchery management was identified as an important factor contributing to the listings of CV spring-run Chinook salmon and CCV steelhead (National Marine Fisheries Service 2014b). Most of California's anadromous fish hatcheries were constructed for mitigation purposes related to loss of habitat due to construction of hydroelectric dams and both SWP and CVP management, and are therefore part of the environmental baseline. Statewide, there are nine hatchery facilities operated by the CDFW and two hatchery facilities operated by the USFWS. California's anadromous fish hatcheries produce ESA-listed Chinook salmon (Sacramento River winter-run Chinook salmon and CV spring-run Chinook salmon) and CCV steelhead. However, production of non-listed Central Valley fall-run Chinook salmon is the largest contributor of hatchery-origin Chinook salmon in the state, with a total combined release of nearly 30 million smolts annually. In the Central Valley, LSNFH, CNFH, FRFH, Nimbus Fish Hatchery, and Mokelumne Fish Hatchery currently produce Chinook salmon and all of them except for LSNFH also produce steelhead. Releasing large numbers of hatchery fish can pose a threat to natural-origin Chinook salmon populations through genetic impacts, displacement, competition for food and other resources, predation of hatchery fish on natural-origin fish, and increased fishing pressure on natural-origin stocks as a result of hatchery production (Waples 1991). The relatively low number of adult spawners needed to sustain a hatchery population can result in high harvest-toescapement ratios in waters where fishing regulations are set according to hatchery population. This can lead to over-exploitation and reduction in the size of natural-origin populations existing 83 Biological Opinion for the Long-Term Operation of the CVP and SWP in the same system as hatchery populations due to incidental bycatch (McEwan 2001). Currently, hatchery produced fall-run Chinook salmon comprise the majority of fall-run adults returning to Central Valley streams. Hatcheries in the Central Valley follow a 25 percent constant fractional marking of hatchery produced fall-run Chinook salmon juveniles. Any returning populations with adipose fin-clipped adult escapement greater than 25 percent, would indicate that hatcheryproduced fish are the predominate source in those spawning populations. To maximize survival, and as a result of the degraded conditions of downstream migration corridors in the Central Valley, most Chinook salmon hatchery production has been routinely released off-site, significantly downstream of the hatchery or in the estuary. The exception is CNFH, where hatchery managers have consistently implemented in-river releases. This approach was temporarily suspended during the recent drought (20 14 and 20 15), when envirorunental conditions in Battle Creek and the upper Sacramento River were likely to result in adverse impacts and significant mortality. [n order to circumvent these unfavorable conditions, the majority of the Chinook salmon produced by CNFH and other Central Valley hatcheries were trucked and released offsite. Although this offsite release practice has improved survival rates and resulted in increased ocean harvest of hatchery fish, it has also led to widespread straying of hatchery fish throughout the Sacramento-San Joaquin system (California Hatchery Scientific Review Group 2012). The impacts of artificial propagation programs in the Central Valley are primarily genetic impacts due to straying of hatchery fish and the subsequent interbreeding of hatchery fish with natural-origin fish. Effects ofthe continuation of producing and releasing salmonids at these hatcheries are considered part of the environmental baseline. Introgression of spring- and fall-run Chinook salmon and significant straying of adults from FRFH have posed a significant threat to the genetic integrity of natural spawning fall- and spring-run Chinook salmon in other watersheds, such as the upper Sacramento River and associated tributaries (National Marine Fisheries Service 2014b). The management of hatcheries, such as Nimbus Fish Hatchery and FRFH, can directly impact Chinook salmon and steelhead populations by oversaturating the natural carrying capacity of the limited habitat available below dams. In the case of the Feather River, significant redd superimposition occurs in-river due to the inability to spatially separate spring- and fall-run Chinook salmon adults. This concurrent spawning has led to hybridization between the spring- and fall-run Chinook salmon in the Feather River. Over the past several decades, the genetic integrity of CCV steelhead has diminished by increases in the proportion of hatchery fish relative to naturally produced fish, use of out-ofbasin stocks for hatchery production, and straying of hatchery produced fish (National Marine Fisheries Service 20 14b). Potential threats to natural-origin steelhead from hatchery programs include: (1) mortality in fisheries targeting hatchery-origin fish; (2) competition for prey and habitat; (3) predation by hatchery-origin fish; (4) disease transmission; and (5) genetic introgression by hatchery-origin fish that spawn naturally and interbreed with local natural-origin populations (National Marine Fisheries Service 2016b, d). High densities of hatchery fish in some rivers may cause competition with natural-origin juvenile parr and smolts. This problem is likely to be greatest when hatchery smolts residualize (those that do not migrate to the ocean). How often this occurs in Central Valley rivers is unknown. What is known is that some hatchery smolts do stray into other rivers. For example, hatchery smolts have been documented in the Vaki Riverwatcher camera, moving upstream/downstream 84 Biological Opinion for the Long-Term Operation of the CVP and SWP ofDaguerre Point Dam on the Yuba River, which most likely originated from the FRFH. They do not appear to be residualizing upstream of the dam, as they do not remain upstream of the dam for long, based on Vaki counts and anecdotal information from angling and snorkel surveys, but their behavior below the dam is not tracked. In the lower American River, some hatchery smolts appear to become "half-pounders", but it is unknown how much time they spend in the river versus in the Delta or Bays. Recent evaluations of these hatchery programs and Hatchery Genetic Management Plans have proposed or recommended changes in hatchery policies and management to address these impacts (State Water Resources Control Board 2017b). Hatcheries may also have short-term positive effects through supporting listed salmonid populations. Artificial propagation has been shown to be effective in bolstering the numbers of naturally-spawning fish in the short-term under specific scenarios. Artificial propagation programs can also aid in conserving genetic resources and guarding against catastrophic loss of naturally spawned populations at critically low abundance levels. For example, LSNFH propagates winter-run Chinook salmon to conserve the genetic resources of a single fish population at low abundance and in danger of extinction. A potential complementary goal of the hatchery program is restoration of the ESU. This goal could be achieved by providing a source of winter-run Chinook salmon to re-establish naturally spawning populations in historical habitats. According to the Central Valley salmonid recovery plan (National Marine Fisheries Service 2014b), "The LSNFH winter-run Chinook salmon conservation program on the upper Sacramento River is one of the most important reasons that Sacramento River winter-run Chinook salmon still persist." Conservation hatcheries like LSNFH can contribute to the recovery oflisted species. However, it is important to note that relative abundance is only one component of a viable salmonid population and managers must also consider the possible adverse impacts ofhatchery influence in the long-run, such as reduced fitness of the population. As described in Appendix C the USFWS has been engaged in efforts regarding CNFH and LSNFH and their contribution to the management and restoration of Chinook salmon in the Sacramento River and Battle Creek. These efforts are: (1) improving LSNFH; (2) implem enting the Battle Creek Reintroduction Plan; (3) designing and fish trapping and sorting facility at CNFH; and (4) studying alternative release strategies for CNFH produced fall-run Chinook salmon. Appendix C includes a brief description of each effort, including progress to date and expectations for completion and funding. All of these efforts are underway and at least partially funded, with most of the funding provided by Reclamation with additional funding and support from other partners. Specific recent and ongoing actions for improving the LSNFH include: 1. During the drought in 2014 and 2015, and at tlhe request ofNMFS and CDFW, LSNFH increased production of winter-run Chinook salmon to compensate for expected high temperature-dependent mortality in the Sacramento River and reinstated the captive broodstock program. Also, Reclamation funded the rental of two commercial-size chiUers to ensure adequate water temperatures for adult holding, egg incubation, and juvenile rearing. Those chillers were rented during the summer and fall and used on a just few occasions. Subsequently Reclamation has funded a small permanent chiller to ensure temperatures for egg incubation only. 85 Biological Opinion for the Long-Term Operation of the CVP and SWP 2. Several years ago, Reclamation funded, and the USFWS operated the ACID trap, a fish trap on the north side of the Sacramento River at Caldwell Park. To date, only two salmon have been collected at that site and the USFWS ceased operating the trap this year. 3. The USFWS partners with the CDFW for much of the monitoring for winter-run Chinook salmon on the Sacramento River. USFWS efforts include coded-wire tagging and marking Livingston Stone NFH-produced winter-run Chinook salmon, acoustic tagging a subset of those fish, rotary screw trapping at Red Bluff Diversion Dam, and carcass surveys on the mainstem Sacramento River. Reclamation covers the costs for all ofUSFWS efforts, mostly out of the operational funding agreement for CNFH and LNFH and the Opinion monitoring agreement with the USFWS ' Red Bluff Fish and Wildlife Office. Both ofthese are long-term agreements with a history of renewal. Specific ongoing actions for improving the implementing the Battle Creek Reintroduction Plan include: 1. In 2017, LSNFH had excess winter-run Chinook salmon broodstock on station. This occurred because extra captive broodstock were being kept in the event additional fish were needed to supplement the mainstem Sacramento River program because of drought conditions. The extra captive broodstock were not needed for the Sacramento program and the agencies decided to use those fish to produce juveniles for release into Battle Creek to jumpstart the reintroduction of winter-run Chinook salmon in advance of the implementation of the Battle Creek Reintroduction Plan and the complete restoration of Battle Creek. In the spring of2018, CNFH released 215,000 juvenile winter-run Chinook salmon into upper Battle Creek. Subsequently, the agencies decided to continue this jumpstart program and CNFH has integrated the production of approximately 200,000 winter-run Chinook salmon juveniles into its annual operations. This currently involves spawning broodstock and rearing eggs at LSNFH, then transferring fry to CNFH for further rearing and release. Specific ongoing actions for constructing a fish trapping and sorting facility at CNFH include: 1. The USFWS assembled a multi-agency team to design a fish trapping and sorting facility at the CNFH Weir to minimize handling and migration delay of listed species during CNFH's fall-run Chinook spawning operations, and to allow for passage, monitoring, and management of fish passage during times when spawning operations are not taking place. The project is currently env isioned to be constructed in two phases, with the first phase establishing the ability to pass fish through the fish sorting facility year round, which would allow for monitoring and management during times when the spawning operations are not being conducted. The second phase would allow for selective bypassing of the spawning building during spawning operations and automation of many of the processes. To date, with Reclamation funding and input from partner agencies, the USFWS has completed 65 percent design ofPhase 1, with anticipated 100 percent design completion in August, 2019. 86 Biological Opinion for the Long-Term Operation of the CVP and SWP Specific ongoing actions for studying alternative release strategies for CNFH produced fallrun Chinook salmon include: 1. Evaluation of alternative release strategies for CNFH fall-run Chinook salmon to determine if trucking to an alternative release site can increase juvenile survival to the ocean and adult returns to the Sacramento River without unacceptable levels of straying. To date, the USFWS has implemented one year of a three-year study, largely through the use of CNFH operational funds, acoustic tags provided by Reclamation, tag surgeries provided by U.C. Davis, and net pen operations provided by stakeholders and the CDFW's Mokelumne River Hatchery. The current plan is to run the study for another two years. 2.4.2.2 Harvest The following discussions of harvest impacts for winter-run and spring-run Chinook salmon, and steelhead were, in large part, taken from the most recent NMFS 5-year status review reports for each species (National Marine Fisheries Service 2016c, b, a). 2.4.2.2.1 Winter-run Chinook salmon 2.4.2.2.1.1 Ocean Harvest Impacts Winter-run Chinook salmon have a more southerly ocean distribution relative to other California Chinook salmon stocks, and are primarily impacted by fisheries south of Point Arena, California. Winter-run Chinook salmon age-3 ocean fishery impact rate estimates for the region south of Point Arena (an approximation of the exploitation rate) are currently available for 2000-2017, and have remained rdatively stable over this period, averaging 16 percent. Fisheries in 2008 and 2009 were closed south of Point Arena owing to the collapse of the Sacramento River fall-run Chinook salmon stock and insufficient data (i.e., insufficient coded-wire tag recoveries) exist for estimating a winter-run Chinook salmon impact rate in 2010. If years 2008-2010 are omitted, the average age-3 impact rate is 18 percent (Pacific Fishery Management Council 20 19). There have been several layers of ocean salmon fishery regulations implemented to protect winter-run Chinook salmon beginning in the early 1990s. For example, a substantial portion of the winter-run Chinook salmon ocean harvest impacts used to occur in February and March recreational fisheries south of Point Arena, but fisheries at that time of the year have been closed since the early 2000s. In general, under the provisions of the Opinions issued since 2004 (National Marine Fisheries Service 2018c), ocean salmon fishing remains closed from late fall through April for the commercial fishery and March for the recreational fishery and sector specific size limits are in place as additional protective measures. O'Farrell and Satterthwaite (2015) hind casted winter-run Chinook salmon age-3 ocean impact rates back to 1978, extending the impact rate time series beyond the range of years where direct estimation is possibl e (2000-2013). Their results suggest that there were substantial reductions in ocean impact rates prior to 2000 and that the highest impact rates occurred in a period between the mid-1980s and late-1990s. NMFS has completed several ESA consultations regarding the impacts of the ocean salmon fishery on winter-run Chinook salmon. The most recent and currently applicable Opinion was 87 Biological Opinion for the Long-Term Operation of the CVP and SWP completed in March 2018. That Opinion analyzed a proposed new abundance-based control. The harvest control rule specifies the maximum allowable age-3 impact rate on the basis of a forecast of the Sacramento River winter-run Chinook salmon age-3 escapement in the absence of fisheries. The limits to the impact rate imposed by the harvest control rule is an additional control on ocean fisheries which still includes previously existing constraints on fishery opening and closing dates and minimum size limits south ofPoint Arena. From 2012 to 2019, the winterrun Chinook salmon harvest control rule has specified maximum allowable forecast impact rates ranging from 12.9 percent to 19.9 percent (Pacific Fishery Management Council2019). 2.4.2.2.1.2 Freshwater Angling Impacts What little winter-run Chinook salmon freshwater harvest that existed historically was essentially eliminated beginning in 2002, when Sacramento Basin Chinook salmon fishery season openings were adjusted so that there would be little temporal overlap with the winter-run Chinook salmon spawning migration and spawning period. However, early arriving fish may still be harvested prior to January 1. Additionally, higher densities of fish in this portion of the river may lead to higher early harvest rates. Higher densities offish, particularly below dams, likely create opportunities for both illegal poaching of salmon and the inadvertent or intentional snagging of fish. In addition, the upper Sacramento River supports substantial angling pressure for rainbow trout. Rainbow trout fishers tend to concentrate in locations and at times where winter-run Chinook salmon are actively spawning (and therefore concentrated and more susceptible to impacts). By law, any winter-run Chinook salmon inadvertently hooked in this section of river must be released without removing it from the water. However, winter-run Chinook salmon are impacted as a result of disturbance and the process of hook-and-release. In addition, because the taking of salmon is permitted after August 1, some late spawning winterrun Chinook salmon may be taken. 2.4.2.2.2 Spring-run Chinook Salmon 2.4.2.2.2.1 Ocean Harvest Impacts The available information indicates that the fishery impacts on the CV spring-run Chinook salmon ESU have not changed appreciably since the 2010 status review (National Marine Fisheries Service 20 16a). Attempts have been made (Grover et al. 2004) to estimate CV springrun Chinook salmon ocean fishery exploitation rates by capturing and tagging natural-origin spring-run Chinook salmon from Butte Creek, but due to the low number of coded-wire tag recoveries, the uncertainty of these estimates is too high for them to be of value. CV spring-run Chinook salmon have a relatively broad ocean distribution from central California to Cape Falcon, Oregon, that is similar to that of Sacramento River fall-run Chinook salmon, thus trends in the fall-run Chinook salmon ocean harvest rate are thought to provide a reasonable proxy for trends in the CV spring-run Chinook salmon ocean harvest rate. While the fall-run Chinook salmon ocean harvest rate can provide information on trends in CV spring-run Chinook salmon fishing mortality, it is likely that CV spring-run Chinook salmon experience lower overall fishing mortality. If maturation rates are similar between CV spring-run and fall-run Chinook salmon, the ocean exploitation rate on CV spring-run Chinook salmon would be lower than fall-run Chinook salmon in the last year of life because CV spring-run Chinook salmon escape ocean fisheries in the spring, prior to the most extensive ocean salmon fisheries in summer. 88 Biological Opinion for the Long-Term Operation of the CVP and SWP The fall-run Chinook salmon ocean harvest rate index peaked in the late 1980s and early 1990s, but then declined. With the closure of nearly all Chinook ocean fisheries south of Cape Falcon in 2008 and 2009, the index dropped to 6 percent and 1 percent respectively. While ocean fisheries resumed in 2010, commercial fishing opportunity was severely constrained, particularly off California, resulting in a harvest rate index of 16 percent. Since 2011, ocean salmon fisheries in California and Oregon have had more typical levels of fishing opportunity. The average Central Valley fall-run Chinook salmon ocean harvest rate from 2011 to 2018 was 46 percent, which is generally similar to levels observed from the late 1990s to 2007. In addition, NMFS determined that the management framework for Sacramento winter-run Chinook that includes the updated harvest control rule and size and season limits contains equivalent and/or additional restrictions on the fishery compared to previous management measures and is more responsive than prior management frameworks to information related to the status of CV spring-run Chinook salmon by accounting for changes in freshwater conditions in the Central Valley for Sacramento River winter-run Chinook salmon. The CV spring-run Chinook salmon spawning migration largely concludes before the mid- to late-summer opening of freshwater salmon fisheries in the Sacramento Basin, and salmon fishing is prohibited altogether on Butte, Deer, and Mill creeks, suggesting in-river fishery impacts on CV spring-run Chinook salmon are relatively minor. Overall, it is highly unlikely that harvest resulted in overutilization of this ESU (National Marine Fisheries Service 20 16a). 2.4.2.2.3 Steelhead In an attempt to minimize potential negative behavioral and genetic interactions with naturalorigin steelhead, CDFW has increased the bag limit for hatchery steelhead on several popular rivers in the Central Valley. Following is a chronological rundown of changes in daily bag and possession limits that have occurred since March 1, 2010, which was the effective date ofthe 2010-201 1 regulations cycle: • • • • Prior to March 1, 2010, the daily bag and possession limit in the Sacramento River system, including the lower Mokelumne River, was one steelhead in the bag and one in possessiOn. Effective March 1, 2010, the steelhead daily bag and possession limit on the mainstem Sacramento and American Rivers increased to a daily bag of two hatchery steelhead and a possession limit of four hatchery steelhead. On the Feather and Mokelumne rivers, the daily bag and possession limit remained at one hatchery steelhead in the bag, and one hatchery steelhead in possession. On March 1, 2013, the steelhead daily bag and possession limit on the Feather River increased to two and four hatchery steelhead, respectively. In the current regulations cycle with an effective date of March 1, 2016, the steelhead daily bag and possession limit remains at two and four, respectively, on the Sacramento, American, and Feather rivers; and at one and one, respectively, on the Mokelumne River. The 2012-2016 drought conditions affected some steelhead fishing opportunities for this DPS. For example, the California Fish and Game Commission imposed an emergency fishery closure on the American River during February of2014. The closure ended in April of that year. The regulation changes reviewed above for steelhead fishing in the Central Valley suggest that there is the potential for a change in harvest dynamic over the past several years. The overall 89 Biological Opinion for the Long-Term Operation of the CVP and SWP trend has been to incrementally increase the opportunity for harvest of hatchery-origin steelhead by increasing the daily bag and possession limits. The rationale behind encouraging more harvest of hatchery-origin steelhead is to minimize potential negative behavioral and genetic interactions with natural-origin steelhead. In addition, retention of hatchery-origin steelhead in the Central Valley is typically very low. Yet, the purpose ofthe hatchery programs is to provide a harvestable fishery resource. Thus, CDFW would like to see more of that resource utilized for its intended consumptive purpose. CDFW performs angler surveys on Central Valley streams, and data from these surveys are used to estimate steelhead harvest and fishing effort. However, these estimates do not appear to be regularly reported. Available data on angler retention of hatchery-origin steelhead suggest an increase in retention since the 2010-2011 regulatory cycle (California Department ofFish and Wildlife 2016d). Mean retention from 2007-2008 through 2009-2010 was 13.1 percent, while mean retention from 2010-2011 through 2015-2016 was 20.4 percent. These means do not differ significantly, however (2-tailed t-test: t = -1.82, p = 0.1 1; no significant departure from normality in sample data; variances not significantly different). This analysis may possibly be jmproved by using expanded catch and retention data for each regulatory year (National Marine Fisheries Service 2016b). Steelhead are rarely caught in ocean fisheries and retention ofsteelhead in nontreaty commercial ocean fisheries is currently prohibited. 2.4.2.2.4 Green Sturgeon Starting in 2006, green sturgeon harvest was prohibited by CDFW. California has established specific rules to protect sDPS green sturgeon, prohibiting fishing for green or white sturgeon year-round in the mainstem Sacramento River from Highway 162 (RK 283) to Keswick Dam (RK 485) andYolo Bypass, prohibiting the removal of incidentally hooked green sturgeon from the water, only allowing the use ofbarbless hooks, prohibiting use of wire leaders and snares, and increasing fines for poaching (National Marine Fisheries Service 2018g). 2.4.2.3 Water Quality Current land use in the Sacramento River basin and Delta has seen a dramatic increase in urbanization, industrial activity, and agriculture in the last century. In a Sacramento River Basinwide study, areas with relatively high concentrations of agricultural activity as well as areas that had previously experienced mining activity showed increased concentrations of dissolved solids and nitrite plus nitrate (Domagalski et al. 2000). Domagalski et al. (2000) also found varying concentrations of mercury and methylmercury throughout the Sacramento River Basin. Concentrations ofthese contaminants were greatest downstream of previous mining sites (primarily Cache Creek). Both studies showed lower concentrations of contaminants in the American River as compared to other sites sampled in the Sacramento River Basin. Multiple studies have documented high levels of contaminants in the Delta such as Polychlorinated biphenyls (PCBs), organochlorine pesticides, polycyclic aromatic hydrocarbons (PAHs), selenium, and mercury, among others (Stewart et al. 2004, Leatherbarrow et al. 2005, Brooks et al. 2012), suggesting that fish are exposed to them. However, the inability to characterize concentrations and loading dynamics makes it difficult to quantify transport and total contaminant loading in the system (Johnson et al. 201 0). Additionally, numerous discharges of treated wastewater from sanitation wastewater treatment plants (e.g., Cities of Tracy, 90 Biological Opinion for the Long-Term Operation of the CVP and SWP Stockton, Manteca, Lathrop, Modesto, Turlock, Riverbank, Oakdale, Ripon, Mountain House, and the Town of Discovery Bay) and the untreated discharge of numerous agricultural wasteways are emptied into the waters of the San Joaquin River and the channels of the south Delta (National Marine Fisheries Service 2014b). This leads to cumulative additions to the system ofthermal effluent loads as well as cumulative loads of potential contaminants (i.e., selenium, boron, endocrine disruptors, pesticides, biostimulatory compounds, etc.). Harmful algal blooms also occur in the Delta and, although toxic exposure of estuarine fish has been documented, the extent oftheir impacts to the aquatic food web is unknown (Lehman et al. 2010). More recently, concerns have been raised about ammonia levels in the Delta (Davis et al. 2018). Central Valley Regional Water Quality Control Board (CVRWQCB) is working with researchers at San Francisco State University and University of California, Davis, to evaluate the impact of ammonia in the Delta (Connon et al. 2011 ). All of the waters within the Delta are listed as impaired by at least one factor, either due to the presence ofunacceptable levels of pollutants or lack of maintaining conditions such as adequate dissolved oxygen levels (U.S. Environmental Protection Agency 20llb). Pesticides are found in the water and bottom sediments throughout the Delta. The more persistent chlorinated hydrocarbon pesticides are consistently found at higher levels than the less persistent organophosphate compounds. Sediments in the western Delta have the highest pesticide content. Pesticides have concentrated in aquatic life, but long-term effects and the effects of intermittent exposure are not known (National Marine Fisheries Service 20 18b). There are now concerns about the aquatic toxicity of pyrethroid-based pesticides (bifenthrin, cyfluthrin, cypermethrin, and permethrin), which have replaced organophosphorus pesticides such as diazinon and chlorpyrifos. Little is known about the potential for interactive toxicity from complex pesticide mixtures and/or pesticides interacting with other chemical, physical, or biological stressors (U.S. Environmental Protection Agency 201la). However, pesticide use for the treatment and elimination of invasive aquatic vegetation may have important consequences for water quality parameters including: amount of light that reaches the water column, temperature, salinity, turbidity, and food availability, which may also influence the migratory paths that green sturgeon salmonids utilize in the Delta (National Marine Fisheries Service 2018g). In December of2018, the State Water Board updated the Bay-Delta Plan to protect beneficial uses in the Bay-Delta watershed. Phase I of this work involved updating San Joaquin River flow and southern Delta water quality requirements included in the Bay-Delta Plan (State Water Resources Control Board 2018). The Environmental Protection Agency (EPA) developed an action plan in 2012 to address water quality concerns in the Delta (U.S. Environmental Protection Agency 2012). This plan included the following actions: (1) Strengthen estuarine habitat protection standards, (2) Advance regional water quality monitoring and assessment, (3) Accelerate water quality restoration through Total Maximum Daily Loads, (4) Strengthen selenium water quality criteria, (5) Prevent pesticide pollution, (6) Restore aquatic habitats while managing methylmercury, and (7) Support the Bay Delta Conservation Plan. 2.4.2.4 Water Temperature Management The environmental baseline considers observed temperature related mortality from the past to the present, including temperature dependent mortality and other mortality factors in the Upper 91 Biological Opinion for the Long-Term Operation of the CVP and SWP Sacramento River. Historical context can be found in the WOA scenario which highlights Reclamation's past actions to manage cold water and insert the temperature control device in Shasta Reservoir. Most recent past exposures include the effects of drought, operations and temperatures on very high mortality of natural winter-run Chinook salmon production in 2014 and 2015. Sacramento River- NMFS' 2009 Opinion required, through Reasonable and Prudent Alternative (RPA) actions, seasonal operations and summer water temperature management to provide cold water habitat for early life stages of winter-run and CV spring-run Chinook salmon each year (National Marine Fisheries Service 2009b). On August 2, 2016, Reclamation requested using the adaptive management provision in the NMFS 2009 Opinion related to Shasta Reservoir operations. The basis for this request included recent, multiple years of drought conditions, new science and modeling, and data demonstrating the low population levels of endangered winter-run Chinook salmon and threatened CV springrun Chinook salmon. NMFS, in consultation with Reclamation, developed a draft proposed amendment to the NMFS' 2011 amendment to the 2009 RPA (National Marine Fisheries Service 2017d). As described in the January 19, 2017, cover letter, NMFS expected the Shasta RPA amendment as a necessary bridge to and part of a phased approach that will inform the ROC on LTO. The draft proposed amendment included a pilot approach to water temperature management that would be implemented starting in 2017. The 2017 pilot approach applied new science on the thermal tolerance of Chinook salmon eggs (Martin et al. 20 16) and was designed to efficiently utilize Shasta Reservoir's limited supply of cold water by basing the spatial distribution of protective temperatures on the within-season spatial distribution of winter-run Chinook salmon redds. The intent was to provide daily average water temperatures of 53°F or less to the furthest downstream redds. The existing RPA requirement was a daily average temperature of 56°F or less at compliance locations between Balls Ferry and Bend Bridge, which are not based on the within-season redd distribution. Although the Shasta RPA amendment was not finalized, the science-based, within season management under the 2017 pilot approach, along with one of the wettest years on record (in water year 2017), resulted in 44 percent egg-to-fry survival, one of the highest estimates on record. The pilot approach was implemented in 2018 and will also be implemented in 2019. Hamda et al. (20 19) recently modeled the effects of Sacramento River water-temperature management for listed spring-run and winter-run Chinook salmon eggs on the growth rate of juvenile green sturgeon, and there was relatively little impact on the growth rate of the species. Clear Creek- RPA Action 1.1.5 Thermal Stress Reduction - requires Reclamation to reduce thermal stress to over-summering CCV steelhead and CV spring-run Chinook salmon during holding, spawning, and embryo incubation by managing Whiskeytown releases to meet a daily water temperature of (1) 60°F at the IGO gage from June 1 through September 15, and (2) 56°F at the IGO gage from September 15 to October 31. Redamation has operated releases for temperature management since implementation of the RPA action, though criteria was not met in some years (see Section 2.5.3.4.1 Clear Creek Temperature Management, that describes effects of higher water temperatures on CV spring-run Chinook salmon adult holding and spawning, as the PA is the same as current operations in the environmental baseline). The RPA also requires Reclamation, in coordination with NMFS, to assess improvements to modeling water temperatures in Clear Creek and identify a schedule for making improvements. In the NMFS, 2011 amendment to the NMFS 2009 Opinion, the need to "explore options to avoid non92 Biological Opinion for the Long-Term Operation of the CVP and SWP compliance with the RPA" was specified for this action. To date, an assessment of and schedule for making improvements to modeling water temperatures in Clear Creek has not been completed. However, beginning in late 2016, Reclamation initiated a temperature model development process, focused on developing a model for Shasta and Keswick reservoirs, with future plans to expand the model to the Trinity Division. RPA Action 1.1.4 Spring Creek Temperature Control Curtain- required Reclamation to replace the Spring Creek Temperature Control Curtain in Whiskeytown Lake by 2011, with the objective to reduce adverse impacts of project operations on water temperature for listed salmonids in the Sacramento River. The curtain was replaced in 2011. In addition, the Oak Bottom Temperature Control Curtain, which is located at the upper end of Whiskeytown Reservoir and intended to enhance coldwater transport from the upper end of the reservoir to the lower reservoir outlets, including Spring Creek Tunnel and Whiskeytown Dam, was replaced in May of 2016. Having both temperature curtains functioning together in tandem enhance cold-water availability in the Spring Creek Tunnel and Whiskeytown Darn outlets, and Reclamation's Technical Service Center is currently evaluating their performance, with a final report expected in 2019. American River- RP A action Il.3 in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b) requires Reclamation to implement physical and structural modifications to the American River Division of the CVP in order to improve water temperature management. The purpose of these physical and structural modifications are to facilitate more control over temperature and amount of water releases into the American River for spawning Chinook salmon and steelhead, and mjgrating and rearingjuveniles ofboth species. Implementation has been delayed, but Reclamation has indicated that some work is being done on the temperature control device at Folsom Dam (http:/I deltacouncil.ca.gov/science-program/20 18-long-term-operations-biologicalopinions-lobo-annual-reports). In addition, annual water temperature management plans for the lower American River have been developed annually starting in 2010. An Iterative Coldwater Pool Management Model was developed by Reclamation in 2010 and is being used annually to evaluate coldwater pool availability in Folsom Reservoir and develop water temperature objectives in the lower American River that are as protective as possible for salmonids. Despite these efforts, current water temperatures in the lower American are annually stressful for juvenile steelhead rearing over the summer and fall-run Chinook salmon adults returning to spawn (see Section 2.5.4.1.2 Juvenile Rearing, and especially Figure 2.5.4-8 on historical water temperatures and effects on juvenile CCV steelhead rearing). 2.4.2.5 Diversions and Entrainment There are over 3,700 water diversions on the Sacramento and San Joaquin rivers, their tributaries, and in the Delta; most of these are unscreened (Mussen et al. 20 13), posing a widespread threat to early life stages offish. A study of 12 unscreened, small to moderate sized diversions (< 150 cfs) in the Sacramento River, found that diversion entrainment was low for listed salmonids and sturgeon, though the study points out that the diversions used were all situated relatively deep in the river channel (Vogel 2013). The study also suggested that the factors affecting fish entrainment at unscreened diversions are complex and poorly understood because ofthe many site-specific variables that influence the exposure and vulnerability offish to entrainment (Vogel2013). 93 Biological Opinion for the Long-Term Operation of the CVP and SWP In a previous mark-recapture study addressing mortality caused by unscreened diversions, Hanson (200 1) observed low mortality in hatchery-produced juvenile Chinook salmon released upstream of four different diversions throughout the Sacramento River 0.1 percent of individuals released). The CVPIA's Anadromous Fish Screen Program (AFSP) was established in 1994 to minimize the impacts of diversions on anadromous fish and provide technical guidance and cost-share funding for fish scre·en projects. The AFSP also supports activities and studies to assess the potential benefits of fish screening, determine the highest priority diversions for screening, improve the effectiveness and efficiency of fish screens, encourage the dissemination of information related to fish screening, and reduce the overall costs offish screens (State Water Resources Control Board 2017b). Through AFSP, as of2019, there have been a total of30 fish screens constructed at diversions on the Sacramento River, 4 fish screens in the San Joaquin and tributaries, and 3 fish screens at Delta diversions, which has resulted in reduced entrainment at those diversions. Currently, screen criteria for green sturgeon has not been developed, and the benefits of projects intended to reduce salmonid impingement and entrainment at diversions to green sturgeon are not fully understood (National Marine Fisheries Service 2018g). A NMFS Opinion on the construction ofNMFS-approved, state-of-the-art fish screens at the Tehama Colusa Canal diversion included a requirement to monitor, evaluate, and adaptively manage the new fish screens to ensure the screens are working properly and impacts to listed species are minimized (National Marine Fisheries Service 2009d). We expect these actions have helped reduce entrainment of listed fish in the upper Sacramento River. In addition, the 2009 RPA included the requirement to identify and implement projects to ensure the M&T Ranch water diversion is adequately screened to protect winter-run Chinook salmon, spring-run Chinook salmon, and steelhead. A short-term screen is currently functioning at the site and a permanent screening option is under development. Gate operations at the RBDD (rkm 391, completed in 1964) created a migration barrier during a critical time for mature adults; operations limited access to spawning habitat for migrating spawning-capable adult green sturgeon (Poytress et al. 2015). In 2013, the RBDD was decommissioned, which permanently lifted the gates and permitted volitional passage for sDPS green sturgeon during all months of river presence (National Marine Fisheries Service 2018g). This action has had a major beneficial impact on spawning distribution for green sturgeon and possibly aided in population recovery (National Marine Fisheries Service 2018g). 2.4.2.6 Predation Predation ofjuvenile salmonids and green sturgeon is thought to be a contributing factor to high mortality at this life stage (Hanson 2009, Vogel2011, Michel et al. 2015). There have been significant alterations to aquatic habitat that are conducive to the success of non-native piscivorous fish such as creating a largely freshwater system out of the naturally estuarine, variable salinity Delta, riverbank armoring, and reduction of habitat complexity (Vogel2011). The altered habitat and modified flow regimes have benefitted non-native striped bass, catfish, largemouth bass, and smallmouth bass, such that predation has been characterized as being, " .. .likely the highest source of mortality to anadromous fish in the Delta" (Vogel 2011 ). The 2009 RPA [RPA Action IV.4.2(2)(a)] requires DWR to implement predator control methods within CCF to reduce salmon and steelhead pre-screen loss to no more than 40 percent. DWR is 94 Biological Opinion for the Long-Term Operation of the CVP and SWP currently implementing four interim methods and conducting studies to reduce predation on listed anadromous fish species in CCF. In March 2019, DWR completed an in-depth study to evaluate dredging alternatives to reduce pre-screen loss of salmonids and sturgeon in CCF. 2.4.2.7 Physical Disturbance from Dredging and Vessel Traffic Dredging operations periodically occur for a variety of purposes including the maintenance of shipping channels; maintenance of diversion intakes; and to remove accumulated sediments from recreational and commercial facilities such as boat docks and marinas. Dredging can have detrimental impacts to listed fish species through physical disturbance, and through the resuspension of sediment. ESA consultations are periodically conducted by NMFS for dredging projects of varying scope and scale in the Central Valley (National Marine Fisheries Service 2018a). Select portions ofthe action area currently experience heavy commercial and recreational vessel traffic, creating hazards to listed fish species through both physical and acoustic disturbance. These impacts may lead to direct mortality or may induce changes in behavior that impair feeding, rearing, migration, and/or predator avoidance. The Stockton Deep Water Ship Channel (DWSC) and Sacramento DWSC experience frequent large commercial vessel traffic. The mainstem Sacramento River; American River; Delta; and remainder of Suisun, San Pablo, and San Francisco bays receive occasional commercial tugboat traffic as construction barges and other heavy equipment are transported upstream. Finally, recreational vessel traffic occurs throughout the action area. In a report on Delta boating needs through the year 2020, the California Department of Boating and Waterways stated an expected increase in boating activity in the Delta area (California Department of Boating andl Waterways 2003). 2.4.2.8 Required Restoration Actions from NMFS (2009) RPA on the Long-term Operations of CVP/SWP Biological Opinion Required restoration actions from the RPA in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b) and the associated 2011 amendments (National Marine Fisheries Service 201ld), are described below, and the status of their implementation. Additional updated information related to restoration actions are available in the Salmon Resiliency Strategy (California National Resources Agency 2017). RPA Action 1.7: Reduce Migratory Delays and Loss of Salmon, Steelhead, and Sturgeon at Fremont Weir and Other Structures in the Yolo Bypass (Improve Yolo Bypass Adult Fish Passage) Pursuant to the RPA in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), Reclamation and DWR shall improve adult salmonid and sturgeon passage through the Yolo Bypass, including the Fremont Weir, by modifying or removing barriers. This action will include preventing straying at Wallace Weir (see Section 2.4.2.9, #6); improving several agricultural road crossings; improving Lisbon Weir; and improving the existing Fremont Weir fish ladder. This is expected to reduce migratory delays and straying of adult salmonids and sturgeon because insufficient adult fish passage at flood bypass weirs combined with attraction flows leads to stranding risk and reduced fish survival, timing, and condition. Improvements to Freemont Weir have resulted in improved fish passage in 2019. Reclamation expects to construct the Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project in 2020 to comply with 95 Biological Opinion for the Long-Term Operation of the CVP and SWP the requirement in RP A Action I. 7. This action is expected to result in improvements to the migration corridor, and help minimize stranding in the Yolo Bypass. Improving access to the Yolo Bypass is also expected to benefit adult sDPS green sturgeon access to habitat (National Marine Fisheries Service 2018g). RPA Action I.6.1: Restoration of Floodplain Rearing Habitat (Increase Juvenile Salmonid Access to Yolo Bypass, and Increase Duration and Frequency of Yolo Bypass Floodplain Inundation) Pursuant to the RPA in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), Reclamation, and DWR shall increase juvenile salmonid access to the Yolo Bypass and improve adult fish passage by constructing an operable gated structure in the Fremont Weir. The facility shall be operated to increase the duration and frequency of Yolo bypass inundation from December through April, providing 17,000+ acres of enhanced floodplain habitat. This is expected to benefit salmonids because lack of floodplain connectivity limits food availability and production and leads to reduced fish growth and subsequent survival. Reclamation expects to construct theYolo Bypass Salmonid Habitat Restoration and Fish Passage Project in 2020, to partially fulfill the requirements in RPA Action I.6.1. This action is expected to result in benefits to juvenile listed salmonids through increased growth and survival. Improving access to theYolo Bypass is also expected to benefit green sturgeon juveniles (National Marine Fisheries Service 2018g). RPA Action Suite V, NF 4: Implementation of Pilot Reintroduction Program (Implementation of Pilot Reintroduction Program above Shasta Dam) Pursuant to the RP A in NMFS 2009 Opinion (National Marine Fisheries Service 2009b), Reclamation, and DWR shall complete all required actions, monitoring, and reporting to guide establishment of an additional population of winter-run Chinook salmon and identify the benefits and risks of reintroduction for CV spring-run Chinook salmon and CCV steelhead in the McCloud River and/or upper Sacramento River. This action is also a Priority 1 NMFS recovery. Additional updated information related to implementation is available in the Salmon Resiliency Strategy (California National Resources Agency 2017). In 2010, pursuant to the requirements ofRPA Action V in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), Reclamation established the Interagency Fish Passage Steering Committee, with representatives from Reclamation, NMFS, USFWS, United States Forest Service (USFS), CDFW, DWR, SWRCB, and U.C. Davis. The Steering Committee focused preliminary evaluation efforts on fish passage above Shasta Dam, Folsom Dam and the upper Stanislaus River. By 2013, focus on the fish passage program was limited to the upper Sacramento and McCloud rivers due in large part to the scope of the RPA and concerns over the endangered status of SR winter-run Chinook salmon. Reclamation prepared a final Environmental Impact Statement (EIS) with a targeted release for the summer of 2018, in anticipation of implementation of the first phase of the pilot reintroduction program scheduled for fall, 2018. To date, the EIS has not been released. Additionally, in 2018, Reclamation awarded DWR 2.7 million dollars as the first installment of a 5-year contract totaling approximately 9 million dollars for the design, construction, installation, and operation of two juvenile fish collection devices in the lower McCloud River and the McCloud arm of Shasta Reservoir. In July, 2018, Reclamation informed the Steering Committee 96 Biological Opinion for the Long-Term Operation of the CVP and SWP that the project was "on hold" and had been defunded for the foreseeable future. Since July, 2018, DWR has continued to move forward with the juvenile collection facilities, but has not received additional financial contributions from Reclamation. Progress on RPA V implementation, aside from DWR's efforts, has stopped!. RPA Action IV.1.3: Consider Engineering Solutions to Further Reduce Diversion of Emigrating Juvenile Salmonids to the Interior and Southern Delta, and Reduce Exposure to CVP and SWP Export Facilities (Including Georgiana Slough Non-Physical Barrier) Pursuant to the RPA in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), DWR, Reclamation and the State and Federal Water Contractors shall increase the overall through-Delta survival of salmonids by reducing juvenile salmon entry into the interior Delta. This action is expected to benefit salmonids because it affects multiple habitat attributes that are hypothesized to affect juvenile survival, including predation and competition, outmigration cues, and entrainment risk. Construction of a non-physical barrier at Georgiana Slough is planned for 2020. This action is consistent with a priority 1 NMFS recovery action for winter-run Chinook salmon. RPA Action 1.2.6: Restore Battle Creek for Winter-Run, Spring-Run, and CV Steelhead (Complete Battle Creek Salmon and Steelhead Restoration Project) Pursuant to the RPA in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), Reclamation, and DWR shall provide improved instream flow releases and safe fish passage to prime salmon and steelhead habitat on Battle Creek for winter-run Chinook salmon, CV springrun Chinook salmon, and CCV stedhead. This is also a Priority 1 NMFS recovery action (National Marine Fisheries Service 2014b). The project has been supported with Federal, State, and private funding. As of2019, implementation of the Battle Creek Salmon and Steelhead Restoration Project has completed construction of phase 1 (of 2), which included removal of one fish passage barrier (dam), and construction ofNMFS-approved fish screens and ladders at the two remaining dams on North Fork Battle Creek. Phase 2 of the project has completed planning, and is currently in design phase. Although implementation has been significantly delayed, we expect benefits to listed salmonids once completed. Additionally, beginning in 2018, winter-run Chinook salmon juveniles produced at LSNFH have been released into North Fork Battle Creek in an effort to jump-start the reintroduction efforts described in the plan (ICF International 2016). These releases are expected to continue until implementation of the full reintroduction plan is underway. Additional updated information related to implementation is available in the Salmon Resiliency Strategy (California National Resources Agency 2017). Other RPA Actions Specific smaller scale fish habitat restoration actions mandated as part ofthe NMFS 2009 Opinion (National Marine Fisheries Service 2009b) are occurring on the upper reaches of the Sacramento River between Keswick Dam and RBDD as well as on the lower American River between Nimbus Dam and the State Route 160 Bridge. At select sites within these areas, the projects involve creation of side channels, addition of spawning gravel, and placement of inwater woody material. NMFS has determined that actions that have been implemented have begun to contribute improvements to aquatic habitat, and are expected to continuing to contribute to the recovery ofESA-listed salmonids in the Central Valley. 97 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.4.2.9 EcoRestore California EcoRestore is a California Natural Resources Agency initiative implemented in coordination with State and Federal agencies to advance the restoration of at least 30,000 acres of Delta habitat by 2020. Driven by world-class science and guided by adaptive management, California EcoRestore will pursue habitat restoration projects with clearly defined goals, measurable objectives, and financial resources to help ensure success. The types of habitat and projects targeted include tidal wetlands, floodplain, upland, riparian, fish passage improvements and others. Specific restoration targets include a focus on implementing a comprehensive suite of habitat restoration actions to support the long-term health of the Delta and its native fish and wildlife species. Specifically, the EcoRestore program aims to create 3,500 acres of managed wetlands created, 17,500 acres of floodplain restoration, 30,000 acres of delta habitat restoration and protection, 9,000 acres of tidal and sub-tidal habitat restoration, and 1,000 acres of proposition 1 and IE funded restoration projects. There have been six completed actions as part ofEcoRestore to date (California National Resources Agency 2017), which has resulted in improved migration and rearing habitats for listed anadromous fish in the lower Sacramento River and Delta. Completed actions include: 1. Knights Landing Outfall Gate- Located one-quarter mile from the confluence with the Sacramento River near Knights Landing, just below RM 90, in Yolo County. This Fish Passage Restoration project is a positive fish barrier (with new concrete wing walls and installation of a metal picket weir) to serve primarily as a fish passage improvement action, preventing salmon entry into the Colusa Basin Drain while also maintaining outflows and appropriate water surface elevations. The project was initiated because adult salmon may be able to enter the Colusa Basin Drain through the Knights Landing Outfall Gates when certain flow velocities are met that attract migrating salmon. Once salmon enter the Colusa Basin Drain, there is no upstream route for salmon to return to the Sacramento River and, absent fish rescue operations, the fish perish and are lost from production. Completion of the project has resulted in increased survival at this location, due to decreased entrainment. 2. Lindsey Slough- Completed in 2014. The project consisted of (I) excavation and debris removal to enlarge an existing north embankment breach on Calhoun Cut at a northern arm ofLindsey Slough; (2) breaching ofthe south embankment of Calhoun Cut; (3) excavation of a 1-mile long channel at the historic southern arm of Lindsey Slough; (4) lowering of an existing earthen causeway on the historic channel; and (5) beneficial reuse of sediment excavated from the channel to create low habitat berms within the marsh and raise the remnant marsh sit,e to a more mature marshplain form. The project was implemented to restore habitat function and connectivity to Delta wetlands and waterways that had been degraded by the construction of dikes and culverts 100 years earlier. Completion of the project has restored habitat function and connectivity to 159 acres of freshwater emergent wetlands and 69 acres of alkali wetlands, and recreated and reconnected a 1-mile tidal channel. 3. Sherman Island: Mayberry Farms- The Mayberry Farms Subsidence Reversal and Carbon Sequestration Project is a permanently flooded wetland on a 307-acre parcel on 98 Biological Opinion for the Long-Term Operation of the CVP and SWP Sherman Island that is owned by the DWR. Completion of this project occurred in 2010, and has restored approximately 192 acres of emergent wetlands and enhanced approximately 115-acres of seasonally flooded wetlands. 4. Sherman Island: Whale's Mouth - The Wetland Restoration Project is to restore approximately 600 acres of palustrine emergent wetlands, within an 877-acre Project boundary, on a nearly 975-acre parcel of property on Sherman Island. Additional project goals include increasing stability and reduced seepage on a threatened section of levee; determining the rates/amounts of carbon sequestered for project; determining the air and water quality impacts of project; and providing recommendations for Delta-wide implementation. This project was initiated in 2013 and was completed in 2015. 5. Sherman Island: Mayberry Slough- Tidal Marsh, Shaded Aquatic Riverine, and Upland Habitats Restoration Targets: 192 acres of emergent wetlands and 115 acres seasonally flooded wetlands. The DWR, in coordination with Reclamation District 341, constructed 6,100 linear feet of habitat setback levee to increase levee stability and provide waterside habitat restoration along Mayberry Slough on Sherman Island. This project was initiated in 2004 and was completed in 2009. 6. Wallace Weir Fish Rescue Facility- This project was completed in 2016, and includes replacing the seasonal earthen dam at Wallace Weir with a permanent, operable structure that would provide year-round operational control. The project also includes a fish rescue facility that would return special status migratory fish species back to the Sacramento River that are unable to pass volitionally over Wallace Weir. Wallace Weir has been treated as a common element to the larger habitat restoration and fish passage projects included as an RPA in the NMFS 2009 Opinion. This project will serve primarily as a fish passage improvement action that will prevent upstream migration of straying adult salmonids and sturgeon into the Colusa Basin Drain. Operational control of water levels would also provide greater flexibility for managing water releases for agriculture and wetlands habitat. As background for this action, in 2013, the CDFW and NMFS documented several hundred adult salmon in dead end agricultural ditches in the Colusa Basin Drain system, and while many of these fish were rescued from the drain, the stress from the poor water quality conditions prevented these salmon from successfully contributing to the reproductive population. In the remainder of2013 and in 2014, CDFW operated a fyke trap with wing walls at Wallace Weir to prevent straying adult salmonids and sturgeon from entering the Colusa Basin Drain; rescued fish were returned to the Sacramento River. These fish rescue operations have proven resource intensive and are not efficient at higher flows in the Knights Landing Ridge Cut (KLRC). Wallace Weir is a key water control structure in the bypass for flood conveyance and irrigation, but it is an obsolete structure, which must be installed and removed annually using inflexible, labor-intensive methods. 2.4.2.10 Ongoing Habitat Restoration and Monitoring Actions There have been a number of habitat restoration actions occurring in the action area,. many of which are expected to continue to benefit listed fish. Some of the restoration actions are ongoing and require repeated annual implementation at a specific site or watershed (e.g., gravel augmentation below Keswick Dam). Others include program level commitments with detailed 99 Biological Opinion for the Long-Term Operation of the CVP and SWP restoration actions to be determined at a later date (e.g., side channel restoration). One such program is the NOAA Restoration Center's Program to Facilitate Restoration Projects in the Central Valley (National Marine Fisheries Service 2018d), which is expected to continue making improvements to aquatic and/or riparian habitat for listed fish. The P A includes restoration actions with annual implementation and are described as conservation measures in Table 4-6 of the ROC on LTO BA (U.S. Bureau ofReclamation 2019). Some of these restoration actions have been consulted on previously such that their past and future beneficial effects to increased spawning and rearing habitat for listed salmonids are factored into the environmental bas eline. Examples of previously consulted restoration actions include the Lower Clear Creek Halbitat Restoration (National Marine Fisheries Service 2014c), Upper Sacramento River Restoration (National Marine Fisheries Servii.ce 2015c), and Lower American River Restoration (National Marine Fisheries Service 2015b) , that are carried out under the Central Valley Project Improvement Act. There are a number of ongoing monitoring and research efforts in the action area, which provide important information on listed anadromous fish. These include monitoring environmental conditions during action implementation (e.g., turbidity or temperature), monitoring fish presence, tagging fish for tracking distribution and survival, monitoring levels of impacts to fish and/or habitat, as examples. The effects of these monitoring and research activities are part of the environmental baseline because they previously have undergone ESA section 7 consultation either through individual or programmatic actions, ESA section 4(d), or section lO(a)(l )(A) incidental take permit. Similarly, any past monitoring that was associated with the NMFS 2009 Opinion is also considered part of the environmental baseline. 2.4.2.11 Conservation/Mitigation Banks There are a number of conservation or mitigation banks with service areas that include the action area for the PA (described below). Conservation banks present a unique factual situation, and this warrants a particular approach as to how they are addressed in an ESA consultation. Specifically, when NMFS is consulting on a proposed action that includes conservation bank credit purchases, it is likely that physical restoration work at the bank site has already occurred and/or that a Section 7 consultation occurred at the time of bank establishment. A traditional interpretation of the "environmental baseline" might suggest that the overall ecological benefits of the conservation bank actions, therefore, belong in the baseline. However, under this interpretation, all proposed actions, whether or not they included proposed credit purchases, would benefit from the environmental ' lift' of the entire conservation bank because it would be factored into the environmental baseline. In addition, where proposed actions did include credit purchases, it would not be possible to attribute their benefits to the proposed action, without double-counting. These consequences undermine the purposes of conservation banks and also do not reflect the unique circumstances under which they are established. Specifically, conservation banks are established based on the expectation of future credit purchases. In addition, credit purchases as part of a proposed action will also be the subject of a future Section 7 consultation. It is therefore appropriate to treat the beneficial effects of the bank as accruing incrementally at the time of specific credit purchases, not at the time of bank establishment or at the time of bank restoration work. Thus, for all projects within the service area of a conservation bank, only the benefits attributable to credits sold are relevant to the environmental baseline. Where a proposed 100 Biological Opinion for the Long-Term Operation of the CVP and SWP action includes credit purchases, the benefits attributable to those credit purchases are considered in the effects of the action. Liberty Island Native Fisheries Conservation Bank: Established in 2010, the Liberty Island Conservation Bank (Bank) is a conservation bank that serves the Delta region. It is located in the southern Yolo Bypass in Yolo County, California. The Bank consists of 186 acres located on the still leveed northernmost tip of Liberty Island. Approved in July 2010 by the NMFS, USFWS, and CDFW, the Bank provides compensatory mitigation for permitted projects affecting specialstatus Delta fish species within the region. The Bank provides habitat for all Delta fish species including: Sacramento River winter-run Chinook salmon; CV spring-run Chinook salmon, CCV steelhead, delta smelt, and Central Valley fall- and late fall-run Chinook salmon. Of the 186 total acres, 139.11 acres can be used for salmonid conservation credits. Ofthe 139.11 acres available for salmonids, approximately 68 acres have been purchased. The habitat includes tidallyinfluenced shallow freshwater habitat, shaded riparian aquatic (SRA) habitat and Tule Marsh SRA habitat. The increased ecological value of the enhanced rearing habitat for juvenile salmonids (and potentially sDPS green sturgeon), which have already been purchased, are part of the environmental baseline for the Project. Features of the bank are designated as critical habitat for CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon. Fremont Landing Conservation Bank: Established in 2006, the Fremont Landing Conservation Bank is 100-acre floodplain site along the Sacramento River (Sacramento RM 80) and is approved by NMFS to provide credits for impacts to Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon and CCV steelhead. There are off-channel shaded aquatic habitat credits, riverine shaded aquatic habitat credits and floodplain credits available. To date, there have been less than 25 percent of the 100 credits sold and the ecological value (increased rearing habitat for juvenile salmonids) of the sold credits are part ofthe environmental baseline. Features of this bank are designated critical habitat for Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon. Bullock Bend Mitigation Bank: Established in 2016, the Bullock Bend Mitigation Bank is a 119.65-acre floodplain site along the Sacramento River at the confluence of the Feather River (Sacramento RM I 06) and is approved by NMFS to provide credits for impacts to Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon and CCV steelhead. There are salmonid floodplain restoration, salmonid floodplain enhancement, and salmonid riparian forest credits available. To date, there have been approximately 10 percent of the 119.65 credits sold and the ecological value (increased rearing habitat for juvenile salmonids) of the sold credits are part of the environmental baseline. Features of this bank are designated critical habitat for the Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon. 2.4.3 Sacramento River Winter-run Chinook Salmon 2.4.3.1 Status of Sacramento River Winter-run Chinook Salmon in the Action Area The action area encompasses almost all freshwater and estuarine habitats utilized by winter-run Chinook salmon. As such, the Status of the Species for winter-run Chinook salmon (see Section 2.2) describes the species' status within the action area. Here, the biological status of winter-run Chinook salmon in the action area is summarized. 101 Biological Opinion for the Long-Term Operation of the CVP and SWP Assessing the temporal occurrence of each life stage is done through monitoring data in the Sacramento River and Delta as well as salvage data from the Tracy and Skinner fish collection facilities in the south Delta (CVP and SWP). Table 2.4.3-1 shows the temporal occurrence of adult and juvenile CCV steelhead at locations in the action area. Darker shades indicate months of greatest relative abundance. Table 2.4.3-1. Tbe Temporal Occurrence of Adult (a) and Juvenile (b) Winter-run in tbe Sacramento River and Delta. Low Sources: • Yoshiyama et al. ( 1998); Moyle (2002) ; bMyers et al. ( 1998); c Williams (2006) ; d Hallock and Fisher (1985), Vogel and Marine (1991); •Martin eta!. (2001) ; rKnights Landing Rotary Screw Trap Data, CDFW (1999-2019); Juvenile Fish Monitoring Program, USFWS (1995-2019), del Rosario et al. (2013). Sacramento River winter-run Chinook salmon are particularly important among California's salmon runs because they exhibit a life- history strategy found nowhere else in the world. These Chinook salmon are unique because they spawn during the summer months when air temperatures usually approach their warmest. As a result, winter-run Chinook salmon require stream reaches with cold-water sources to protect their incubating eggs from the warm ambient conditions. Because ofthis need for cold water during the summer, winter-run Chinook salmon historically spawned only in rivers and creeks fed by cold water springs, such as the Little Sacramento, McCloud, and Pit rivers, and Battle Creek (Lindley et al. 2004). The construction of Shasta and Keswick dams eliminated access to the Little Sacramento, McCloud, and Pit rivers, ,extirpating the winter-run Chinook salmon populations that spawned and reared tlhere. The fish from these three different populations above Shasta Dam were forced to mix and spawn as one population downstream of Keswick Dam on the Sacramento River. Construction and operation of hydropower facilities in Battle Creek made the creek inhospitable to winter-run Chinook salmon, which resulted in extirpation of the population from that area. 102 Biological Opinion for the Long-Term Operation of the CVP and SWP Currently, only the one small population of winter-run Chinook salmon spawning downstream of Keswick Dam exists, making this species particularly vulnerable to environmental pressures such the 2012-2015 drought. This vulnerability manifested during the drought with nearly two consecutive year class failures due to an inability to provide cold water throughout the egg and fry life stages. Warm water releases from Shasta Reservoir in 2014 and 2015 contributed to 5.9 percent and 4.2 percent egg-to-fry survival rates respectively, to RBDD. Under varying hydrologic conditions from 2002 to 2013, winter-run Chinook salmon egg-to-fry survival ranged from three to nearly 10 times higher than in 2014 and 2015. Survival improved after the drought ended with 24 percent survival in 2016, 44 percent survival in 2017, and 26 percent survival in 2018. Estimates of hatchery-origin winter-run Chinook salmon survival to age 2 are low relative to relevant benchmarks. For winter-run Chinook salmon, the mean smolt-to-adult ratio (SAR) from 1999 to 2012 was 0.64 percent (SE 0.18), well below the Columbia River Basin Fish and Wildlife Program suggested minimum of2 percent SAR required for population survival and 4 percent for population recovery for Upper Columbia River and Snake River Chinook salmon populations (Michel 20 18). SAR should be treated as an index of survival that primarily represents survival from hatchery release to age 2. Lindley et al. (2007) developed extinction risk criteria for Central Valley salmonid populations based on viability parameters for abundance, population decline rate, and hatchery influence, and using data through 2004, found that the mainstem Sacramento River population was at low risk of extinction, but that the ESU as a whole remained at a high risk of extinction because there is only one naturally-spawning population, and it is not within its historical range. The overall extinction risk of winter-run Chinook salmon has increased since the 2007 and 2010 assessments (Table 2.4.3-2). Based on the Lindley et al. (2007) criteria, the population is at high extinction risk in 2019. High extinction risk for the population was triggered by the hatchery influence criterion, with a mean of 66 percent hatchery origin spawners from 2016 through 2018. The threshold for high risk associated with hatchery influence is 50 percent hatchery origin spawners. The recent increase in hatchery influence was expected as production from LSNFH was increased during the drought to buffer against low adult returns resulting from poor survival of the 2014- and 2015-year class. Tlris buffering appears to have been successful in the sense that adult escapement through 2018 met the low extinction risk criterion for abundance (i.e., census population size of2,500). Table 2.4.3-2. Winter-run Chinook salmon extinction risk based on the criteria established in Lindley et al. (2007). 2007 1 Sacramento River Low Low Moderate 1 Lindley et a!. (2007), 2 Wi lliams et a!. (20 I I) 3Williams et al. (20 16), 3Williams eta!. (20 16) 2.4.3.2 Status of Sacramento River Winter-run Chinook Critical Habitat in the Action Area The proposed action area encompasses the entire range wide riverine and estuarine critical habitat PBFs for winter-run. Widespread degradation to these PBFs has had a major contribution 103 Biological Opinion for the Long-Term Operation of the CVP and SWP to the status of the winter-run Chinook salmon ESU, which is at high risk of extinction (National Marine Fisheries Service 2016c). PBFs (as discussed in the Section 2.2 Range wide Status of the Species) include: (1) access from the Pacific Ocean to appropriate spawning areas in the upper Sacramento River, (2) the availability of clean gravel for spawning substrate (3) adequate river flows for successful spawning, incubation of eggs, fry dlevelopment and emergence, and downstream transport of juveniles, (4) water temperatures between 42.5 and 57.5°F (5.8 and 14.1 °C) for successful spawning, egg incubation, and fry development:, (5) habitat and adequate prey that are not contaminated, (6) riparian habitat that provides for successful juvenile development and survival, and (7) access downstream so that juveniles can migrate from the spawning grounds to San Francisco Bay and the Pacific Ocean. Passage impediments in the northern region of the Central Valley are [argely responsible for isolating the existing population from historical spawning reaches, which occurred upstream of Keswick and Shasta dams and included the upper Sacramento River, McCloud River, Pit River, Fall River and Hat Creek (Yoshiyama et al. 1996, Lindley et al. 2004), (National Marine Fisheries Service 20 14b). Due to the installation of Keswick and Shasta dams, the winter-run ESU is now relegated to spawning downstream, in the Sacramento River. The majority of spawning occurs between RBDD and Redding (below Keswick Dam) (Vogel and Marine 1991, National Marine Fisheries Service 2014b). PBFs #2-4 for this ESU have been degraded in a number of ways. Spatially, the total area of usable spawning habitat has been significantly diminished. Physical features that are essential to the functionality of existing spawning habitat have also been degraded such as: loss of spawning gravel, and elevated water temperatures during summer months when spawning events occur (National Marine Fisheries Service 2014b). Degradation of these features has been actively mitigated through real-time temperature and flow management at Shasta and Keswick dams (National Marine Fisheries Service 2009b) as well as gravel augmentation projects in the affected area, which have been occurring as described in a multi-year programmatic biological opinion (National Marine Fisheries Service 20 16b). PBFs related to the rearing and migration ofjuveniles and adults have been degraded from their historical condition within the action area as well. Adult passage impediments on the Sacramento River existed for many years at the RBDD and ACID diversion dam (National Marine Fisheries Service 2014b). However, the RBDD was decommissioned in 2013, providing unimpaired juvenile and adult fish passage and a fish passage improvement project at the ACID was completed in 2015, so that adult winter-run Chinook salmon could migrate through the structure at a broader range of flows in order to reach spawning habitat upstream of that structure. Juvenile migration corridors are impacted by reverse flows in the Delta that become exacerbated by waiter export operations at the CVP/SWP pumping plants. This results in impaired routing and timing for outrnigrating juveniles and is evidenced by the presence of juvenile winter-run Chinook salmon at the State and Federal fish salvage facilities. Shoreline armoring and development has reduced the quality and quantity of floodplain habitat for rearing juveniles in the Delta and Sacramento River (Williams et al. 2009, Boughton and Pike 2013). Juveniles have access to floodplain habitat in the Yolo Bypass only during mid to high water years, and the quantity of floodplain available for rearing during drought years is currently limited. The Yolo Bypass Salmonid Habitat Restoration and Fish Passage Implementation Plan includes notching the Fremont Weir, which will provide access to floodplain habitat for juvenile salmon over a longer period (California Department of Water Resources and U.S. Bureau of Reclamation 2012). 104 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.4.4 Central Valley Spring-run Chinook Salmon and California Central Valley Steelhead 2.4.4.1 Status of Central Valley Spring-run Chinook Salmon in the Action Area Various life stages of CV spring-run Chinook salmon are found in the Sacramento River, Clear Creek, American River, San Joaquin River, Stanislaus River, and the Delta, though the American River only currently supports non-natal rearing of juveniles. Assessing the temporal occurrence of eaclh life stage of spring-run Chinook salmon is done through analysis of monitoring data in the Sacramento River and select tributaries; monitoring in the Delta; and salvage data from the Tracy Fish Collection Facility (TFCF)and Skinner Delta Fish Protection Facility (SDFPF) in the south Delta (CVP and SWP, respectively). Darker shades indicate months of greatest relative abundance. Table 2.4.4-1 The Temporal Occurren,ce of Adult (a) and Juvenile (b) Central Valley Spring-run Chinook Salmon in the Mainstem Sacramento River. Relative Abundance High Low (a) Adult Migration Location Nov Dec D elta" San Joaquin Basin Sac. River Basinb,c Sac. River Mainstemc,d b) Adult Holdingb,c c) Adult Spawningb,c,d (b) Juvenile Migration Location Jun Jul Aug Sep Oct Sac. River at RBDDd Sac. River at K.Li San Joaquin basin Deltai Sources: "CDFG (1998); bYoshiyama et al. ( 1998); c Moyle (2002); d Myers et al. ( 1998); e Lindley et al. (2004); f California Deparitment ofFish and Game (1998); g McReynolds et al. (2007); h Ward et al. (2003); iSnider and Titus (2000b); iU.S. Fish and WildLife Service (20 19) Note: Yearling spring-run Chinook salmon rear in their natal streams through the first summer following their birth. Downstream emigration generaLly occurs the following fall and winter. Most young-of-the-year spring-run Chinook salmon emigrate during the first spring after they hatch. Adult spring-run Chinook salmon enter the San Francisco estuary to begin their upstream spawning migration in late January and early February (California Department ofFish and Game 1998). They enter the Sacramento River from March to September, primarily in May and June (Yoshiyama et al. 1998, Moyle 2002). Generally, adult spring-run Chinook salmon are sexually immature when they enter freshwater habitat and must hold in deep pools for up to several 105 Biological Opinion for the Long-Term Operation of the CVP and SWP months in preparation for spawning (Moyle 2002). The Delta and Sacramento River provide a critical migration corridor for spawning adults, allowing them access to spawning grounds upstream. Monitoring of the Sacramento River mainstem during spring-run Chinook salmon spawning timing indicates that some spawning occurs in the river. Although habitat conditions can support spring-run Chinook salmon spawning and incubation in the mainstem, significant hybridization/introgression with fall-run Chinook salmon due to lack of spatiaVtemporal separation, makes identification of spring-run Chinook salmon in the mainstem very difficult (California Department of Fish and Game 1998). However, counts of Chinook salmon redds in September are typically used as an indicator of the Sacramento River spring-run Chinook salmon population abundance. Less than 15 Chinook salmon redds per year were observed in the Sacramento River from 1989 to 1993, during September aerial redd counts. Redd surveys conducted in September from 200 l to 2011 have observed an average of 36 Chinook salmon redds from Keswick Dam downstr.eam to the RBDD, ranging from 3 to 105 redds; from 2012 to 2015, redds observed were close to zero except in 2013, when 57 redds were observed in September (California Department ofFish and Wildlife 2017c). Currently, Clear Creek is the only tributary within the action area that has a population of spring-run Chinook salmon. The Sacramento River mainly functions as both rearing habitat for juveniles and the primary migratory corridor for outmigrating juveniles and spawning adults for all the Sacramento River basin populations. The juvenile life stage of CV spring-run Chinook salmon exhibits varied rearing behavior and outmigration timing. Juveniles may reside in the action area for 12-16 months (these individuals are characterized as "yearlings"), while some may migrate to the ocean as young-of-the-year (National Marine Fisheries Service 2014b). The Delta is utilized by juveniles prior to entering the ocean. Juvenile spring-run Chinook salmon use Suisun Marsh extensively as a migratory pathway, though they likely move through quickly based on their size upon entering the bay (as compared to fall-run, which enter this area at a smaller size and likely exhibit rearing behavior prior to continuing their outward migration) (Brandes and McLain 2001) (Williams 2012). Some non-natal juvenile rearing has been observed in the Lower American River (Snider and Titus 2000a). However, there is no longer a spawning population of CV spring-run Chinook associated with that system. An experimental population of spring-run Chinook salmon has been designated under section I O(j) of the ESA in the San Joaquin River from Friant Dam downstream to its confluence with the Merced River (Snider and Titus 2000a, 78 FR 79622 20 13), and spring-run Chinook salmon are currently being r·eintroduced to the San Joaquin River. The experimental population area in the San Joaquin River is outside the action area. However, when these fish migrate to and from the ocean, they will pass through the action area, where they are considered part of the nonexperimental CV spring-run Chinook salmon ESU. A conservation stock of spring-run Chinook is being developed at the San Joaquin River Interim Conservation and Research Facility at Friant Dam and juveniles have been released annually since 2014 to the lower San Joaquin River (CDFW 2014). In 2019, the San Joaquin River Restoration Program released 168,495 San Joaquin River Conservation and Research Facility spring-run Chinook salmon juveniles to the San Joaquin River in Reach 5 of the Restoration Area (Ferguson 2019). As of May 2019, more than 10 adult fish have been detected returning to the San Joaquin River. In the spring of 20 18, 106 Biological Opinion for the Long-Term Operation of the CVP and SWP juveniles released in Reach 1 of the Restoration Area were detected at the TFCF, demonstrating volitional passage ofjuvenile spring-run through the San Joaquin River for the first time in 60 years (National Marine Fisheries Service 2019c). In addition, observations in the last decade suggest that spring-running populations may currently occur in the Stanislaus and Tuolumne rivers (Franks 2014), tributary rivers to the mainstem San Joaquin River. Although the exact number of spring-running Chinook salmon in the San Joaquin basin is unknown, juvenile and adult spring-run Chinook salmon use the portion of the lower San Joaquin River within the Delta as a migratory pathway. Spring-run Chinook salmon adults are vulnerable to climate change because they over-summer in freshwater streams before spawning in autumn (Thompson et al. 2011). Currently, CV springrun Chinook salmon spawn primarily in the tributaries to the Sacramento River, and without cold water refugia (usually those in higher elevation, input from springs, or snowmelt), those tributaries will be more susceptible to impacts of climate change. Even in tributaries with cool water springs, in years of extended drought and warming water temperatures, unsuitable conditions may occur. Additionally, juveniles often rear in their natal stream over the summer prior to emigrating (McReynolds et al. 2007), and would be susceptible to warming water temperatures. Overall, the SWFSC concluded in their viability report that the status of CV spring-run Chinook salmon (until2014) has probably improved since the 2010/2011 status review and that the ESU's extinction risk may have decreased during that timeframe (Williams et al. 2016). However, the CV spring-run Chinook salmon ESU remains at moderate risk of extinction based on the severity of the drought and the low escapements, as well as increased pre-spawn mortality in Butte, Mill, and Deer creeks in 2015. There is concern that these CV spring-run Chinook salmon strongholds will deteriorate into high extinction risk in the coming years based on the population size or rate of decline criteria (National Marine Fisheries Service 20 16a). This predicted trend has been validated in recent years through escapement data collected by CDFW for Mill and Deer creeks (California Departrn,ent ofFish and Wildlife 2019), with adult returns below 500 individuals for the fourth consecutive year (20 15-20 18)(Figure 2.4.4-1 ). 107 Biological Opinion for the Long-Term Operation of the CVP and SWP Battle Creek 1.000 Butte Creek 20.000 18.000 • , 16.000 1\ .I . 14.000 12.000 500 10.000 400 8 .000 300 6 .000 200 100 L 2 .00: 0 2001 2003 2005 2007 20011 2011 2013 2015 Clear Creek 700 2017 1 1 2001 3 .000 II 2 .500 500 2 .000 400 1.500 300 1.000 200 ./ 2001 2003 2005 500 2007 20011 2011 2013 2015 2017 Feather River Hatchery 10.000 2007 20011 2011 • 2013 2017 2015 Dee r Creek .. -- 0 ..._ 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 Mill Creek 1.500 .. 6 .000 ' 4 .000 • 2005 \/\ i 2 .000 8.000 2003 • .I 4 .000 / . 1.000 .,; _.., 2 .000 ,.. 500 • j'·. ...,/ 0 0 2001 2003 2005 2007 20011 2011 2013 2015 \ .. . "' 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2017 Figure 2.4.4-1 Spring-run Chinook Salmon Adult Abundance. All populations are at or near all-time low levels for adult abundance. Data points from 2018 are preliminary estimates from the California Department of Fish and Wildlife and are subject to change. The status of spring-run critical habitat in the action area is discussed in Section 2.4.2.2.2 below. 2.4.4.2 Status of California Central Valley Steelhead in the Action Area Assessing the temporal occurrence of each life stage of CCV steelhead in the action area is done through analysis of monitoring data in the Sacramento River and select tributaries; monitoring in the Delta; and salvage data from the TFCF and SDFPF in the south Delta (CVP and SWP). Table 2.4.4-2 shows the temporal occurrence of adult and juvenile CCV steelhead at locations in the action area. 108 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.4.4-2 The Temporal Occurrence of (a) Adult and (b) Juvenile California Central VaHey Steelhead at Locations in the Action Area. Darker shades indicate months of greatest relative abundance. ll-ligh Relative Abundance Low (a) Adult migration Location Jan Feb Mar Apr May Jun Jul Delta 1 Sacramento R. at Fremont Weir 2 Sacramento R. at RBDD 3 San Joaquin River (b) Juvenile migration Location Jul Aug Sep Dec '.2Sacramento R. near Fremont Weir 4 Sacramento R. at Knights Landing 5Chipps Island (clipped) 5 Chipps Island (unclipped) 6 San Joaquin R. at Mossdale Sources: 1 (Hallock et a!. 1957) ); 2 (McEwan 200 I); 3 (Califomia Department of Fish and Game 2007); 4NMFS. analysis of 1998-2018 CDFW data; 5NMFS analysis of 1998-2018 USFWS data; 6NMFS analysis of2003-2018 USFWS data. Spawning adults enter the San Francisco Bay estuary and Delta from August to November (with a peak in September (Hallock et al. 1961). Spawning occurs in a number of tributaries to the Sacramento River, to which the Delta and Sacramento River serve as key migratory corridors. Spawning occurs from December to April, with a peak in January through March, in rivers and streams where cold, well oxygenated water is available (Hallock et al. 1961 ), (McEwan and Jackson 1996), (Williams 2006). Adults typically spend a few months in freshwater before spawning (Williams 2006) but very little is known about where they hold between entering freshwater and spawning in rivers and streams. Utilization of the Delta by adults is also poorly understood. Juvenile CCV steelhead rear in cool, clear, fast-flowing streams and are known to prefer riffle habitat over slower-moving pools. Little is known about the rearing behavior ofjuveniles in the Delta. However, they are thought to exhibit short periods of rearing and foraging in tidal and non-tidal marshes and other shallow areas prior to their final entry into the ocean. The Lower American River contains a naturally spawning population of CCV steel head, which spawn downstream ofNimbus Dam. The dam is an impassable barrier to anadromous fish, isolating historical spawning habitat located in the North, Middle and South forks of the upper American River. The American River population is small, with only a few hundred individuals 109 Biological Opinion for the Long-Term Operation of the CVP and SWP returning to spawn each year (U.S. Bureau of Reclamation 2015). Spawning adults have been observed with intact adipose fins indicating that a portion of the in-river spawning population is ofwild origin (Hannon 2013). Juvenile 0. mykiss (anadromous and resident forms) have been observed to occupy fast-flowing riffle habitat in the Lower American River, which is consistent with known life history traits of this species. Nimbus Fish Hatchery, located on the Lower American River adjacent to Nimbus Dam, produces the anadromous form of 0. mykiss. However, steelhead from Nimbus Fish Hatchery are not included in the CCV steelhead DPS due to genetic integrity concerns from use of out-ofbasin broodstock (71 FR 834 2006). To specifically address this issue and in response to RPA Action 11.6.1 contained in the NMFS 2009 Opinion (National Marine Fisheries Service 2009b), genetic testing of American River 0. mykiss population was completed in 2014 to inform the planning for Nimbus Fish Hatchery broodstock replacement that will support the CCV steelhead DPS (National Marine Fisheries Service 2016b). The portion of the lower San Joaquin River within the Delta is used by migrating adult and juvenile CCV steelhead to reach spawning and rearing grounds in the tributaries (FISHBIO 2012, California Department ofFish and Wildlife 2013b). Although steelhead will experience similar effects of climate change to Chinook salmon, as they are also blocked from the vast majority of their historic spawning and rearing habitat, the effects may be even greater in some cases., as juvenile steelhead may rear in freshwater over the summer prior to emigrating as smolts (Snider and Titus 2000b). Several studies have found that steelhead require colder water temperatures for spawning and embryo incubation than salmon (McCullough et al. 2001 ). McCullough et al. (200 1) recommended an optimal incubation temperature at or below 11 °C to l3°C (52°F to 55°F), and successful smoltification in steelhead may be impaired by temperatures above l2°C (54°F) (Richter and Ko[mes 2005). In some areas, stream temperatures that currently provide marginal habitat for spawning and rearing may become too warm to support naturally spawning steelhead populations in the future. Information on the status of CCV steelhead consist of three types of data sources: direct adult counts, redd counts, and smolt counts. Adult data are the best source, but are complicated by inconsistent counting methods and reporting formats among the hatcheries and weirs. Redd counts represent valuable information from rivers where there are no dams or weirs to block adult migration, but the actual number of adults represented by each redd are unknown. Sampling of smolts in trawls and at the salvage facilities gives us an idea of relative productivity for a region and between hatchery and wild sources, but the survival of these smolts is unknown, and the counts cannot give us estimates of adult abundance. Implementation of CDFW's Central Valley Steelhead Monitoring Program should result in greater consistency in reporting of adult escapement and estimates of abundance that are currently lacking (National Marine Fisheries Service 2016b). Hatchery production and returns are dominant over natural-origin fish. Continued decline in the ratio b etween naturally-produced juvenile steelhead to hatchery juvenile steelhead in fish monitoring efforts indicates that the wild population abundance is declining. Hatchery releases (100 percent adipose fin-clipped fish since 1998) have remained relatively constant over the past decade, yet the proportion of adipose fin-clipped hatchery smolts to unclipped naturally produced smolts has steadily increased over the past several years (National Marine Fisheries Service 2016b). 110 Biological Opinion for the Long-Term Operation of the CVP and SWP One continuing strength of the CCV steelhead DPS is the widespread distribution of this species throughout the rivers of the Central Valley. While most of the measured populations are small, steelhead can be found in most of the major rivers and streams of the Sacramento River, San Joaquin River, and eastside tributaries including the Mokelumne River and Calaveras River. Although there have been recent restoration efforts in the San Joaquin River tributaries, CCV steelhead populations in the San Joaquin Basin continue to show an overall very low abundance, and fluctuating return rates (National Marine Fisheries Service 2016b). Many watersheds in the Central Valley are experiencing decreased abundance of CCV steelhead. Dam removal and habitat restoration efforts in Clear Creek appear to be benefiting CCV steelhead as recent increases in non-clipped (wild) abundance have been observed. Despite the positive trend in Clear Creek, all other concerns raised in the previous status review remain, including low adult abundances, loss and degradation of a large percentage of the historic spawning and rearing habitat, and domination of smolt production by hatchery fish. Many other planned restoration and reintroduction efforts have yet to be implemented or completed, or are focused on Chinook salmon, and have yet to yield demonstrable improvements in habitat, let alone documented increases in naturally produced steelhead. There are indications that natural production of steelhead continues to decline and is now at a very low levels. Their continued low numbers in most hatcheries, domination by hatchery fish, and relatively sparse monitoring makes the continued existence of naturally reproduced steelhead a concern (National Marine Fisheries Service 2016b). 2.4.4.3 Status of Central Valley Spring-run Chinook Salmon and California Central Valley Steelhead Critical Habitat in the Action Area A significant portion of designated critical habitat for both CV spring-run Chinook salmon and CCV steelhead is contained within the proposed project action area. PBFs for both species are concurrently defined in (70 FR 52488 2005) and the following PBFs, in summary, for these species are present in the proposed action area: (1) freshwater spawning sites, (2) freshwater rearing sites, (3) freshwater migration corridors, and (4) estuarine areas. Critical habitat for CV spring-run Chinook includes portions of the north Delta, as well as the Sacramento River and the lower American River (from the confluence with the Sacramento River to the Watt Avenue Bridge). With the exception of Clifton Court Forebay, the entirety of the proposed action area in the Central Valley is designated critical habitat for CCV steelhead. Historically, both CV spring-run Chinook salmon and CCV steelhead spawned in many ofthe headwaters and upstream portions of the Sacramento River and San Joaquin River basins. Similar to winter-run Chinook salmon, passage impediments have contributed to substantial reductions in the populations of these species by isolating them from much of their historical spawning habitat. Naturally-spawning spring-run Chinook salmon had been extirpated from the San Joaquin River basin entirely. However, an experimental population has been reintroduced to the river under section 1O(j) ofthe ESA and "spring-running" adults have been documented migrating into the San Joaquin tributaries (Franks 2014). Within the action area, spawning habitat for CV spring-run is currently limited to the mainstem of the Sacramento River between Red Bluff and Keswick Dam, and Clear Creek. CCV steelhead spawn in this reach of the upper accessible Sacramento River, and Clear Creek, as well as throughout the lower American River between its confluence with the Sacramento River up to Nimbus Dam. The PBFs of freshwater 111 Biological Opinion for the Long-Term Operation of the CVP and SWP spawning sites has been degraded within the action area due to high water temperatures, redd dewatering, and loss of spawning gravel recruitment in reaches below Keswick Dam (Wright and Schoellhamer 2004, Good et al. 2005, National Marine Fisheries Service 2009b, Jarrett and Killam 201 4). These issues are actively addressed by adaptive flow management in both rivers as well as spawning gravel augmentation projects in both reaches. Freshwater rearing and migration PBFs have been degraded from their historical condition within the action area. In the Sacramento and San Joaquin rivers, bank armoring has significantly reduced the quantity of floodplain rearing habitat for juvenile salmonids and has altered the natural geomorphology of the river (National Marine Fisheries Service 201 4b). Similar to winter-run Chinook salmon, CV spring-run and CCV steelhead are only able to access large floodplain areas, such as the Yolo Bypass, under certain hydrologic conditions which do not occur in drier years. However, the Yolo Bypass Restoration Salmonid Habitat Restoration and Fish Passage Implementation Plan includes notching the Fremont Weir, which will provide access to floodplain habitat for juvenile spring-run Chinook salmon and steelhead over a longer period (California Department of Water Resources and U.S. Bureau of Reclamation 20 16). Levee construction involves the removal of riparian vegetation, resulting in reduced habitat complexity and shading, making juveniles more susceptible to predation. Additionally, loss of riparian vegetation reduces aquatic macroinvertebrate recruitment resulting in decreased food availability forrearingjuveniles (Anderson and Sedell 1979, Pusey and Arthington 2003). The lower American River has experienced similar losses of rearing habitat. However, projects sponsored by Reclamation are restoring rearing habitat for juvenile CCV steelhead through the creation of side channels and placement of instream woody material (U.S. Bureau of Reclamation 201 5). Within the action area ofthe PA, the estuarine PBFs include the legal Delta, encompassing significant reaches of the Sacramento and San Joaquin rivers that are tidally influenced (70 FR 52488 2005). Estuarine habitat in the Delta is significantly degraded from its historical condition due to levee construction, shoreline development, and dramatic alterations to the natural hydrology of the system due to water export operations (National Marine Fisheries Service 20 14b). Though critical habitat for CV spring-run occurs in the north Delta and not the interior or south Delta, entrainment into the interior Delta may occur during DCC gate openings if coinciding with migration. However, the 2014 drought year prompted protections for CV springrun at the DCC (National Marine Fisheries Service 2016a). Reverse flows in the central and south Delta resulting from water exports may exacerbate interior Delta entrainment by confounding flow and temperature-related migratory cues in outmigratingjuveniles. The presence of these stressors, which cause altered migration timing and routing, degrade critical habitat PBFs related to rearing and migration. 2.4.5 sDPS North American Green Sturgeon 2.4.5.1 Status of sDPS North American Green Sturgeon in the Action Area The sDPS green sturgeon exhibit a more complex life history with respect to salmon ids and less is known about the ecology and behavior of their various life cycle stages in the action area. Some acoustic telemetry (Kelly et al. 2007, Heublein et al. 2009, Thomas et al. 2014, Wyman et al. 201 7, Steel et al. 2018, Chapman et al. 20 19) and multi-frequency acoustic survey work 112 Biological Opinion for the Long-Term Operation of the CVP and SWP (Mora et al. 20 15) has been done to study adult migration patterns and habitat use in the action area (Delta and Sacramento River). Field surveys have also been conducted on the Sacramento River to study spatial and temporal occurrence of early life stages (Poytress et al. 20 10, Poytress et al. 2011,2012, 2013) (Table 2.4.5-1). These studies have documented some spatial patterns in spawning events on the upper reaches of the Sacramento River. Spawning occurs in cool sections of the upper Sacramento, Feather, and Yuba rivers in deep pools (>5 meters) with small to medium sized sand, gravel, cobble, or boulder substrate (National Marine Fisheries Service 2018g). Although Seesholtz et al. (2014) and (Beccio 2018) observed spawning in the Feather River and Yuba River, respectively, no known spawning events have been observed in the lower American River or in the portion of the lower San Joaquin River that is included in the Delta. Recently, an eDNA and video-confirmed green sturgeon was observed in the Stanislaus River occupying a pool downstream of Knights Ferry, CA (RK 86.1) (Anderson et al. 2018). Additionally, several lab studies have been conducted using early life stages to investigate ontogenic responses to elevated thermal regimes as well as foraging behavior as a function of substrate type (Allen et al. 2006, Nguyen and Crocker 2006, Linares-Casenave et al. 2013, Poletto et al. 2018). However, due to sparse monitoring data for juvenile, sub-adult and adult life stages in the Sacramento River and Delta, there are significant data gaps to describe the ecology of this species in the action area. Spawning occurs in the upper reaches of the Sacramento River and Feather River (Seesholtz et al. 2014, Poytress et al. 2015). Mainstem Sacramento and Delta serve as rearing habitat and a migratory corridor for this species. Some rearing also may occur in the lowest reaches of the lower American River where deep pools occur for rearing of older life stages (downstream ofSR-160 bridge) (Thomas et al. 2013). However, CDFW is currently performing a juvenile monitoring study in the Delta using acoustic telemetry (Beccio 20 18). Juvenile green sturgeon rear from 1 to 5 years in the Delta and San Francisco Estuary before entering the ocean as sub-adults. Around age 15, mature adults migrate into the San Francisco Estuary in late winter through early spring to spawn in the Sacramento River and its tributaries primarily from April to July, and generally, adults spawn every 3 to 4 years. Elevated Delta outflow is a likely spawning cue for mature adults to enter the river system. Following spawning, adults may remain in the Sacramento River Basin for up to a year; elevated water flows in the late fall and winter signal outmigration in adults that over-summer in spawning habitats (National Marine Fisheries Service 2018g). Information gaps encountered in efforts to summarize information on sDPS green sturgeon life history are often addressed using known information about the nDPS. 113 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.4.5-1 The Temporal Occurrence of (a) Spawning Adult, (b) Larval, (c) Young Juvenile, (d) Juvenile, and (e) Sub-adlult and Non-spawning Adult Southern DPS Green Sturgeon at Locations in the Action Area. Darker shades indicate months of greatest relative abundance. (a) matm·e (2:145 em TL females, 2: 120 em TL males), including pr·e- a nd postindhiduals. J an Sac River (< rkm 332. Sac-SJ-SF Location SAC-SJ-SF Estuaty Pacific Coast Coas tal Bays & Estuaries' Relative Abundance: =High = Medium Sources: (a) (Heublein et a l. 2009, Kl irnley et al. 20 15a, Mora et al. 2015, Poytress et aL 20 I 5, DuBois and Danos 20 I 8, Mora et aL 2018) (b) (Poytress et al. 2015, Heublein et al. 2017); (c) (Poytress et al. 2015, Heublein et aL 20 17); (d) (Radtke 1966, California Department ofFish and Game 2002, Poytress et al. 2015, Heublein et al. 2017); (e) (Erickson and Webb 2007, Moser and Lindley 2007, Lindley et al. 2008, Huff et aL 20 II , Lindley et aL 20 I I , DuBois and Danos 20 18). Outside of Sac-SJ-SF estuary (e.g. Columbia R., Grays Harbor, Willapa Bay). Southern DPS green sturgeon spawn primarily in the Sacramento River from April to July, with the farthest upstream spawning event in the Sacramento River documented near Ink's Creek at river km 426 (Poytress et at. 2015). However, Heublein (2009) detected adults as far upstream as river km 451 near Cow Creek, suggesting that their spawning range may extend farther upstream 114 Biological Opinion for the Long-Term Operation of the CVP and SWP than previously documented. The upstream extent of their spawning range lies somewhere below ACID (RM 299, or RK 480) as that dam impedes passage for green sturgeon in the Sacramento River (Heublein et al. 2009). However, it is uncertain if green sturgeon spawning habitat exists closer to ACID, which could allow spawning to shift upstream in response to climate change effects. Successful spawning of green sturgeon in other accessible habitats in the Central Valley (i.e., the Feather and Yuba rivers) is limited, in part, by late spring and summer water temperatures and water flow. Similar to salmonids in the Central Valley, green sturgeon spawning in the major lower river tributaries to the Sacramento River are likely to be further limited if water temperatures increase over time. In a bioenergetics study, 15-l9°C was the optimal thermal range for age-0 green sturgeon (Mayfield and Cech 2004). Iftemperatures in spawning habitat exceed that range in the future, it may reduce the fitness of early life stages. 2.4.5.2 Status of sDPS North American Green Sturgeon Critical Habitat in the Action Area Critical habitat for sDPS green sturgeon is contained in nearly all ofthe PA's action area for listed anadromous fish with the exception of Clear Creek, the lower American River from the SR-160 bridge upstream to Nimbus Dam, and the Stanislaus River. A11 PBFs for sDPS green sturgeon critical habitat are present in the action area, except PBFs for nearshore coastal marine areas. The PBFs in the action area include, in summary: (1) food resources; (2) substrate type or size; (3) water flow; (4) water quality; (5) migratory corridor; (6) depth; and (7) sediment quality. These PBFs apply to both riverine and estuarine areas except "substrate type or size," which pertains to spawning habitats and only applies to riverine areas. These PBFs are described in detail in the range wide status of sDPS green sturgeon in Appendix B. The historical spawning range of sDPS green sturgeon is not well known, though they are thought to have spawned in many of the major tributaries of the Sacramento River basin, many of which are isolated due to passage impediments (Beamesderfer et al. 2004). Green sturgeon utilize the lower Sacramento River for spawning and are known to spawn in its upper reaches between RBDD and Keswick Dam (Poytress et al. 2015). Similar to the listed salmonid species addressed in this Opinion, PBFs related to spawning and egg incubation have been degraded as discussed in Sections 2.2.8. Changes in flow regimes and the installation of Keswick and Shasta dams have significantly reduced the recruitment of spawning gravel in the upper reaches of the lower Sacramento River. Flow conditions in the Sacramento River have also been significantly altered from their historical condition. The degree to which these altered flow regimes affects outrnigration dynamics of juveniles is unknown. However, some suitable habitat exists and spawning events have been consistently observed annually (Poytress et al. 2015). PBFs for sDPS green sturgeon in the lower reaches of the Sacramento River and the Delta have also been significantly altered from their historical condition, similar to the impacts described in Sections 2.4.1.2 and 2.4.2.3. However, green sturgeon exhibit very different life history characteristics from those of salmonids and therefore utilize habitat within the proposed action area differently as follows. Green sturgeon are thought to exhibit rearing behavior in the lower reaches of the Sacramento River and the Delta as juveniles and subadults prior to migrating to the ocean, though little is known about the behavior of these life stages in the Delta (Radtke 1966, National Marine Fisheries Service 2015a). Loss ofriparian habitat complexity in the Sacramento River and Delta has likely posed less of a threat to green sturgeon because these life stages are benthically oriented. However, it is likely that reverse flows generated by Delta water 115 Biological Opinion for the Long-Term Operation of the CVP and SWP exports affect the green sturgeon juvenile and subadult life stages to some degree as evidenced by juvenile captures at CVP/SWP salvage facilities during high water years (California Department ofFish and Wildlife 2018a). 2.4.6 Importance of the Action Area for the Survival and Recovery of Listed Fish Species The action area defmed for this PA includes critical habitat designated for all species ofESAlisted fish addressed in this Opinion. It includes spawning habitat that is critical for the natural production of these species; rearing habitat that is essential for growth and survival during early life stages and enhances overall productivity and population health; migratory corridors that facilitate anadromous life history strategies; and estuarine habitat that serves as additional rearing habitat and provides a gateway to marine phases of their lifecycle. The NMFS Recovery Plan for Central Valley salmonids (National Marine Fisheries Service 20 14b) provides region-specific recovery actions that were identified by NMFS in order to facilitate recovery of these species. Implementation of some of these actions has already begun and more are in the planning phase. Recovery criteria for the winter-run Chinook salmon ESU identified in the Recovery Plan for Central Valley salmonids (National Marine Fisheries Service 2014b), includes three viable populations. The Recovery Plan further identified which populations/watersheds have the likely potential to become viable. These include the current population downstream of Keswick Dam on the Sacramento River, reintroducing a population to Battle Creek (tributary to the Sacramento River), and reintroducing a population to the Little Sacramento River or McCloud River upstream of Shasta Dam. As mentioned above, the only current population is being managed by CVP operations. However, implementation of a ' jump start" to the reintroduction plan to Battle Creek began in 2018. Reintroduction to McCloud River was part of the 2009 RP A, but has not been implemented past initial studies to date (further description is provided above in Section 2.4.2.9 Restoration Actions from 2009 NMFS RPA). Recovery criteria for the spring-run Chinook salmon ESU identified in the Recovery Plan for Central Valley salmonids (National Marine Fisheries Service 2014b), includes a total of nine viable populations, spread among four distinct geographical regions (or diversity groups). The Recovery Plan further identified which populations/watersheds have the likely potential to become viable. These include Clear Creek (in the Northwestern California Diversity Group); Battle Creek, and one population upstream of Shasta Dam (in the Basalt and Porous Lava Diversity Group); Butte, Mill, and Deer creeks, as well as upper Yuba River (in the Northern Sierra Nevada Diversity Group); and in the Southern Sierra Nevada Diversity Group - the San Joaquin River below Friant Dam, and one additional population above current impassible dams in either the Stanislaus or Tuolumne rivers. Currently, only three popu lations, all in the Northern Sierra Nevada Diversity Group, are considered to be both genetically independent and sufficiently high in abundance in most years to warrant "viable or close to viable status." However, these three stronghold populations have been heavily affected by the recent years of drought, such that numbers of returning adults have been extremely low. Additionally, recent expansive and destructive timber fires in anadromous watersheds have left behind large amounts of ash, debris, mountainous bare terrain, and mixed stands of dead and scarred trees/vegetation. Resulting effects of fire can lead to local impacts and alteration of freshwater ecological function (Bisson et al. 2003, Bixby et al. 2015). Years offuture impacts are expected associated with 116 Biological Opinion for the Long-Term Operation of the CVP and SWP terrain devoid of vegetation, resulting in accelerated erosion/runoff, and physiochemical changes to soil/water chemistry (Johnson et al. 2012). Recovery criteria for the CCV steelhead DPS identified in the Recovery Plan for Central Valley salmonids (National Marine Fisheries Service 2014b), include a total of nine viable populations, spread among four distinct geographical regions (or diversity groups). The Recovery Plan further identified which populations/watersheds have the likely potential to become viable. Most of the identified steelhead populations are the same as CV spring-run Chinook salmon described above. Some differences include Antelope Creek instead of Butte Creek (for the Northern Sierra Nevada Diversity Group); and Calaveras River instead ofthe San Joaquin River. Currently, there is still a general lack of data on the status of wild populations. However, the catch of unmarked (wild) steelhead at Chipps Island has been less than 5 percent of the total smolt catch during recent years, which indicates that natural production of steelhead throughout the Central Valley remains at very low levels. Despite the positive trend on Clear Creek and encouraging signs from Mill Creek (both Core 1 Populations), concerns such as low adult abundances, loss and degradation of a large percentage of the historic spawning and rearing habitat, and domination of smolt production by hatchery fish still remain (National Marine Fisheries Service 20 16b). Recovery criteria for sDPS green sturgeon identified in the Recovery Plan for the Southern Distinct Population Segment ofNorth American Green Sturgeon (National Marine Fisheries Service 2018g) include demographic recovery criteria (abundance, distribution, productivity, and diversity) and threat-based recovery criteria (significant known threats impeding recovery). The action area of the PA includes sDPS green sturgeon spawning habitat, adult and juvenile migratory corridors, juvenile rearing habitat, and adult post-spawning holding areas. 2.4.7 Southern Resident Killer Whale 2.4.7.1 Status of Southern Resident Killer Whale in the Action Area The federally listed SRKW DPS occurs in the action area and may be affected by the proposed action. Please refer to Southern Resident Killer Whale Recovery Plan (National Marine Fisheries Service 2008b) and the most recent 5-year status review (National Marine Fisheries Service 2016e) for more detailed information on the state of knowledge about the status ofSRKW and overall threats that are currently facing the species. In killer whale populations, groups of related matrilines form pods, and three pods (J, K, and L) make up the Southern Resident community. The historical abundance of SRKW is estimated from a low population level of 140 animals to an unknown upper bound. The minimum historical included whales killed or removed for public display in the 1960s and 1970s, estimate which were added to the remaining population at the time the captures ended (National Marine Fisheries Service 2008b). Several lines of evidence (i.e., known kills and removals (Olesiuk et al. 1990), salmon declines (Krahn et al. 2002), and genetics (Krahn et al. 2002, Ford et al. 2011) all indicate that the population used to be much larger than it is now, but there is currently no reliable estimate of the upper bound of the historical population size. Over the last 5 decades, the SRKW population has remained at a similarly low population size fluctuating from about 80-90 individuals (Olesiuk et al. 1990, Center for Whale Research 2008). NMFS has continued to fund the Center for Whale Research (CWR) to conduct an annual census of the SRKW population, and census data are now available through December 2018. At the end 117 Biological Opinion for the Long-Term Operation of the CVP and SWP of December 2018, the population numbered 74 individuals; K Pod=18, L Pod=34, J Pod=22. The SRKW population has experienced an increase in reproductive females since the beginning of the annual censuses in the 1970s. There is weak evidence of a decline in fecundity rates through time for reproductive females. This decline is linked to fluctuations in abundance of Chinook salmon prey, and possibly other factors (Ward 2014). However, there were six births in 2015, which is higher than observed in recent times. It is unclear yet how these additions to the population will affect the SRKW population dynamics. As of December 2018, the population has decreased to only 74 whales, a historical low in the last 30 years with a current realized growth rate (from 1974 to 2017) at half of the previous estimate described in the science panel report; 0.29 percent. SRKW spend a substantial amount of time from late spring to early autumn in inland waterways of Washington State and British Columbia, including the Strait of Georgia, Strait of Juan de Fuca, and Puget Sound (Bigg 1982, Krahn et al. 2002). SRKW occur throughout the coastal waters of Washington, Oregon, and Vancouver Island and are known to travel as far south as central California and as far north as southeast Alaska. Although the entire SRKW DPS has the potential to occur in coastal waters at any time during the year, occurrence in coastal waters is more hkely from November to May. Satellite-linked tag deployments on K and L pod animals indicate that those pods in particular use the coastal waters along Washington, Oregon, and California during non-summer months (Hanson 2015). Detection rates ofK and L pods on passive acoustic recorders indicate the whales occur with greater frequency off the Columbia River delta and Westport, Oregon, and are most common in March (Hanson et al. 2013). Results of recent satellite tagging indicate the limited occurrence along the outer coast by J pod (Hanson 20 15) where J pod has also only been detected on one of seven passive acoustic recorders positioned along the outer coast; members of the J pod do not appear to travel to Oregon or California like K and L pods (Hanson et al. 20 13). As described in the final Recovery Plan for SRKW (National Marine Fisheries Service 2008b), several factors may be limiting recovery of the SRKW DPS. These factors include: quantity and quality of prey, toxic chemicals that accumulate in top predators, and disturbance from sound and vessels. Oil spills are also a risk factor. It is likely that multiple threats are acting together to impact the whales. Although it is not clear which threat or threats are most significant to the survival and recovery of SRKW, all identified threats are potential limiting factors in their population dynamics (National Marine Fisheries Service 2008b). Significant attention has been paid in recent years to the relationship between the Southern Resident population and the abundance of important prey, especially Chinook salmon. Recently, Ford et al. (2016) confirmed the importance of Chinook salmon to SRKW in the summer months using DNA sequencing from whale feces. The researchers found that salmonids made up to over 98 percent of the whales inferred diet, of which almost 80 percent were Chinook salmon. Researchers also found evidence of prey shifting at the end of summer towards coho salmon for all years analyzed; coho salmon contributed to over 40 percent of the diet in late summer. Chum, sockeye, and steelhead made up relatively small contributions to the sequences (less than 3 percent each). Although less is known about the diet of SRKW offthe Pacific coast during winter, the available information from observation of predation events indicates that salmon, and Chinook salmon in particular, are also important when the whales occur in coastal waters (Hanson et al. 201 0). 118 Biological Opinion for the Long-Term Operation of the CVP and SWP One hypothesis as to why killer whales primarily consume Chinook salmon even when they are not the most abundant salmon available is because of the Chinook salmon's relatively high energy content (Ford and Ellis 2006). Chinook salmon have the highest value of total energy content compared to other salmonids because of their larger body size and higher energy density (expressed in kcal/kg) (O'Neill et al. 2014). For example, in order for a killer whale to obtain the total energy value of one average size adult Chinook salmon, it would need to consume approximately 2.7 averaged size coho salmon, 3.1 chum salmon, 3.1 sockeye salmon, or 6.4 pink salmon (O'Neill et al. 2014). Ford et al. (2005, 20 10) evaluated 25 years of demographic data from Southern and Northern Resident killer whales and found that changes in survival largely drive their population, and the populations' survival rates were strongly correlated with coast-wide availability of Chinook salmon. Ward et al. (2009) found that Northern and SRKW fecundity was highly correlated with Chinook salmon abundance indices, and reported the probability of calving increased by 50 percent between low and high Chinook salmon abundance years. More recently, Ward et al. (2013) considered new stock-specific Chinook salmon indices and found strong correlations between the indices of Chinook salmon abundance, such as the West Coast Vancouver Island (WCVI) used by the Pacific Salmon Commission, and killer whale demographic rates. However, no single stock or group of stocks was identified as being most correlated with the whales' demographic rates. Further, they stress that the relative importance of specific stocks to the whales likely changes over time (Ward et al. 2013). The health of individual SRKW is being studied closely. As a chronic condition, nutritional stress can lead to reduced body size and condition of individuals, and lower reproductive and survival rates of a population (Trites and Donnelly 2003). Very poor body condition is detectable by a depression behind the blowhole that presents as a "peanut-head" appearance. There have been several SRKW that have been observed in recent years with the " peanut-head" condition, and the majority of these individuals died relatively soon after these observations (Durban et al. 2017, Fearnbach et al. 20 18). The bodies of the SRKW that died following these observations were not recovered and therefore a definitive cause of death could not be identified. More recently, photographs of whales from an unmanned aerial system (i.e., a drone) have been collected and individual whales in poor condition have been observed. Both females and males across a range of ages were found in poor body condition. Killer whales are exposed to persistent pollutants primarily through their diet, including Chinook salmon. These harmful pollutants are stored in blubber and can later be released and become redistributed to other tissues when the whales metabolize the blubber in response to food shortages or reduced acquisition of food energy that could occur for a variety of other reasons including during gestation or lactation. High levels of these pollutants have been measured in blubber biopsy samples from SRKW (Ross et al. 2000, Krahn et al. 2007, Krahn et al. 2009), and more recently these pollutants wer·e measured in scat samples collected from the whales, providing another potential opportunity to evaluate exposure of SRKW to these pollutants (Lundin et al. 2016). High levels of persistent pollutants have the potential to affect the whales' endocrine and immune systems and reproductive fitness (Krahn et al. 2002), Mongillo et al. in review). As described in National Marine Fisheries Service (2016e), vessel activities may affect foraging efficiency, communication, and/or energy expenditure through the physical presence of the vessels, underwater sound created by the vessels, or both. Houghton et al. (20 15) found that the noise levels killer whales receive are largely determined by the speed of the vessel. Thus, to 119 Biological Opinion for the Long-Term Operation of the CVP and SWP reduce noise exposure to the whales, they had recommended reduced vessel speeds. In 201 1, NMFS announced final regulations to protect killer whales in Washington State from the effects ofvarious vessel activities (76 FR 20870 2011). 2.4.7.2 Summary of Southern Resident Killer Whale DPS Viability The viability ofthe SRKW DPS is. evaluated through the consideration of the threats identified in the recovery plan and the population status relative to downlisting criteria. Since completing the recovery plan, NMFS has prioritized actions to address the threats with highest potential for mitigation: salmon recovery, oil spill response, and reducing vessel impacts. Several threats criteria have been met, but many w ill take years of research and dedicated conservation efforts to satisfy. Salmon recovery is a high priority on the West Coast and there are numerous actions underway to address threats to salmon populations and monitor their status. Recovery of depleted salmon populations is complex and a long-term process. NMFS and partners have successfully developed an oil spi11 response plan for killer whales (National Marine Fisheries Service 20 16e). However, we still have additional work to prepare for a major spill event. NMFS has developed special vessel regulations intended to reduce disturbance of killer whales from vessel traffic. It will take time to evaluate the effectiveness of any new regulations in improving conditions for the whales. Even with progress toward minimizing the impacts of the threats, each of the threats still pose a risk to the survival and recovery of the whales (National Marine Fisheries Service 2016e). At the time of listing in 2005, there were 88 whales in the population and at the end of 2016, there were 78 whales. Population growth has varied during this time with both increasing and decreasing years. The most recent assessment including data through 2016 now suggests a downward trend in population growth projected over the next 50 years, in part due to the changing age and sex structure of the population, but also related to the relatively low fecundity rate observed over the period from 2011 to 2016 (National Marine Fisheries Service 2016e). The biological downlisting and delisting criteria, including sustained growth over 14 and 28 years, respectively, have not been met (National Marine Fisheries Service 2016e). While some ofthe biological downlisting and delisting criteria have been met (i.e., representation in all three pods, multiple mature males in each pod), the overall status of the population is not consistent with a healthy, recovered population. Considering the status and continuing threats, the SRKW remain in danger of extinction (National Marine Fisheries Service 2011f). 2.4.7.3 Critical Habitat and Physical or Biological Features for Southern Resident Killer Whale Designated critical habitat for the SRKW DPS consists of three specific marine areas ofPuget Sound, Washington: (1) the Summer Core Area in Haro Strait and waters around the San Juan Islands; (2) Puget Sound; and (3) the Strait of Juan de Fuca (71 FR 69054 2006). These areas are not part of the action area, and are not expected to be affected by the proposed action; therefore, critical habitat for the SRKW DPS will not be discussed further in this Opinion. 2.4.7.4 Factors Affecting the Prey of Southern Residents in the Action Area In the Rangewide Status of the Species and Critical Habitat and Environmental Baseline sections for ESA-listed Chinook salmon, we discussed the impacts of various activities and factors 120 Biological Opinion for the Long-Term Operation of the CVP and SWP affecting Chinook salmon populations in the freshwater environment and, specifically, the action area in the Central Valley, including major influences such as water operations and climate change. In the past, NMFS has consulted on the effects of the long-term operations ofthe CVP/SWP in California (National Marine Fisheries Service 2009b). In that analysis, NMFS found that the long-term operations of the CVP and SWP, as proposed, were likely to jeopardize the continued existence of several ESA-listed Chinook salmon ESUs. NMFS concluded that the increased risk of extinction of the winter- and spring-run Chinook salmon, along with loss of diversity in fall-run, as a long-term consequence of the proposed action is likely to reduce the likelihood of survival and recovery ofthe SRKW DPS, although implementation of the RPA actions for reducing adverse impacts to Chinook salmon was determined sufficient to also reduce adverse impacts on SRKW and avoid jeopardy. In general, the factors affecting non-listed Chinook salmon (fall-run and late fall-run) in the freshwater environment are identical or very similar to what is discussed for ESA-listed Chinook salmon in the Central Valley. All of these important influences on Chinook salmon in the freshwater environment contribute to the health, productivity, and abundance of Chinook salmon that ultimately survive to reach the ocean environment and influence the prey base and health of SRKW. Given that the factors that affect salmon in the freshwater environment of the Central Valley have already been discussed, this section focuses on important factors for Chinook salmon and for SRKW in the marine environment. Significance ofPrey As described in the Rangewide Status ofSouthern Resident Killer Whale section (Section 2.2.9), statistical correlations between various Chinook salmon abundance indices and the vital rates (fecundity and survival) of SRKW have been outlined in several papers. In addition to examining whether any fundamental linkages between vital rates and prey abundance are evident, another primary purpose of many of these analyses has been aimed at distinguishing which Chinook salmon stocks, or grouping of Chinook salmon stocks, may be the most closely related to these vital rates for SRKW. Largely, attempts to compare the relative importance of any specific Chinook salmon stocks or stock groups using the strengths of these statistical relationships have not produced clear distinctions as to which are most influential, as most Chinook salmon stock indices are highly correlated with each other. It is also possible that different populations may be more important in different years. Large aggregations of Chinook salmon stocks that reflect abundance on a coastwide scale appear to be as equally or better correlated with Southern Resident vital rates than any specific or smaller aggregations of Chinook salmon stocks, including those that originate from the Fraser River that have been positively identified as key sources of prey for SRKW during certain times of the year in specific areas (see Hilborn et al. 2012, Ward et al. 2013). However, there are still questions about the diet preferences of SRKW throughout the entire year, as well as the relative exposure of SRKW to varioll!s Chinook salmon or other salmon stocks outside of inland waters during the summer and fall. To help answer some of these questions, NMFS and Washington Department ofFish and Wildlife (WDFW) recently released a report to help evaluate and identify which Chinook stocks, including Central Valley Chinook salmon, should be priorities for recovery actions to help increase SRKWs' prey base (NMFS and WDFW 2018; described in more detail in Appendix B). As referenced above, the independent science panel found good evidence that Chinook salmon are a very important part of the SRKW diet and that some SRKW have been in poor condition 121 Biological Opinion for the Long-Term Operation of the CVP and SWP recently, which is associated with higher mortality rates. They further found that the data and correlations developed to date provide some support for a cause and effect relationship between salmon abundance and SRKW survival and reproduction. They identified "reasonably strong" evidence that vital rates of SRKW are, to some degree, ultimately affected by broad-scale changes in their primary Chinook salmon prey. They suggested that the effect is likely not linear, however, and that predicted improvements in SRKW Slllrvival with increasing abundances of Chinook salmon may not be realistic or may diminish at Chinook salmon abundance levels that are above their historical average (Hilborn et al. 2012). Given all the available information, and considering the uncertainty that has been highlighted, we assume that the overall abundance of Chinook salmon as experienced by foraging SRKW throughout their range may be as influential on their vital rates as any other relationships with any specific Chinook salmon stocks. Link between Southern Resident Killer Whales and Central Valley Chinook as Prey As described in the Rangewide Status ofSouthern Resident Killer Whale section (Section 2.2.9), SRKW (particularly K and L pod) are known to reside in coastal waters along the west coast of U.S. and Canada during the winter and spring, including at least occasional visits to California. The BA describes in general some of what is known about the distribution of Central Valley Chinook salmon in the Pacific Ocean in comparison to the distribution of Southern Residents. Largely, our knowledge of the distribution of these Chinook salmon in the ocean comes from the data obtained from coded wire tags (CWT) and genetic stock information (GSI) obtained from fish harvested in ocean fisheries that generally occur sometime between April and October. Unfortunately, the timing of ocean salmon fisheries does not overlap well with the occurrence of SRKW in coastal waters during the winter and spring, especially in the last few decades. Ocean distribution of Chinook salmon populations based on summer time fishery interactions generally indicates northern movements of Chinook salmon from their spawning origins (Weitkamp 2010), although the range ofthese movements is quite variable between populations and run timings, and the distribution of Chinook salmon populations in the winter and spring when SRKW are likely to encounter Central Valley Chinook salmon stocks is not as well known. Recently, Shelton et al. (2019) did estimate the seasonal ocean distribution, survivorship, and aggregate abundance of fall-run Chinook salmon stocks from California to British Columbia. While their analysis did not appear to reveal significant seasonal variance in the relative distribution of Chinook salmon stocks from California during the winter and spring compared to the summer and fa11, they generally concluded that fall-run Chinook salmon stocks tended to be more northerly distributed in summer than in winter-spring, and ocean distributions also tend to be spatially less concentrated in the winter-spring (Figure 3 in Shelton et al. 20 19). Without any additional information available that would suggest the distribution of Central Valley Chinook salmon shifts substantially during the winter or spring, we assume the distribution of Central Valley Chinook salmon during the winter and spring is similar to what has been documented during the summer and fall, and that data collected from hatchery fish (usually where CWTs are applied) are representative of the distribution ofboth wild and hatchery populations. The available data from CWT and GSI confirm that Chinook salmon from the Central Valley (particularly fall-run) occur in small numbers as far north as Vancouver Island, British Columbia, but are primarily encountered by ocean salmon fisheries south of the Columbia River (Weitkamp 2010, Bellinger et al. 2015, Shelton et al. 201 9). Recent GSI studies by Bellinger et al. (2015) indicated that Central Valley Chinook salmon (primarily fall-run) constituted sizeable 122 Biological Opinion for the Long-Term Operation of the CVP and SWP proportions of Chinook salmon sampled off the coast of Oregon and California during the 2010 fishing season where comprehensive GSJ data were collected. 2 In total, the available data suggest that Central Valley Chinook salmon constitute a sizeable percentage of Chinook salmon that would be expected to be encountered by SRKW in coastal waters off California and Oregon, and at least a small portion of Chinook salmon in the ocean as far north as British Columbia. In addition, ratios of contaminants in blubber biopsies found that the blubber ofK and L pod match with similar ratios of contaminants in Chinook salmon from California, which was indicated by the relatively high concentrations of dichlorodiphenyltrichloroethane (DDT). These DDT fingerprints suggest fish from Califomia3 form a significant component of their diets (Krahn et al. 2007, Krahn et al. 2009, O'Neill et al. 2012). As a result, we conclude that Central Valley Chinook salmon are an important part ofthe diet for most SRKW during portions of the year when SRKW occur in coastal waters off the North American coast, especially south of the Columbia River, which includes the times of potential reduced body condition and increased diet diversity that received additional weight during a recent prey prioritization process described above. Relationship of Central Valley Chinook to the Total Abundance of Chinook within the Ocean Range ofSRKW Given that the best information available links SRKW population dynamics to the abundance of Chinook salmon available to SRKW at a coast-wide level, and that impacts from the proposed action are expected to occur only to salmon from the California Central Valley, it is important to understand how significant Central Valley Chinook salmon are to the abundance of Chinook salmon within the range of SRKW. Currently, there is no capability to generate specific estimates of the number of Chinook salmon that may be found in the ocean within any defined boundary that would include likely or possible coastal migrations of SRKW during the winter and spring. There are many different management and monitoring schemes that are employed for Chinook salmon along the western North American coast that make it difficult to directly relate and compare metrics of Chinook salmon abundance. A commonly used approach involves use of relative indexes as opposed to absolute measures of abundance, such as the WCVI index that has been previously related to Southern Resident population dynamics (Ward et at. 2013). In addition, many of the estimates or forecasts of Chinook salmon abundance used for management are related to escapements that are not inclusive of adult Chinook salmon that remain in the ocean to mature, or succumb to predation or other forms of mortality. In combination, use of catch and escapement data from Chinook salmon populations that occur in the range of SRKW could provide some minimum measure of the absolute abundance of Chinook salmon that are available, although all of these Chinook salmon individuals would not necessarily always overlap with SRKW during any specific time period given the uncertain and variable migratory nature of Chinook salmon and Southern Residents. Without any comprehensive and consistent monitoring and assessment methodology across Chinook salmon populations throughout the 2 Bellinger et al. 2015 estimated that Central Valley Chinook salmon made up about 22% of the Chinook salmon sampled off the Oregon coast and about 50% of those sampled off the California coast (south to Big Sur) during that one-year study. 2010 was a very low year for Central Valley harvest and escapement (PFMC 2019). 3 The research does not specify if or how much fish from the Central Valley specifically contribute to the diet: only that SRKW must feed in areas where Chinook with California origins occur. Consistent with the information reviewed, Central Valley Chinook salmon overlap in space and time with Chinook from other California origins like the Klamath River (Shelton et al. 20 18). 123 Biological Opinion for the Long-Term Operation of the CVP and SWP range of SRKW, we will combine the data and information that are available for use in generally characterizing the abundance of coast-wide Chinook salmon potentialRy available to SRKW, as well as the relative importance of Central Valley Chinook salmon to that total. In general, ocean abundance estimates for Chinook salmon that originate from U.S. systems are provided by the Pacific Fisheries Management Council (PFMC 20 19). The estimated 2019 ocean abundance of Sacramento River fall-run Chinook salmon (Sacramento Index, or SI), which constitutes most of the Chinook salmon that are harvested in the ocean or return to the Central Valley in terms of abundance, is 379,600 fish (PFMC 2019)4 . Winter, spring, and late fall-run Chinook salmon are not included in the SI index. These runs combined collectively constitute approximately I 0 percent of all Central Valley Chinook salmon returns on average; ranging from 5-27 percent of Central Valley Chinook salmon returns over the last two decades (California Department ofFish and Wildlife 2019). Since the early 1980s, SI values commonly range from 500,000 to 1 million fish, although recent abundances have been much smaller than historical averages, and SI values have exceeded 300,000 only 3 times in the last 12 years (PFMC 2019). In 2019, the Klamath River was estimated to have an ocean abundance of274,00 fish; which is generally consistent with the average ocean abundance of Klamath over the last 10 years (PFMC 2019).lncluding escapement forecasts for Columbia River Chinook salmon stocks (514,400 fish) with other stocks south ofthe Strait of Juan de Fuca (48,800 fish); along with Puget Sound, Hood Canal, and the Strait of Juan de Fuca combined (243,800 fish); the total Chinook salmon abundance from these sources equals 1,460,800 fish in 2019 (PFMC 2019), ofwhich 379,600/ 1,460,800=26 percent originate from the Central Valley. As mentioned, 2019 is expected to be a relatively low abundance year compared to historical perspectives for Sacramento River fall-run Chinook salmon based on the SI forecast, which historically would be more significant to the overall abundance especially in the action area. While the estimated proportion of Chinook salmon originating from the Central VaHey for 2019 does include accounting of most of the significant populations of Chinook salmon along the U.S. coast, this does not include any totals from significant Canadian Chinook salmon populations that are likely encountered by SRKW to some degree, in particular Fraser River and West Coast Vancouver Island stocks. Although abundance estimates or escapement forecasts for 2019 are not readily available for these Chinook salmon stocks (largely managed through relative abundance indices), it is possible to look at historical catch and escapement numbers to get a sense of at least the minimum number ofthese fish that are in the ocean in the range ofSRKW at some point each year. During the independent science panel, historical estimates of catch and escapement for most all major Chinook salmon stocks from British Columbia to California were produced (Kope and Parken 2011). Across all major Chinook salmon populations, Kope and Parken (20 11) reported that the total number of Chinook salmon that were either captured or escaped annually from 1979-2010 ranged from about 2-6 million; commonly between 3 and 4 million fish. Although these totals are certainly an underestimate of al1 the Chinook salmon that could be present in coastal waters along the west coast associated with these populations, and the 4 The Sacramento Index (SI) is limited to a measure of catch and escapement abundance, and not absolute abundance in the ocean. The SI index is the sum of (I) adult Sacramento River Fall Chinook (SRFC) salmon ocean fishery harvest south of Cape Falcon, OR (2) adult SRFC impacts from non-retention ocean fisheries when they occur, (3) the recreational harvest of adult SRFC in the Sacramento River Basin, and (4) the SRFC adult spawner escapement. The SI forecasting approach uses jack escapement estimates to predict the SI (PFMC 2019). 124 Biological Opinion for the Long-Term Operation of the CVP and SWP precise overlap of SRKW with all these populations at all times during the year is not well established, we conclude based on the historical catch and escapement data presented above that the relative magnitude of Chinook salmon in the range of SRKW each year is likely at least several million fish. Based on the tabulations of catch and escapement conducted by Kope and Parken (20 11 ), we can get a sense of the relative contribution of Central Valley Chinook salmon (as represented by the SI) to the total abundance of Chinook salmon in the range ofSRKW. On average since the early 1980s, it appears that the SI constitutes about 20 percent of the total catch and escapement of all these Chinook salmon populations that are likely encountered by SRKW to some degree, although this proportion varies from about 10-30 percent each year depending on varying strengths in run size (Kope and Parken 2011 ). As a result, we conclude that Central Valley Chinook salmon make up a sizeable and significant portion of the total abundance of Chinook salmon available to SRKW throughout their range in most if not all years; likely at least several hundred thousand individual fish other than during years of exceptionally low abundance for Central Valley Chinook salmon. In addition, the known distributions of Chinook salmon along the coast suggest that Central Valley Chinook salmon are an increasingly significant prey source (as SRKW move south along the U.S. West Coast) during any southerly movements of SRKW along the coast of Oregon and California that may occur during the winter and spring (Weitkamp 2010, Bellinger et al. 2015, Shelton et al. 2019). Climate Change and Environmental Factors in the Ocean The availability of Chinook salmon to SRKW is affected by a number of environmental factors and climate change. Predation in the ocean contributes to natural mortality of salmon in addition to predation in freshwater and estuarine habitats, and salmonids are prey for pelagic fishes, birds, and a wide variety of marine mammals (including SRKW). Recent work by Chasco et al. (20 17) estimated that marine mammal predation of Chinook salmon off the West Coast ofNorth America has more than doubled over the last 40 years. They found that resident salmon-eating killer whales consume the most Chinook salmon by biomass, but harbor seals consume the most individual Chinook salmon (typically smolts). In particular, they noted that southern Chinook salmon stocks ranging south from the Columbia River have been subject to the largest increases in predation, and that SRKW may be the most disadvantaged compared to other more northern resident killer whale populations given the northern migrations of Chinook salmon stocks in the ocean. Ultimately, Chasco et al. (2017) concluded that these increases in marine mammal predation of Chinook salmon could be masking recovery efforts for salmon stocks, and that competition with other marine mammals may be limiting the growth of the SRKW population. Recent studies have provided evidence that growth and survival rates of salmon in the California Current off the Pacific Northwest can be linked to fluctuations in ocean conditions related to Pacific Decadal Oscillation and the El Nino-Southern Oscillation conditions and events, as well as the recent northeast Pacific marine warming phenomenon (aka "the blob") (Peterson et al. 2006, Wells et al. 2008). Evidence exists that suggests early marine survival for juvenile salmon is a critical phase in their survival and development into adults. The correlation between various environmental indices that track ocean conditions and salmon productivity in the Pacific Ocean, both on a broad and a local scale, provides an indication of the role they play in salmon survival in the ocean. Moreover, when discussing the potential extinctions of salmon populations, Francis and Mantua (2003) point out that climate patterns would not likely be the sole cause, but could certainly increase the risk of extinction when combined with other factors, especially in ecosystems under stress from humans. 125 Biological Opinion for the Long-Term Operation of the CVP and SWP Salmon Harvest Actions NMFS has consulted on the effects of numerous salmon fishery harvest actions that may affect Chinook salmon availability in coastal waters for SRKW, including the Pacific Coast Salmon Plan fisheries (National Marine Fisheries Service 2009a), the 10-year term of the Pacific Salmon Treaty [term ofbiological opinion from 2009-2018; (National Marine Fisheries Service 2008a), and 2019-2028; (National Marine Fisheries Service 2019b) and the United States v. Oregon 2018 Management Agreement (term of biological opinion from 2018-2027; National Marine Fisheries Service 201 8t)]. In these past harvest Opinions, NMFS has considered the short-term effects to SRKW resulting from reductions in Chinook salmon abundance that occur during a specified time period and the long-term effects to whales that could result if harvest affected viability of the salmon stock over time by decreasing the number of fish that escape to spawn. These past analyses suggested tihat short-term prey reductions were small relative to remaining prey available to the whales. In the long term, harvest actions have been designed or modified via RPAs to meet the conservation objectives of harvested stocks in a manner determined not likely to appreciably reduce the survival and recovery of listed Chinook salmon, and therefore ultimately not likely to jeopardize the continued existence of listed Chinook salmon. The harvest Opinions referenced above that considered potential effects to SRKW have all concluded that the to jeopardize the continued existence harvest actions cause prey reductions, but were not ofESA-listed Chinook salmon or SRKW. Ocean harvest rates of Chinook salmon throughout the range of SRKW are highly variable on a stock-by-stock basis as influenced by factors that include variable management goals or limits for different stocks and/or geographic areas, along with variable overlap in fishing effort and the abundance and distribution of stocks and fishing effort. Overall, Hilborn et al. (2012) generally assumed that all salmon fisheries reduced Chinook salmon abundance for SRKW by approximately 20 percent each year under current harvest management regimes. Although precise estimates of exploitation rates for all Central Valley Chinook salmon populations are not readily available, the estimated harvest of Sacramento River fall-run Chinook salmon typically is equal il:o or exceeds the estimated escapement of fall-run Chinook salmon in the Sacramento River as represented SI used for fisheries management each year (Pacific Fishery Management Council 2019). As part of the recent the Pacific Salmon Treaty negotiation, the U.S. agreed to develop a targeted funding initiative to mitigate the effects of harvest and other limiting factors by investing in habitat and hatchery actions to increase prey available for SRKW (NMFS 2019a). Those actions are anticipated to increase Chinook salmon abundance and prey for SRKW by four to five percent throughout their range in Puget Sound waters during the summer, and in coastal areas during the winter when prey is believed to be most limiting. It is expected that an additional 20 million Chinook salmon smolts will be produced by facilities in Puget Sound and along the Washington coast and Columbia River. To a large degree, Chinook salmon from these origins will only overlap with the small percentage of Chinook salmon from the Central Valley that range up to the Columbia River area and northward. Water Operations Recently, NMFS completed consultation on the operation of the Klamath River water project from 2019-2024, which included measures to address disease concerns for juvenile Chinook and coho salmon in the Klamath Basin (National Marine Fisheries Service 2019a). The analysis of 126 Biological Opinion for the Long-Term Operation of the CVP and SWP the proposed action indicated that the juvenile survival rates to ocean entry for Chinook salmon would improve overall; by as much as 18 percent during years (typica1ly drier) when disease may be a significant threat. As a result, we expect hundreds or thousands of more adult Chinook salmon from the Klamath River will be available for SRKW off the coast of California and Oregon during some years over the next decade, especially for brood years that may have been exposed to more stressful conditions. Scientific Research Research activities on SRKW are typically conducted between May and October in inland waters, and some permits include authorization to conduct research in coastal waters as well. In general, the primary objective of this research is population monitoring or data gathering for behavioral and ecological studies. Recent permits issued by NMFS include research to characterize the population size, structure, feeding, ecology, behavior, movement patterns and habitat use of the SRKW, especially during the winter and spring when SRKW are using coastal waters extensively. Impacts from permitted research include temporary disturbance and potential short-term disruptions or changes in behavior such as feeding or social interactions with researchers in close proximity, and any minor injuries that may be associated with biopsy samplings or attachment oftags for tracking movements and behavior. We note that in 2016, a SRKW (L95) was found to have died of a fungal infection that may have been related to a satellite tag deployment approximately 5 weeks prior to its death (Carretta et al. 20 18). Other Factors Affecting SRK.Win the Action Area As described above in the Section 2.2.9. Rangewide Status of the Species, SRKW are affected by a number of activities and stresses in marine environment, including vessel activity, anthropogenic sounds resulting from various sources, and potential exposure to oil spills. All of these potential impacts are occurring or remain constant stresses or threats to SRKW throughout their range, including when they occur in coastal waters within the action area. Summary ofEnvironmental Baseline SRKW are exposed to a wide variety of human activities and environmental factors in the action area. All the activities discussed above in Section 2.2.9 Rangewide Status of the Species are likely to have some level of impact on SRKW when they are in the action area. No single threat has been directly linked to or identified as the cause of the relative lack of growth of the SRKW population over time, although three primary threats that have been identified are: prey availability, environmental contaminants, and vessel effects and sound (Krahn et al. 2002). There is limited information on how these factors or additional unknown factors may be affecting SRKW when in coastal waters. However, the small size of the population increases the level of concern about all of these risks (National Marine Fisheries Service 2008b). 2.5 Effects of the Action on the Species In Table 4-6 ofthe BA (U.S. Bureau of Reclamation 2019), Reclamation identified a number of restoration actions or programs that have been occurring, and which are expected to continue into future. An analysis of any negative and/or beneficial effects to fish and their habitat has been completed for those actions or programs that previously underwent separate ESA section 7 consultations, and are therefore described in the environmental baseline section. For those programs or actions Reclamation identified as linked to the PA, and will continue into the future, 127 Biological Opinion for the Long-Term Operation of the CVP and SWP we consider any expected continued negative and/or beneficial effects to listed fish and habitat at a broader scale- or "framework-level" only. For any identified new restoration programs or actions that lack sufficient detail to analyze and quantify level of impact at the level of incidental take, the program or action would require a separate section 7 consultation when sufficient details are available. Any "conservation measure" type actions in Table 4-6 of the BA, would be handled in the same manner described above. Reclamation also identified existing monitoring and research programs and actions linked to the PA in Appendix C ofthe BA (U.S. Bureau of Reclamation 20 19). Effects of any existing research and monitoring programs and actions that have been previously analyzed through an ESA Section 7, 4(d), or 10 process are considered to be in the environmental baseline. For those research or monitoring programs proposed to continue into the future, we consider any expected continued negative and/or beneficial effects to listed fish and habitat at a "framework-level" only. for any identified new research or monitoring programs or actions that lack sufficient detail to analyze and quantify level of impact at the level of incidental take, the program or action would require a separate ESA compliance when sufficient details are available. All modeling used to inform the following effects analysis reflects the incorporation of a 2030 scenario of climate conditions, water demands, and build-out, as discussed in Section 2.1 Analytical Approach. Therefore, the evaluation implicitly includes a climate change condition (Section 2.5.10 Climate Change). However, considering the 4th California Climate Assessment, NMFS expects that in-river temperatures will be even greater than what was presented in the BA modeling. NMFS cannot quantify the effect of this on species, but will assume that the provided modeling represents a scenario of lower effect and will layer additional qualitative evaluations of increased climate effects to the species based on the updated assessments. Regarding sea level rise, NMFS considers the modeling ofthe PA as the scenario of lower effect and consistent with the 4th CA Assessment for 2030; however, it is considered as an absolute lower effect for late 2000s when the assessment projects much greater increases than those captured in the modeling of 2030 in the BA. Detailed descriptions of the modeling used to inform the effects analysis are available as appendices to this Opinion. Specifically, Appendix H--WRLCM is the model description for the Sacramento River Winter-run Chinook Salmon Life Cycle Model (WRLCM). Appendix D provides descriptions ofthe Delta Passage Model (DPM), the Interactive Object-Oriented Simulation (lOS) and the SALMOD Model. These were extracted from Appendix 5.D of(U.S. Bureau ofReclamation 2016a) because the same methods, without modification, were applied in Reclamation's analysis of that project and the documentation is still accurate. Likewise, Appendix G, describing the Salvage Density Model, was also extracted from the CWF biological assessment Appendix S.D. Appendix E contains a description of the Reclamation Salmon Mortality Model (SacSalMort) which was included in Attachment S.D. I of the ROC on LTO biological assessment. Lastly, Appendix F describes the methods used for the Science Integration Team's (SIT) Model Floodplain Habitat Analyses for the rivers and bypasses considered in the analysis of the ROC on LTO. The effects of the PA is organized by Division and species. Table 2.5-1 provides an overview of the species for which the effects are analyzed in each Division. 128 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5-1 : Overview of the species for which the effects are analyzed in each Division. An "X" indicates the species will be analyzed for that Division and a "-" indiicates that effects are not analyzed because the species is not present in the Division. A"*" indicates that while no etlects analysis is done tor that species in that Division, NMFS acknowledges that some life stage of the species may occasionaUy be there (for example, adult winter-run Chinook salmon in Clear Creek, winter-run juveniles in the American River, or adult green sturgeon in the Stanislaus River). Division Sacramento River winter-run Chinook salmon X * X Central Valley spring-run Chinook salmon X X X X X California Central Valley steelhead X X X X X Southern Distinct Population Segment ofNorth American green sturgeon X X X X Southern Resident Killer Whale 8 2.5.1 Stressors and Species Response The following stressors are considered in the analysis of effects of the proposed action: Passage Impediments/Barriers, Harvest and Angling Impacts, Water Temperature, Water Quality, Flow Conditions, Loss of Natural River Morphology and Function, Loss of Floodplain Habitats, Spawning Habitat Availability, Physical Habitat Alteration, Invasive Species/Food Web Disruption, Predation, and Hatchery Effects. These stressors were previously identified during the development of the Central Valley salmonid and green sturgeon recovery plans as being the 5 In this Opinion, this area is defined as the reach of the San Joaquin River between the confluence with the Stanislaus River and approximately Mossdale. 6 In addition to the Sacramento River, juvenile winter-run Chinook salmon have also been found to rear in areas including the lower American River, lower Feather River, Battle Creek, Mill Creek, Deer Creek, and the Delta (Phillis et al. 20 18). Phillis et al (20 18) found with isotope data that 44 to 65 percent of surviving winter-run Chinook salmon adults reared in non-natal habitats as juveniles. 7 Records of green sturgeon in the San Joaquin River and its tributaries are rare and limited to information from angler report cards. However, Anderson eta!. (2018) recently confirmed an adult green sturgeon holding in a deep pool near Knights Ferry in the Stanislaus River in the fall of2017. 8 Effects to Southern Resident killer whale prey analyzed in Section 2.5.8. 129 Biological Opinion for the Long-Term Operation of the CVP and SWP primary stressors affecting the recovery of the species. In the analysis of the effects ofthe action, NMFS uses the description of each stressor as the standard against which to measure the severity or magnitude of impact associated with a particular action component. In this way NMFS measures the effects of the action against the factors known to affect recovery of the species, and where the effect ofthe PA either increases, decreases, or has an unknown or indiscernible effect on those stressors. 2.5.1.1 Passage Impediments/Barriers Passage Impediments/Barriers was identified as a primary stressor affecting the recovery of Central Valley salmonid species (National Marine Fisheries Service 2014b) because construction ofbarriers since the 1800s has caused a 95 percent reduction in river and stream spawning habitat available to Central Valley salmon and steelhead (California Department offish and Game 1993). Construction of new impediments can further limit access to spawning habitats in a way that reduces habitat connectivity. Passage impediments and barriers are considered to be threats affecting adult immigration and staging, spawning, embryo incubation, and juvenile rearing and outrnigration life stages of Chinook salmon, steelhead, and sturgeon from the Delta to the upper river reaches. Effects of the action that contribute to Passage Impediments/Barriers are likely to result in a probable change in fitness of: reduced reproductive success and reduced lifetime reproductive success. Natural and artificial barriers can delay the upstream passage and increase energetic costs to migration for salmon. These impediments physically block access to upstream historic holding and spawning habitats, alter downstream habitat (by disrupting water velocity, temperature, and sediment transport) and eliminate the spatial segregation of spawning habitat that historically existed. This can create cascading effects of fragmented! habitat, constrained species distributions, isolate genetic pools, increased competition for spawning sites, and favoring generalist over specialist life histories which poses a particular risk to endemic species (Poff et at. 2007, Liermann et at. 2012). For sturgeon Passage Impediments/Barriers to migration caused by impoundments were recognized as a high threat to the sDPS green sturgeon (Acipenser medirostris) in the Sacramento River Basin (National Marine Fisheries Service 2018g). Large dams constructed on the Sacramento, Feather, and Yuba rivers have restricted spawning and rearing areas for green sturgeon by presenting a physical barrier to migration. Impassible barriers were recognized as a main threat to the green sturgeon in the original listing decision as well as in subsequent status reviews. These barri,ers, along with water management actions that divert water for other uses and restrict water at certain times of year, affect river flow volumes and temperatures throughout the year. Flow may be an important cue for migration and can factor into successful spawning, egg deposition, and early life stage development. Passage Impediments/Barriers also includes temporary or operable barriers such as the Delta Cross Channel Gate, which can negatively impact migration. Operation ofthe Delta Cross Channel Gate may influence downstream migration by providing false migration cues for juvenile and adult salmon and sturgeon to move from lower Sacramento River to the central Delta rather than their intended destination of the western Delta and San Francisco Bay. Likewise temporary agricultural barriers, constructed in the spring to provide water surface elevation protection for Delta agricultural diverters (U.S. Bureau of Reclamation 2019), can 130 Biological Opinion for the Long-Term Operation of the CVP and SWP cause delays to migration or result in the isolation of fish, preventing them from reaching suitable habitats. DWR issued a report regarding the effects of the south Delta agricultural barriers on the survival of emigrating juvenile salrnonids, including both Chinook salmon and steelhead (California Department of Water Resources 2018b). This study showed that by delaying migration and increasing the time that juvenile salmonids spent in the vicinity of the barriers, the fish were increasingly exposed to elevated water temperat ures as the season progressed. This could in turn diminish the physiological state of the fish making them more vulnerable to predation. Some impediments have been alleviated in recent years through efforts like the fish passage improvement project at RBDD which reduces impacts to both salmonids and sturgeon. 2.5.1.2 Harvest and Angling Impacts During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), the Harvest and Angling Impacts stressor was identified as affecting the recovery of the species. Angliing Impacts primarily affect the adult immigration and staging life stages from the Ocean, Bay, and Delta, to lower, middle, and upper reaches of the Central Valley rivers; as well as impacts to the spawning and embryo incubation life stages in the upper rivers. Effects of the action that contribute to Harvest and Angling Impacts are likely to result in a probable change in fitness of: reduced survival probability, reduced reproductive success and reduced lifetime reproductive success. Harvest and Angling Impacts refers to the total number or weight of fish caught and kept from an area over a period of time including commercial landings and recreational angling. Harvest and Angling Impacts also includes incidental impacts such as bycatch in mixed stock fisheries or anglers disturbing incubating embryos if they wade through redds. The multi-agency Salmon and Sturgeon Assessment of Indicators by Life Stage (SAIL) synthesis teams also identified the relevant pathways by which Harvest and Angling Impacts is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) noted that harvest is one of the three primary factors affect salmon survival during the ocean phase of their lifecycle (along with food supply and predation) and that mortality is highest during the first year of the ocean phase, which strongly influences spawning. The number of Chinook salmon harvested in the California commercial salmon fishery dramatically declined starting in 2006. From 1978 to 2005, the annual salmon harvest for the California commercial fishery exceeded 300,000 in all but one year (2001). In 2006 the fishery collapsed resulting in complete fishery closures in 2008 and 2009, and a heavily restricted fishery in 2010 (NMFS 2014). Sacramento River adult fall Chinook salmon escapement has now remained below the 180,000 goal 8 of the past 12 years [Figure II-1, (Pacific Fishery Management Council2019)]. It is now possible for this ocean fishery to be managed for specific river fisheries through genetic sampling of the ocean harvest along the Pacific Coast. This change has altered the way ocean harvest is regulated, and protects critical species in that life stage. Seasonal time/area restrictions and minimum size limits for the sport and commercial ocean salmon fisheries are in place for the protection of winter-run Chinook salmon. Additionally, there is a regulatory management framework to further reduce ocean fishery impacts when the status of winter-run is declining or unfavorable (National Marine Fisheries Service 20 12). In rivers, potential impacts of anglers include the capture of adults or incidentally physically disturbing incubating embryos while wading through the river. The State has 131 Biological Opinion for the Long-Term Operation of the CVP and SWP established specific in-river fishing regulations and no-retention prohibitions designed to protect winter-run Chinook salmon during their freshwater life stages. Harvest protective measures benefiting spring-run Chinook salmon include seasonal constraints on sport and commercial fisheries south of Point Arena. In addition, the State has listed springrun Chinook under the California Endangered Species Act (CESA), and has thus established specific in-river fishing regulations and no-retention prohibitions designed to protect this ESU (e.g., fishing method restrictions, gear restrictions, bait limitations, seasonal closures, and zero bag limits), in tributaries such as Deer, Big Chico, Mill, and Butte creeks. Because there is no commercial fishery for Central Valley steelhead and the recreational fishery is regulated to protect wild steelhead, there is some reason to think that fishing impacts would not be a significant problem for this species. However, because the sizes of Central Valley steelhead populations are largely unknown, it is difficult to make conclusions about the impact of the recreational fishery (Good et al. 2005). The State also works closely with NMFS to review and improve inland fishing regulations. As a result, zero bag limits for unmarked steelhead, gear restrictions, closures, and size limits designed to protect smelts are additional inland harvest measures that protect CCV steelhead. 2.5.1.3 Water Temperature During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Water Temperature was identified as a primary stressor affecting the recovery of the species. This threat affects all life stages: adult immigration, staging, juvenile rearing and outmigration in the Delta and rivers of the Central Valley; and spawning and embryo incubation in the upper reaches. Effects ofthe action that contribute to the Water Temperature are likely to result in a probable change in fitness of: reduced growth, reduced survival probability, reduced reproductive success and reduced lifetime reproductive success. Water Temperature in this context refers to thermal stress that can affect the physiology of ectothermic organisms like salmon and sturgeon. These effects can impact the organism directly (e.g. altered metabolic demand), as well as indirectly by altering their habitat (e.g. decreased dissolved oxygen or increased water chemistry reaction rates). Water temperatures can be affected by a number of factors, including air temperatures, elevation, flow and velocity, and presence of riparian vegetation. Riparian vegetation, specifically SRA habitat, provides overhead cover, which results in shade and protection, increases large woody material recruitment, provides slower flow velocities for resting spots, and provides substrate for food production (such as aquatic and terrestrial invertebrates) for anadromous fish (Anderson and Sedell1979, Pusey and Arthington 2003). A vibrant riparian corridor provides important water temperature cooling, especially in smaller streams. The loss of riparian vegetation can therefore increase predation rates and reduce food production and feeding rates for juveniles. This interaction with the Loss ofRiparian Habitat and Instream Cover stressor may also expose anadromous fish juveniles to increased water temperatures when the riparian corridor has been degraded, which may result in decreased growth and survival (U.S. Fish and Wildlife Service 1992, Michel 2010). There is also a high threat posed by altered water temperatures due to climate change. In the Sacramento River Basin, climate change models predict increased air temperatures in the Central Valley and surrounding mountains (Ficklin et al. 2012), altered precipitation patterns with a higher frequency of dry years, reduced spring snowpack, and reduced spring flows (Knowles and 132 Biological Opinion for the Long-Term Operation of the CVP and SWP Cayan 2002, CH2M HILL 2014). Water temperatures in the Sacramento River Basin could also increase (CH2M HILL 2014). A warming climate with continued changes in precipitation patterns may influence reservoir operations and thus influence water temperature and flow that fish experience in the Central Valley. The multi-agency SAIL synthesis teams also identified the relevant pathways by which Water Temperature is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) focused on the effects of water temperature on the rate of development of embryos and alevins (Rombough 1988, Beacham and Murray 1989), temperature thresholds, and interactions with dissolved oxygen saturation concentration which has been positively correlated with Chinook salmon larval growth. Chinook salmon, CCV steelhead, and sDPS green sturgeon are dependent on a range of optimal water temperatures for survival, which vary depending on life stage. Central Valley dams currently block Chinook salmon, CCV steelhead, and sDPS green sturgeon from their historical habitat, confming them to a limited amount of thermally suitable habitat for adult holding, spawning, and rearing. As a result, flow releases combined with cold-water temperature management downstream of dams is necessary to provide habitat suitable for fresh-water life stages. Spawning and holding winter-run and CV spring-run Chinook salmon are dependent on cold water releases because they hold and spawn during the summer months. Based on several studies on CV Chinook salmon, temperatures between 43°F and 54°F (6°C and 12°C) appear best suited to Chinook salmon egg and larval development (Myrick and Cech 2004). Several studies indicated that daily temperatures over 56°F (13.3°C) would lead to sub-lethal and lethal effects to incubating eggs (Seymour 1956, Boles 1988a, U.S. Fish and Wildlife Service 1999, U.S. Environmental Protection Agency 2003). A 56°F (13.3°C) temperature compliance target was included in the NMFS 2009 Opinion to protect the sensitive life-stages of listed Chinook salmon in Clear Creek and the Sacramento River (National Marine Fisheries Service 2009b). However, recent investigations into causes of mortality upstream also revealed that the 56°F (13.3°C) daily average temperature may not be adequate to protect the earliest life stages (Swart 20 16). The Martinet al. (2016) egg mortality model found strong evidence that significant thermal mortality occurs at temperatures >53.5°F (12°C), supporting the conclusion that the 56°F (13.3°C) daily temperature criteria mandated in the NMFS 2009 Opinion is likely not sufficiently protective. To improve Sacramento River water temperature management for Chinook salmon, a 2016 pilot study was implemented where the temperature criterion was adjusted to the U.S. Environmental Protection Agency (2003) recommendation of 55°F 7DADM metric and applying it to the Bonneyview Bridge temperature control point which was roughly equivalent to a daily average temperature of 53.5°F at Clear Creek (Swart 2016). Every salmonid life stage is dependent on suitable temperatures. Besides spawning and egg incubation, juvenile rearing also occurs in the upper Sacramento River. Salmonids with a stream life history, such as spring-run Chilnook salmon and steelhead, need suitable spawning and rearing temperatures to be maintained year round. The larger salmonidjuvenile life stages are less sensitive to temperature than the alevins and yolk-sac fry, but will suffer lethal and sublethal effects when not in optimal instream temperatures. The EPA guidelines recommend water temperatures do not exceed 61 °F ( 16°C) 7 -day average daily maximum (7DADM) for juvenile rearing salmonids in the upper basin of natal rivers and do not exceed 64°F (l8°C) in the lower 133 Biological Opinion for the Long-Term Operation of the CVP and SWP basin of natal rivers (U.S. Environmental Protection Agency 2003). Potential sub-lethal temperature effects on juvenile salmonids include slowed growth, delayed smoltification, desmoltification, and extreme physiological changes, which can lead to disease and increased predation. Myrick and Cech (2004) reviewed the published information on Central Valley salmon and steelhead temperature tolerance and growth and noted that several studies suggest that the optimal temperature for Chinook salmon growth lies within the 63°F to 68°F (17 to 20°C) range (Brett et al. 1982, Clarke and Shelbourn 1985, Myrick and Cech Jr 2002, Marine and Cech 2004, Myrick and Cech 2004). Green sturgeon have different temperature requirements than salmonids in the upper Sacramento River. The majority of green sturgeon spawn above Red Bluff Diversion Dam. Suitable spawning temperatures must remain below 63°F (17.5°C) to reduce sub-lethal and lethal effects. Temperatures in the range of57° to 62°F (14 to l7°C) appear to be optimal for embryonic development (Van Eenennaam et al. 2005). Juvenile sturgeon can tolerate higher temperatures and optimal bioenergetics performance was found to be between 59 to 66°F (15 to l9°C) (Mayfield and Cech 2004). Although optimal temperatures for green sturgeon are typical1y higher than temperatures suitable for salmon egg incubation green sturgeon energy budget modelling has found that water-temperature management for the eggs of the endangered Sacramento River winter-run Chinook salmon have a relatively small impact on the growth rate of green sturgeon (Hamda et al. 2019). The threat posed to sDPS green sturgeon by altered water temperatures due to impoundments was ranked high in the Sacramento River Basin for eggs and juveniles. Impoundments alter flow regimes, which in turn affect the water temperature of the river downstream of the impoundment. If water released from the impoundments results in water temperatures that are not within the optimal thermal window for development, survival and growth will be limited. Sacramento River temperature management was rated as a medium threat to all life stages of sDPS green sturgeon. Under laboratory conditions, Mayfield and Cech (2004) reported optimal bio-energetic performance of age-0 and age-l Northern DPS green sturgeon at 15 to l9°C. Summer water temperatures in the upper Sacramento River have typically been below this range, within lab-based optima for green sturgeon egg development but below lab-based optima for green sturgeon larval and juvenile growth (Mayfield and Cech 2004, Van Eenennaam et al. 2005, Allen et al. 2006). Notably, temperatures throughout the upper Sacramento River were in excess of 13.3°C during periods of2014 and 2015 due to historic drought but the effect of this on sDPS green sturgeon production remains unclear. Although the first successful season of directed juvenile green sturgeon sampling near RBDD occurred during elevated temperatures in 2015, juveniles were subsequently collected in 2016 and 2017 sampling efforts [As cited in (National Marine Fisheries Service 2018g)]. Furthermore, high larval sDPS green sturgeon catch at RBDD has occurred in years with relatively low water temperatures (1995, 2011, 2016, and 2017; [As cited in (National Marine Fisheries Service 20 18g)]). The effect of cold-water releases from Keswick Dam may have a greater impact on green sturgeon spawning and incubation in the uppermost accessible reach of the Sacramento River below Anderson-Cottonwood Irrigation District (ACID) Dam. The ACID Dam currently serves as a migration barrier, but low water temperature could deter green sturgeon spawning even if passage was restored to this reach. 134 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.1.4 Water Quality Water Quality is identified as a primary stressor affecting the recovery of the species in the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 20 14b). This threat includes dissolved oxygen, heavy metals, and agricultural and urban runoff affecting adult immigration and staging and juvenile rearing and outmigration from the San Francisco Bay through the Delta and the Sacramento River. Especially threatening is the stress of water pollution in the Upper Sacramento River impacting embryo incubation. Effects of the action that contribute to the Water Quality are likely to result in a probable change in fitness of: reduced growth, reduced survival probability, reduced reproductive success, and/or reduced lifetime reproductive success. Water Quality encompasses the physical, chemical, and biological properties of aquatic environments. Physical properties include temperature, turbidity, and dissolved gases. Chemical properties include pH, hardness, organic and inorganic contaminants, and metals. Biological properties include pathogens, fishes, insects, algae, and other organisms. The Water Quality stressor discussed below focuses on threats from Contaminants and Oxygen is the crucial final electron acceptor in the Krebs Cycle energy-producing pathway, but despite efficient physiological mechanisms for obtaining and using oxygen, it is often a limiting factor for fish who spend considerable energy in perfusion, ventilation, and/or locomotion to extract dissolved oxygen from dense and viscous water (Kramer 1987). In order to avoid suffocation, fish can potentially compensate for hypoxia behaviorally with increases in air or surface breathing or changes in activity or habitat use (Breitburg 2002). Dissolved oxygen impacts on all fish lifestages, including embryos, juveniles, and adults. The embryonic stage is particularly vulnerable due to their immobility, as studies depriving salmon eggs of adequate oxygen observed deformities, premature hatching or delay in emergence, smaller and weaker sac fry, and death (Alderdice et al. 1958, Silver et al. 1963, Geist et al. 2006). Reductions in swimming performance and preference/avoidance behavior can impose costs on fish, for example migrating adult Chinook exhibited an avoidance response when dissolved oxygen was below 4.2 mg/L and most waited to migrate until dissolved oxygen levels were at 5 mg/L or higher (Hallock et al. 1970, Bjomn and Reiser 1991, Carter 2005). Turbidity. The multi-agency SAIL synthesis teams also identified the relevant pathways by which Water Quality is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) focused on water quality gradients and poor water quality factors such as low dissolved oxygen, noting that these factors influence fish condition and behavior. 2.5.1.4.1 Contaminants Many freshwater taxa in the Central Valley are in noticeable decline. This includes ESA-listed species and their designated critical habitat, which are susceptible to contaminants, many of which interact with other stressors such as pathogens to cause mortality, reproductive failure, and other losses to individual fitness. Many ESA-listed fish species in the Central Valley are highly mobile and traverse hundreds of kilometers of freshwater habitat from the Sacramento-San Joaquin River Delta on their migration path to and from the ocean (Quinn 2005). 135 Biological Opinion for the Long-Term Operation of the CVP and SWP Chemical forms of water pollution are a major cause of freshwater habitat degradation worldwide. There ar,e many sources of contaminants, and these reflect past and present human activities and land use (Scholz and Mcintyre 20 15). Contaminants are typically associated with areas of urban development, agriculture, or other anthropogenic activities (e.g., mercury contamination as a result of gold mining or processing). Organic contaminants from agricultural drain water, urban and agricultural runoff from storm events, and high trace element (i.e., heavy metals) concentrations may deleteriously affect early life-stage survival of fish in the Central Valley watersheds (National Marine Fisheries Service 20llc, 2013b). Legacy contaminants such as mercury, PCBs, heavy metals, and persistent organochlorine pesticides, however, continue to be found in watersheds throughout the Central Valley. Persistent organic pollutants such as PCBs disrupt immune system function in exposed fish, thereby rendering exposed fish more susceptible to disease. PCBs are considered persistent pollutants because they resist degradation in the environment, by processes that are either biotic (e.g., microbial breakdown) or abiotic (e.g., photolysis in response to sunlight). They accumulate in sediments and can be resuspended and redistributed in aquatic habitat by dredging and similar forms of human disturbance. Alterations of flow into the San Francisco Bay Delta Estuary can also effect related water quality measures (e.g. salinity, sediment, nutrients, metals, and phytoplankton growth) (Cloern and Jassby 201 2). These hydrologic alterations can impact the fate and transport of pollutants (e.g. sequestering or resuspending, diluting or concentrating, and increasing or decreasing bioavailability). The resulting toxicity can kill or impede fish (e.g. degrading movements essential to predator avoidance, reproduction, social behaviors, or migration). The degree to which this is a threat is difficult to quantify and often site-specific. Zones of degraded water quality, such as chemical or thermal plumes or hypoxic zones without adequate zones of passage (Environmental Protection Agency 2014), can impede fish movement (Sprague and Drury 1969 , Giatt:ina and Garton 1983, Scott and Sloman 2004). Adult salmonid exposure within the Delta is limited and not likely to affect reproduction. However, survival and growth of juvenile salmonids wi11 potentially be affected. In contrast, green sturgeon may remain in or return to the Delta at all life stages such that survival, growth, and reproduction are all important characteristics to consider for green sturgeon. Metals, PCBs, and hydrocarbons (typically oil and grease) are common urban contaminants that are introduced to aquatic systems via nonpoint-source stormwater drainage, industrial discharges, and municipal wastewater discharges. Many of these contaminants readily adhere to sediment particles and tend to settle out of solution relatively close to the primary source of contaminants. PCBs are persistent, adsorb to soil and organic matter, and accumulate in the food web. Lead and other metals also will adhere to particulates and can bioaccumulate to levels sufficient to cause adverse biological effects. Mercury is also present in the Sacramento River system and could be sequestered in riverbed sediments. Hydrocarbons biodegrade over time in an aqueous environment and do not tend to bioaccumulate or persist in aquatic systems. Ifbioaccumulative contaminants such as organochlorines are resuspended from sediments into the water column, they can biomagnify in aquatic food webs. That is, they become proportionately more concentrated at higher trophic levels. Consequently, they present a greater risk to fish that feed at or near the top of aquatic food webs. Exposure to contaminated food sources and bioaccumulation of contaminants from feeding on them may create delayed sublethal effects that negatively affect the growth, reproductive development, and reproductive 136 Biological Opinion for the Long-Term Operation of the CVP and SWP success of listed anadromous fishes, thereby reducing their overall fitness and survival (Laetz et al. 2009). The effects ofbioaccumulation are of particular concern as pollutants can reach concentrations in higher trophic level organisms (e.g., salmonids) that far exceed ambient environmental levels (Allen and Hardy 1980). Bioaccumulation may therefore cause delayed stress, injury, or death as contaminants are transported from lower trophic levds (e.g., benthic invertebrates or other prey species) to predators long after the contaminants have entered the environment or food chain. Many contaminants lack defined regulatory exposure criteria that are relevant to listed salmonids and yet may have effects on salmonids (Ewing 1999). It follows that some organisms may be negatively affected by contaminants while regulatory thresholds for the contaminants are not exceeded during measurements of water or sediments. Rand (1995) stated that the most common sublethal endpoints in aquatic organisms are behavioral (e.g., swimming, feeding, attraction-avoidance, and predator-prey interactions), physiological (e.g., growth, reproduction, and development), biochemical (e.g., blood enzyme and ion levels), and histological changes. Some sublethal effects may result in indirect mortality, for example, when a fish already stressed due to toxicity encounters an additional stressor and the combination of those causes death. Changes in certain behaviors, such as swimming or olfactory responses, may diminish the ability of listed fish to find food or escape from predators and may ultimately result in death. Some sublethal effects may have little or no long-term consequences to the fish because they are rapidly reversible or diminish and cease with time. Individual fish of the same species may exhibit different responses to the same concentration of toxicant. In addition, the individual condition of the fish can significantly influence the outcome of the toxicant exposure. Fish with greater energy stores will be better able to survive a temporary decline in foraging ability or have sufficient metabolic stores to swim to areas with better environmental conditions. Fish that are already stressed are more susceptible to the deleterious effects of contaminants and may succumb to toxicant levels that are considered sublethal to a healthy fish. Exposure to sublethal levels of contaminants has been shown to have serious implications for salmonid health and survival. Studies have shown that low concentrations of commonly available pesticides can induce significant sublethal effects on salmonids. Scholz et al. (2000) and Moore and Waring (1996) have found that diazinon interferes with a range of physiological biochemical pathways that regulate olfaction, negatively affecting homing, reproductive, and anti-predator behavior of salmonids. Waring and Moore ( 1997) also found that the carbofuran had significant effects on olfactory mediated behavior and physiology in Atlantic salmon (Salmo salar). Scientific literature on the effects of pesticides on salmonids and identified a wide range of sublethal effects such as impaired swimming performance, increased predation ofjuveniles, altered temperature selection behavior, reduced schooling behavior, impaired migratory abilities, and impaired seawater adaptation (Sandahl et al. 2007, Baldwin et al. 2009, Laetz et al. 2009, Mcintyre et al. 2012, Laetz et al. 2013) are reviewed Ewing (1999). Other non-pesticide compounds that are common constituents of urban pollution and agricultural runoff also have the potential to negatively affect salmonids. Green sturgeon are expected to be more vulnerable than salmonids to sediment contamination due to their benthic-oriented behavior, which conceivably put them in closer proximity to the contaminated sediment horizon, although it is presently unclear if juveniles exhibit this behavior 137 Biological Opinion for the Long-Term Operation of the CVP and SWP to the same extent that adults do (Presser and Luoma 2010b, 2013). Their " inactive" resting behavior on substrate may potentially put them in dermal contact with contaminated sites, which can lead to lesions and the production of tumors from materials in the substrate. Sturgeon are also benthic invertebrate feeders that forage on organisms that can sequester contaminants at much higher levels than the ambient water or sediment content, such as the Asian clams Corbicula and Potamocorbula that are prevalent in the action area, a non-native species known to bioaccumulate selenium (California Department of Fish and Game 2002, Linville et al. 2002). Laboratory research has revealed that green sturgeon are highly sensitive to selenium with potential impacts including reduced growth and organ abnormalities (Bakke et al. 20 10, Silvestre et al. 2010, Lee et al. 2011, De Riu et al. 2014). The great longevity of sturgeons also places them at risk for the bioaccumulation of contaminants to levels that create physiologically adverse conditions within the body of the fish. Contaminants found in the Sacramento River Basin were determined to pose the greatest threat to green sturgeon eggs, larvae, and juveniles, resulting in reduced growth, injury, or mortality. Contaminants could also negatively affect the reproductive capacity of female adults during spawning. In addition, pyrethroid insecticides used in crop protection and home pest control may affect aquatic invertebrates and the prey base of the green sturgeon. A recent Biological Opinion found that the pesticides chlorpyrifos, diazinon, and malathion jeopardize green sturgeon and adversely modify their critical habitat (National Marine Fisheries Service 2017a). These pesticides were found to potentially cause direct mortality, impaired behavior, and a reduced prey base and could impact green sturgeon in the Sacramento River Basin and San Francisco Bay D elta Estuary environments (National Marine Fisheries Service 2017a). 2.5.1.4.2 Dissolved Oxygen Oxygen is the crucial final electron acceptor in the Krebs Cycle energy-producing pathway, but despite efficient physiological mechanisms for obtaining and using oxygen, it is often a limiting factor for fish who spend considerable energy in perfusion, ventilation, and/or locomotion to extract dissolved oxygen from dense and viscous water (Kramer 1987). In order to avoid suffocation, fish can potentially compensate for hypoxia behaviorally with increases in air or surface breathing or changes in activity or habitat use (Breitburg 2002). Dissolved oxygen impacts on all fish 1i festages, including embryos, juveniles, and adults . The embryonic stage is particularly vulnerable due to their immobility, as studies depriving salmon eggs of adequate oxygen observed deformities, premature hatching or delay in emergence, smaller and weaker sac fry, and death (Alderdice et al. 1958, Silver et al. 1963, Geist et al. 2006). Reductions in swimming performance and preference/avoidance behavior can impose costs on fish, for example migrating adult Chinook exhibited an avoidance response when dissolved oxygen was below 4.2 mg/L and most waited to migrate until dissolved oxygen levels were at 5 mg/L or higher (Hallock et al. 1970, Bjornn and Reiser 1991 , Carter 2005). 2.5.1.4.3 Turbidity Elevated turbidity and suspended sediment levels have the potential to adversely affect salmonids during all freshwater life stages. Specifically increased turbidity can clog or abrade gill surfaces, adhering to eggs, hamper fry emergence (Phillips and Campbell 1961 ), bury eggs or alevins, scour and fill in pools and riffles, reduce primary productivity and photosynthesis 138 Biological Opinion for the Long-Term Operation of the CVP and SWP activity (Cordone and Kelley 1961), and affect intergravel permeability and dissolved oxygen levels (Lisle and Eads 1991, Zimmermann and Lapointe 2005). Fish behavioral and physiological responses indicative of stress include: gill flaring, coughing, avoidance, and increased blood sugar levels (Berg and Northcote 1985, Servizi and Martens 1992). Excessive sedimentation over time can cause substrates to become embedded, which reduces successful salmonid spawning and egg and fry survival (Waters 1995). Changes in turbidity and suspended sediment levels associated with water operations may negatively impact fish populations temporarily when deposition of fine sediments fills interstitial substrate spaces in food-producing riffles, reducing the abundance and availability of aquatic insects and cover for juvenile salmonids (Bjornn and Reiser 1991). Suspended solids and turbidity generally do not acutely affect aquatic organisms unless they reach extremely high levels (i.e., levels of suspended solids reaching 25 mg/L). At these high levels, suspended solids can adversely affect the physiology and behavior of aquatic organisms and may suppress photosynthetic activity at the base of food webs, affecting aquatic organisms either directly or indirectly (Alabaster and Lloyd 1980, Lloyd 1987, Waters 1995). Increased sediment concentrations can also affect fish by reducing feeding efficiency or success and stimulating behavioral changes. Sigler et al. (1984) found that turbidities between 25 and 50 Nephelometric Turbidity Units (NTU) reduced growth of juvenile coho salmon and steelhead, and Bisson and Bilby ( 1982) reported that juvenile coho salmon avoid turbidities exceeding 70 NTUs. Turbidity likely affects Chinook salmon in much the same way it affects juvenile steelhead and coho salmon because of similar physiological and life hjstory requirements between the species. Newcombe and Jensen (1996) also found increases in turbidity could lead to reduced feeding rate and behavioral changes such as alarm reactions, displacement or abandonment of cover, and avoidance, which can lead to increased predation and reduced feeding. At high suspended sediment concentrations for prolonged periods, lethal effects can occur. Conversely, impoundments upstream of bays and estuaries may result in a long-term reduction in turbidity by holding back sediment and this could conceivably increase interactions between green sturgeon and large predators. such as marine mammals and sharks. This can impact green sturgeon feeding habitat quality and quantity through changes in sediment deposition and composition and subsequent changes in prey resources or through changes in turbidity that could impact habitat use and predation by sight-predators. 2.5.1.5 Flow Conditions During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Flow Conditions was identified as a primary stressor affecting the recovery ofthe species. This threat primarily affects the adult immigration and staging (with Lower Sacramento River low flows for attraction and migratory cues, and flood flows for non-natal area attraction, as well as in the Middle & Upper Sacramento River low flows for attraction and migratory cues), Spawning and Embryo Incubation (with upper Sacramento River flow fluctuations), and Juvenile Rearing and Outrnigration (with Changes in Delta Hydrology, Diversions into the Central Delta, Reverse Flow Conditions in the Delta, Flow Dependent Habitat Availability in the Lower Sacramento River, Flow Dependent Habitat Availability in the Middle and Upper Sacramento River). 139 Biological Opinion for the Long-Term Operation of the CVP and SWP Effects of the action that contribute to the Flow Conditions are likely 1to result in a probable change in fitness of: reduced growth, reduced survival probability, reduced reproductive success and/or reduced lifetime reproductive success. Flow Conditions refer here to the quantity, timing, and quality of water flows required to sustain fishes and the ecosystems upon which they depend. Numerous other stressors are superimposed on flow conditions (e.g. water temperature, water quality, loss of natural river morphology and function, and loss of floodplain habitats), so the discussion below focuses on the following specific facets: hydrologic alteration, redd dewatering, isolation and stranding, travel time & outmigration, and delta survival. The multi-agency SAIL synthesis teams also identified the relevant pathways by which Flow Conditions is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (20 17) focused on the impacts of flow to migration, spawning, and growth. The authors discuss how flows impact: migration (by altering contaminant concentration, reducing water temperatures, thereby affecting dissolved oxygen, food availability, predation, pathogens, and disease), entrainment and stranding risk, and cues to stimulate outrnigration. They also discuss how flow can diminish natural channel formation, alter food web processes, slow regeneration of riparian vegetation, reduce bedload movement causing gravels to become embedded, and decrease channel widlth due to incision, all of which can decrease the availability and variability of spawning and rearing habitat. Additionally, reduced flows can weaken fish during periods of holding prior to spawning by concentrating fish within a smaller habitat area, thereby increasing the potential for lateral transmission of disease and prespawn mortality; while increased flows can move weakened fish downstream out of the temperature-controlled section of river, reducing spawning success, or laterally to the stream margins, making them more vulnerable to predation, harassment, or poaching. Finally, the synthesis notes that juvenile salmon growth is influenced by water temperature and access to floodplain habitats- both of which are strongly related to flow. 2.5.1.5.1 Hydrologic Alteration The natural flow regime of a water body is defined by its flow magnitude, timing, duration, frequency, and rate of change (Poff et al. 1997). Anthropogenic flow modifications are ubiquitous in running waters, and tend to be most aggressive in locations with highly variable flow regimes, like California, where water storage and flood control is most needed (Dudgeon et al. 2006). Across the major basins of California's Central Valley, mean monthly flows have been depleted at 80 percent or more of gages (Zimmerman et al. 20 18). These changes in flow can have cascading effects that alter geomorphology (channel incision, widening, bed armoring, etc.) and connectivity (latera11y with the flood-plain, longitudinal upstream-downstream, or vertically between surface water and groundwater)- ultimately impacting the chemical, physical, and biological properties of the ecosystem (Novak et al. 2016). Literature reviews have shown that fish abundance, diversity and demographic rates consistently decline in response to both elevated and reduced flow magnitude (Poff and Zimmerman 201 0). Changes in abundance in the Delta and estuary of juvenile Central Valley Chinook salmon appear related to flow (Brandes and McLain 2001) with recruitment in San Joaquin River Basin being highly correlated with the magnitude and duration of spring flows when the fish were subyearling juveniles (Sturrock et al. 2015). Studies in the Southern Sacramento-San Joaquin Delta observed that fish communities at each river location were consistently different each year, and correlated with river flow and turbidity (Feyrer and Healey 2003). 140 Biological Opinion for the Long-Term Operation of the CVP and SWP Flows may also be a migration cue for green sturgeon, so altered flows could impact adult in or out migration. Flows could also impact the number of deep pools in the river as well as those with specific characteristics (possibly including flow) that are necessary for spawning. Flow is also li.ikely important for egg development and larval dispersal, but specific, appropriate flow rates are not determined. Reduced spring flows could negatively impact recruitment, given the likely relationship between high spring flows and high green sturgeon recruitment seen in 2006 (Heublein et al. 2017). Successful spawning in the Feather River has also been linked to high spring flows (2011 and 2017; (Heublein et al. 2017). Within the San Francisco Bay Delta Estuary, channel control structures, impoundments, and upstream diversions were recognized as specific threats that have altered and impacted juvenile and subadult/adult green sturgeon. The San Francisco Bay Delta Estuary environment has been highly impacted by structures built to divert water and by 11.1pstream impoundments, which have changed flow patterns, channel morphology, and water depth/presence and salinity in certain areas. Localized flow patterns can impact habitat quality for green sturgeon and flow may impact migration and movement. 2.5.1.5.2 Redd Dewatering Redd dewatering is a risk to incubating salmonid eggs and alevin. Salmonid redds require cool, oxygenated, low turbidity water for approximately three to four months to complete the eggalevin life stages (Williams 2006). Water must move through a reddat a swift enough velocity to sweep out fme sediment and metabolic waste. Otherwise, incubating eggs do not receive sufficiently clean, oxygenated water to support proper d!evelopment (Vaux 1968). Salmonid redd dewatering can occur when water levels decrease after redd construction, exposing buried and otherwise submerged eggs or alevilns to air. Dewatering can affect eggs and alevins in multiple ways. Studies have shown that dewatering can impair egg and alevin development and cause direct mortality due to desiccation, insufficient oxygen levels, waste metabolite toxicity, and thermal stress (Reiser and White 1983, Becker and Neitzel 1985). Because instream flows on the Sacramento River, Clear Creek, Stanislaus River, and American River are dependent on reservoir releases, redd dewatering can occur through water operations. On the Sacramento River, winter-run and spring-run are particularly susceptible to operational flow decreases when releases are reduced in the fall due to decreased water demands for irriga6on and the need for Shasta-cold water storage conservation. Releases are further reduced in the winter to a minimum of 3,250 cubic feet per second (cfs), the amount depending on water year type and storage conservation needs, which may redd dewater Central Valley steelhead, fall-run, and late-fall run redds. Dewatering of green sturgeon spawning areas is not a concern because of the location in which eggs are deposited and develop. green sturgeon spawning primarily occurs in cool sections of the upper mainstem Sacramento River in deep pools containing small to medium sized gravel, cobble or boulder substrate (Klimley et al. 2015a, Klimley et al. 2015b, Poytress et al. 2015). Sturgeon eggs primarily adhere to gravel or cobble substrates, or settle into crevices (Moyle 1995, Van Eenennaam et al. 2001, Poytress et al. 20 15) where they incubate for a period of seven to nine days. Newly hatched sturgeon fry remain near the hatching area for 18 to 35 days prior to dispersing (Van Eenennaam et al. 2001, Deng et al. 2002, Poytress et al. 2015). 141 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.1.5.3 Redd Scour Streambed scour resulting from high flows is a physical factor that can cause salmonid egg mortality. High flows can mobilize sediments in the river bed causing direct egg mortality, if scour occurs to the depth of the redd egg pocket. Scour can also increase fine sediment infiltration and indirectly decrease egg survival (DeVries 1997). Increased water releases for flood control, and for scheduled pulse flows for geomorphic benefit and salmonid migration cues, may be high enough to mobilize sediments, and scour Chinook salmon and steelhead redds. 2.5.1.5.4 Isolation and Stranding Rapid reductions in flow can adversely affect fish. Juvenile salmonids are particularly susceptible to isolation or stranding during rapid reductions in flow. Isolation can occur when the rate of reductions in stream flow inhibits an individual's ability to escape an area that becomes isolated from the main channel or dewatered (U.S. Fish and Wildlife Service 2006). The effect of juvenile isolation on production of Chinook salmon and steelhead populations is not well understood, but isolation is frequently identified as a potentially important mortality factor for the populations in the Sacramento River and its tributaries (U.S. Fish and Wildlife Service 2001, Water Forum 2005, U.S. Bureau of Reclamation 2008, National Marine Fisheries Service 2009b, Jarrett and Killam 2014, Jarrett and Killam 2015). Juveniles typically rest in shallow, slow-moving water between feeding forays into swifter water. These shallower, low-velocity margin areas are more likely than other areas to dewater and become isolated with flow changes (Jarrett and Killam 2015). Accordingly, juveniles are most vulnerable to isolation during periods of high and fluctuating flow when they typically move into inundated side channel habitats. Isolation can lead to direct mortality when these areas drain or dry up or to indirect mortality from predators or rising water temperatures and deteriorating water quality. Isolation is currently a potential stressor in the upper Sacramento River, though mechanisms such as ramping restrictions exist that are intended to reduce the risk of occurrence. The upper Sacramento River has numerous side channel-like gravel bars that are used by juveniles as resting stops when inundated by higher flows. These areas can become isolated pools or even completely dewatered when reservoir releases are reduced. Although the NMFS 2009 Opinion (National Marine Fisheries Service 2009b) includes ramping restrictions for reservoir releases, CDFW rescues fish from these channel margin pools every year (California Department ofFish and Wildlife 2013b, 2015b, 2016b)(Azat 2018,). CDFW monitoring reports show a range of numbers of different species and runs of anadromous fish observed and rescued in these efforts. The dependence of isolation risk on factors such as rate of sediment mobilization, rate of sediment settling in channel margin areas, and timing and rate of flow reductions makes the quantification of stranding risk difficult. 2.5.1.5.5 Travel Time & Outmigration Patterns of anadromous fish migration are influenced by a number of variables, including flow velocity, direction, volume, and source. When velocities along migratory corridors are reduced, juvenile outmigration takes longer and smolts are more likely to be vulnerable to increased predation risk (Anderson et al. 2005, Muthukumarana et al. 2008, Cavallo et al. 2013). The amount of time outmigrating juvenile salmonids spend traveling throll!gh migratory corridors in 142 Biological Opinion for the Long-Term Operation of the CVP and SWP the Delta is one indicator of predation risk, with longer travel time through the Delta often resulting in higher mortality rates. Studies of Delta inflow and Juvenile Survival help to define the relationship of Sacramento River flow (at Freeport) and survival of juvenile salmon through the Delta, as well as the importance that fish migration routing has on migratory success. The acoustic tag studies (Perry and Skalski 2010, Perry et at. 2015, Perry 2016) indicate that survival probability increases with increasing flows, and changes in survival are steepest when flows are below 30,000 cfs at Freeport. The flow-survival relationship is strongest at lower flows, and in the reaches that transition from riverine to strong tidal influence. The relationship between flow and survival is in agreement with the assumptions and results of the velocity and entrainment analyses that indicated low, slack, and reverse velocities increase entrainment risk and increase travel time, which reduce survival probabilities. For example, entrainment into the interior Delta via Georgiana Slough or DCC is increased when flows in the mainstem Sacramento River are low, reversing, or stagnant, and the proportion offish remaining in the Sacramento River or entering Sutter or Steamboat Slough are increased under high (Perry and Skalski 2010, Perry et at. 2015, Perry 20 16). While the mechanisms causing reduced survival probabilities are likely combinations of reduced velocities, route selection, and increased entrainment into the interior Delta, the flow-survival relationship can be used to collectively evaluate effects of flow changes on through-Delta survival. 2.5.1.5.6 Delta Survival There are two primary categories of effects in the south Delta due to water export: (l) salvage and entrainment at the south Delta export facilities, and (2) water-project-related changes to south Delta hydrodynamics that may reduce the suitability of the south Delta for supporting successful rearing or migration of salmonids and sturgeon from increased predation probability and exposure to poor water quality conditions. Key water-project-related drivers of south Delta hydrodynamics are Vernalis inflow, CVP and SWP exports from the south Delta export facilities, and the construction of the Head of Old River Barrier (HORB) or other agricultural barriers; these drivers interact with tidal influences over much of the central and southern Delta. In day-to-day operations, these drivers are often correlated with one another (for example, exports tend to be higher at higher San Joaquin River inflows) and regulatory constraints on multiple drivers may simultaneously be in effect. The Salmonid Scoping Team, a technical team associated with the Collaborative Adaptive Management Team (CAMT) process, evaluated how the relative influence of these drivers on hydrodynamic conditions varied temporally and spatially throughout the south Delta, [(Salmonid Scoping Team 2017b): Appendix B: Effects of Water Project Operations on Delta Hydrodynamics)]. In order to describe the driver-specific effects on south Delta hydrodynamics which are relevant to the types of operations anticipated in the PA, highlights of that report are provided below. The Delta flow regime can have effects on a wide range of factors such as productivity, food webs, or invasive species, and management actions related to CVP and SWP operations, which are just a few of many interacting drivers (Monismith et at. 2014, Delta Independent Science Board 2015). Export effects in the south Delta are expected to reduce the probability that juvenile salmonids in the south Delta will successfully migrate out past Chipps Island, either via entrainment or mortality at the export facilities, or by changes to migration rates or routes that increase residence time ofjuvenile salmonids in the south Delta and thus increase exposure time to agents 143 Biological Opinion for the Long-Term Operation of the CVP and SWP of mortality such as predators, contaminants, and impaired water quality parameters (such as dissolved oxygen or water temperature). Effects of exports and HORB construction depend on location within the south Delta. For example, the HORB improves migratory conditions in the mainstem San Joaquin River but adversely impacts conditions in Old River if exports remain static with no concurrent reductions. Export effects of ongoing diversions from the south Delta export facilities adversely impact hydrodynamic conditions in the south Delta. If export diversions remain static with the HOR gate closed, the supply of water to maintain exports at the south Delta facilities must come from the channels to the north of the export facilities (i.e., Old River, Middle River, Columbia Cut and Turner Cut) which will increase flows towards the export facilities and thus make cumulative flows more negative. This reduces the likelihood of fish successfully migrating out of these channels should they be present, and increases the likelihood that fish from the mainstem San Joaquin River to the north that are entrained into these river channels by tides or other mechanisms will have a higher probability of moving southwards towards the export facilities under the influence of reverse flows. Much uncertainty remains about how reach-scale hydrodynamic effects link to salmonid migration behavior in the south Delta. More data are available on both through-Delta survival and reach-scale survival for Chinook salmon and CCV steelhead. Recent reports summarize select data relevant to water-project-related effects on juvenile salmonid migration and survival in the south Delta (see in particular Appendices D and E of Volume 1 (Salmonid Scoping Team 2017a). These reports summarize the latest information on salmonid behavior and survival in the south Delta in the context of water project operations and so offer relevant information. Some overarching findings, summarized in Volume 1, are: • • • • • • Spatial variability in the relative influence of Delta inflow and exports on hydrodynamic conditions means that any given set of operational conditions may differentially affect fish routing and survival in different Delta regions. Gates and barriers influence fish routing away from specific migration corridors. The relationship between San Joaquin River inflow and survival is variable, and depends on barrier status and region of the Delta. Juvenile salmonid migration rates tend to be higher in the riverine reaches and lower in the tidal reaches. The extent to which management actions such as reduced negative OMR reverse flows, ratio of San Joaquin River inflow to exports, and ratio of exports to Delta inflow affect through-Delta survival is uncertain. Uncertainty in the relationships between south Delta hydrodynamics and through-Delta survival may be caused by the concurrent and confounding influence of correlated variables, overall low survival, and low power to detect differences. The first four findings highlight that effects on routing and survival differ across the Delta and are sensitive to inflow and barrier status; as discussed earlier, the HORB effects tend to be positive on the mainstem San Joaquin River but negative in Old River mediated in part by the effect of inflow on tidal extent. As described by National Marine Fisheries Service (2009b), entrainment of juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead at the south Delta export facilities may result in mortality. "Loss" is a term used to refer to the estimated number offish that experience mortality within the export facilities, and is estimated based on the number of 144 Biological Opinion for the Long-Term Operation of the CVP and SWP salvaged fish (fish observed within the fish collection facilities at the export facilities) and a number of components related to facility efficiency and handling. Percentages refer to the percent of fish reaching a specific stage in the salvage process that are assumed to experience mortality during that stage. For example, the 75 percent loss associated with prescreen loss at the SWP means that 75 percent of the fish entering Clifton Court Forebay at the radial gates are assumed to die before reaching the primary louvers at the Skinner Fish Protection Facility. Of those fish that do reach the louvers, another 25 percent are lost, and so on. The total loss percentages represent the overall percent loss across all stages, that is, the percent of all fish entering the facility that die somewhere during the salvage process. • • SWP: (1) Pr,escreen loss (from Clifton Court Forebay radial gates to primary louvers at the Skinner Fish Protection Facility): 75 percent loss, (2) Louver efficiency: 25 percent loss; (3) Collection, handling, trucking, and release: 2 percent loss; (4) Post release: I 0 percent loss; and (5) Total loss (combination ofthe above): 83.5 percent. CVP: (1) Prescreen loss (in front of trash racks and primary louvers): 15 percent loss; (2) Louver efficiency: 53.2 percent loss; (3) Collection, handling, trucking, and release: 2 percent loss; (4) Post release: 10 percent loss; and (5) Total loss (combination ofthe above): 3 5.1 percent. 2.5.1.6 Entrainment During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Entrainment was identified as a primary stressor affecting the recovery of the species. In the Recovery Plan Entrainment is defined as the redirection of fish from their natural migratory pathway into areas or pathways not normally used. Entrainment also includes the take, or removal, of juvenile fish from their habitat through the operation of water diversion devices and structures such as siphons, pumps and gravity diversjons (National Marine Fisheries Service 2014b). While the former definition of Entrainment, the flow mediated Entrainment, is discussed in the previous section under Flow Conditions: Travel Time & Outmigration (2.5.1.5.5), and Delta Survival (2.5.1.5.6), here the discussion of the effects of Entrainment is limited to those associated with unscreened or inadequately screened water diversions. This threat primarily affects the juvenile rearing and outrnigration life stage of these species, from the upper reaches of their watershed of origin through the Delta and Bays. Effects of the action that contribute to Entrainment are likely to result in a probable change in fitness of: reduced survival probability; or in cases where the P A would mitigate an unscreened or poorly screened water diversion the effect of the action would be to: increase survival probability. The exact number of unscreened diversions in the Central Valley is not known as a recent assessment of water diversions has not been made. However, a dated but oft-cited assessment of water diversions in California's Central Valley identified 3,356 water diversions, 98.5 percent of which were either unscreened or screened insufficiently to prevent fish entrainment (Herren and Kawasaki 200 1). And while quantification of the effect of small unscreened diversions is limited, there is no doubt that at times large numbers of juvenile salmonids are entrained by diversions, especially by large and small diversions on tributaries important for spawning and rearing (Moyle and Israel 2005). NMFS fish screen criteria (National Marine Fisheries Service 1997a, 2011 e) intended to limit entrainment for waters which may contain salmonid fry (<60 mm in total length), identifies a maximum gap between bars of 0.069 in. (1.75 mm). Screens of these 145 Biological Opinion for the Long-Term Operation of the CVP and SWP dimensions are designed to minimize the entrainment of alevins, fry, juvenile, and larger salmonids. Juvenile fish with a head width ofless than or slightly greater than 1.75 mm have the potential to pass through screen openings and get entrained into the diversions. It is possible that juvenile fish with heads larger than the 1.75 mm screen openings may pass through the fish screen if they become impinged on the fish screen and, during the process of trying to free themselves, change their orientation and are pulled through the fish screen openings by the current passing through the slot openings of the fish screen. Since ossification of the bones is not yet complete during the early life stages of teleost fish (Van den Boogaart et al. 2012, Mork and Crump 2015, Witten and Hall2015), the plasticity of the cranium, opercular, and axial skeletal structures of larvae and fry may allow these otherwise bony structures to deform, allowing the fish to pass through a screen. Also, juvenile fish that exceed the minimum size criteria for exclusion and that are impinged on the fish screen may pass through the fish screen ifthey are pushed through by a screen cleaner brushes (ICF International 2015). It is expected that all fish entrained through a screen would be lost to the population, as an attempt to salvage any of these fish from behind the screens is not expected. These fish are effectively considered as mortalities, even if they survive their entrainment through the screens. Impingement may occur when the approach velocity exceeds the swimming capability of a fish, creating substantial body contact with the surface of a fish screen. Whether or not impingement would occur depends on screen approach velocity, screen sweeping velocity, and the swimming capacity of juvenile fish. Injury resulting from impingement may be minor and create no longterm harm to the fish, or result in injuries leading to mortality either directly or at some time in the future after contact with the screen, including predation or infections from wounds and abrasions associated with the screen contact. Approach velocity is the vector component of the channel's water velocity immediately adjacent to a screen face that is perpendicular to and upstream of the vertical projection of a screen face, calculated by dividing the maximum screened flow by the effective screen area. Fish screens with approach velocities less than or equal to 0.33 ft/sec would minimize screen contact and impingement of juvenile salmonids (National Marine Fisheries Service 1997a). Sweeping velocity is the vector component of channel flow velocity that is parallel and adjacent to the screen face, measured as close as physically possible to the boundary layer turbulence generated by the screen face. Screening criteria from California Department ofFish and Game (2000) requires a sweeping flow velocity/approach velocity of 2:1 for in river fish screens while National Marine Fisheries Service (20 11 e) recommends that for screens longer than 6 feet, the optimal sweeping velocity should be at least 0.8 ft/sec and less than 3ft/sec, with sweeping velocity not decreasing along the length of the screen. These criteria are such that they will reduce exposure time of fish to a screen and therefor the potential for impingement as fish move past it. Historically, of the four Sacramento River Chinook salmon races, winter-run Chinook salmon have probably been the most vulnerable to entrainment ibecause newly emerged fry would occur in the vicinity of water diversions during the July through August time periods of high agricultural diversion. However, juvenile emigration data suggest that peak winter-run Chinook salmon movement occurs in October and November, when pumping volume is decreasing or has ceased for the season. Fish screens, when meeting speci fie design criteria for screen materials, sweeping flows, and approach velocities described in the NMFS fish screen criteria (National Marine Fisheries Service 1997a, 2011 e) , have shown guidance efficiencies of greater than 98 percent for juvenile salmonids (i.e., less than 2 percent entrainment). In a field study ofjuvenile 146 Biological Opinion for the Long-Term Operation of the CVP and SWP salrnonid injury and mortality related to contact with a vertical profile bar screen at John Day Darn (1.75 mrn opening) resulted in an overall average of2.5 percent for injury and 3.7 percent for mortality (Brege et al. 2005). These results likely represent the high end ofjuvenile fish injury and mortality rates at vertical profile bar screens. For green sturgeon a study by Mussen et al. (2014a) indicated that juvenile green sturgeon (350mrn mean fork length) appear to lack avoidance behavior when encountering unscre,ened waterdiversion structures. In this study sturgeon entrainment ranged from 26-61 percent and they estimated green sturgeon entrainment of up to 52 percent if they passed within 5 ft of an active diversion three times. The studies examined the rate of entrainment wiith different intake flows through the pipe inlet and sweeping flows past the unscreened diversions, where there did not appear to be significant differences in the entrainment risk at different sweeping velocities of 0.4, 1.2, and 2.0 ftfs. However, there was a trend towards less entrainment at higher sweeping flows, which appeared to be related to the swimming behavior of the experimental fish. At lower sweeping flows, fish were more actively swimming, and thus encountered the inlet to the pipe more frequently. In contrast, very low numbers of sturgeon were entrained in a monitoring project that sampled 12 unscreened diversions (<150 cfs) on the Sacramento River between Colusa and Knights Landing (Vogel2013). During Vogel's study, green sturgeon were entrained at the South Steiner diversion during the irrigation seasons in 2010 (n=3 [extrapolated]; FL = 86 rnrn; approach velocity = 2.17 ftlsec) and 2011 (n= 1; FL = 70 rnm; approach velocity = 0.08 ftlsec); and at the Tisdale diversion in 2011 (n=l; FL = 106 rnm; approach velocity = 0.40 ftlsec) but not in the 2012 (n=O) irrigation season. The multi-agency Salmon and Sturgeon Assessment oflndicators by Life Stage (SAIL) synthesis teams also identified the relevant pathways by which Entrainment is likely to affect species as well as how it is likely to interact with other stressors. Windell et al. (20 17) note survival across all life stages and in all geographic regions can be affected by entrainment, particularly within the rearing to outrnigrating juveniles stage in the Upper and Middle Sacramento River and the Bay-Delta. 2.5.1.7 Loss of Riparian Habitat and Instream Cover During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Loss ofRiparian Habitat and Instream Cover was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the juvenile rearing and outrnigrati!on life stage of these species, from the upper reaches of their watershed of origin through the Delta. Effects of the action that contribute to the Loss of Riparian Habitat and Instream Cover are likely to result in a probable change in fitness of: reduced growth and/or reduced survival probability. Loss of Riparian Habitat and Instream Cover refers to the process by which access to riparian habitat and instrearn cover is lost either by the construction of river features (i.e. levees, or flood control structures), or by river channelization due to the geological formation and controlled flow regimes that result in disconnection of the river from its historic floodplain. Construction of river features involves rip-rapping the river bank and removing vegetation along the bank and upper levees which removes most instrearn and overhead cover in nearshore areas. This has negative effects on riparian habitat due to the river's inability to naturally recruit riparian species seedlings as well as woody debris to deposit elsewhere. Woody debris and overhanging 147 Biological Opinion for the Long-Term Operation of the CVP and SWP vegetation within shaded riverine aquatic (SRA) habitat provide escape cover for juvenile salmonids from predators as well as thermal refugia. Aquatic invertebrates are dependent on the organic material provided be a healthy riparian habitat and many terrestrial invertebrates also depend on this habitat. Studies by the California Department of Fish and Game (CDFG) as reported in NMFS (National Marine Fisheries Service 1997b) demonstrated that a significant portion of juvenile Chinook salmon diet is composed of terrestrial insects, particularly aphids which are dependent on riparian habitat. The multi-agency SAIL synthesis teams also identified the relevant pathways by which Loss of Riparian Habitat and Instream Cover is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) focused on the growth and condition of juveniles as being affected by access to riparian habitats. Habitats that provide refuge from high water velocity or predators, without depleting food supply, function to increase growth rates by reducing energy demand to obtain a given food supply. Growth rate may then, influence migration timing and success, where a higher growth rate is associated with earlier smolti fication and faster downstream migration (Beckman et al. 2007). However, the inability of a juvenile in a particular habitat to supply its metabolic demand and achieve some threshold growth rate may also serve as a strong cue to leave that habitat and migrate downstream, and a satisfactory food supply may induce a juvenile to remain in the habitat for a longer duration of time to rear. 2.5.1.8 Loss of Natural River Morphology and Function During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 20 14b), Loss ofNatural River Morphology and Function was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the juvenile rearing and outmigration life stage of these species, from the upper reaches oftheir watershed of origin through the Delta. Effects of the action that contribute to the Loss ofNatural River Morphology and Function are likely to result in a probable change in fitness of: reduced growth, reduced survival probability, reduced reproductive success, and/or reduced lifetime reproductive success. Loss of Natural River Morphology and Function is the result of river channelization and confinement, which leads to a decrease in riverine habitat complexity, and thus, a decrease in the quantity and quality of juvenile rearing habitat. Additionally, this primary stressor category includes the effect that dams have on the aquatic invertebrate species composition and distribution, which may have an effect on the quality and quantity of food resources available to juvenile salmonids. For example, in a natural river system without one or more large dams, there is an upstream source oflotic aquatic invertebrate species available to juvenile salmonids, whereas on a river with a large terminal dam, the upstream drift of food resources to juvenile salmonids is drastically altered. The multi-agency SAIL synthesis teams also identified the relevant pathways by which Loss of Natural River Morphology and Function is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) focused the impact of channelized, leveed, and riprapped reaches potentially having low habitat complexity, low abundance of food organisms, and offer little protection from predators - factors which juveniles are dependent for growth and successful survival. 148 Biological Opinion for the Long-Term Operation of the CVP and SWP Water depth modification caused by non-point source sediment was ranked in the Recovery Plan as a high threat to green sturgeon adults within the Sacramento River Basin and a medium threat to other life stages in the Sacramento River Basin. Impoundments and mitigation and restoration efforts were also considered as contributing to the water depth modification threat to all life stages in the Sacramento River Basin. Non-point source sediment includes runoff from urban areas, agriculture, forests, irrigated lands, landfills, livestock, mining operations, nurseries, orchards, etc. Removal of riparian vegetation results in increased erosion and input of fine grain material into the water. Sediment from these sources can be deposited in pools. green sturgeon requires deep pools for spawning and holding in the Sacramento River Basin. Large impoundments (e.g., Oroville, Shasta reservoirs) that reduce the frequency of high flow events may limit pool scouring and result in a reduction of pool depth. Survival and development of early life stages within the Sacramento River Basin may also be impacted by non-point source sediments through altered turbidity and substrate composition. At the time that the Recovery Team conducted its assessment, the High ranking for adults was attributed, in part, to the impact of water depth modification on the quantity and habitat quality of deep pools. The work of Mora (20 16b) indicates 50-125 areas with greater than 5m depth available on the mainstern Sacramento River depending upon the year. It is uncertain as to whether all of these pools supply sufficient habitat for spawning and holding in terms of depth and substrate. 2.5.1.9 Loss of Floodplain Habiitats Loss ofFloodplain Habitat and Loss of Wetland Function have been identified as primary stressors affecting the recovery of Central Valley salmonid species (National Marine Fisheries Service 2014b), and sDPS green sturgeon (National Marine Fisheries Service 2018g). This threat primarily affects the juvenile rearing and outmigration life stage of these species, from the upper reaches of their watershed of origin through the Delta. Effects of the action that contribute to the Loss ofFloodplain Habitat are likely to result in a probable change in fitness of: reduced growth and/or reduced survival probability. Although riverine floodplains support high levels ofbiodiversity and productivity, they are also among the most converted and threatened ecosystems globally (Opperman et al. 2010). In California, more than 90 percent of wetlands have been lost since the mid-1800s (Hanak et al. 2011, Garone 2011 ). Loss ofFloodplain Habitat within the Central Valley is a result of controlled flows and decreases in peak flows which have reduced the frequency of floodplain inundation resulting in a separation of the river channel from its natural floodplain. Channelizing the rivers and Delta ihas also resulted in a loss of river connectivity with the floodplains that otherwise provide woody debris and gravels, that aid in establishing a diverse riverine habitat, and that provide juvenile salmonid rearing habitat. The importance of connectivity for juvenile Chinook salmon to floodplain rearing habitat has been observed in several river systems. Research on the Yolo Bypass, the primary floodplain on the lower Sacramento River, indicates that floodplain are key juvenile rearing habitats supporting significantly higher drift invertebrate consumption and therefore faster growth rates (Sommer et al. 2001a, Katz et al. 2017). Otolith microstructure studies near the City of Chico recorded increased fall run Chinook Salmon growth, higher prey densities, and warmer water temperatures in off-channel ponds and non-natal seasonal tributaries compared to the main-channel Sacramento River (Limm and Marchetti 2009). Research of juvenile Chinook salmon on the Cosumnes River noted that ephemeral floodplain habitats supported hjgher growth rates for 149 Biological Opinion for the Long-Term Operation of the CVP and SWP juvenile Chinook salmon than more permanent habitats in either the floodplain or river (Jeffres et al. 2008). This growth is important to first year and estuarine survival, factors which may be key influences of a Chinook cohort's success (Kareiva et al. 2000). As with other stressors the SAIL synthesis teams referenced the relevant pathways by which Loss of Floodplain Habitat could affect species as well as how it may interact with other stressors. However, instead of describing the negative effects caused by a Loss ofFloodplain Habitat, Windell et al. (2017) examined the benefit of juvenile rearing on floodplains as it relates to survival, residence time and migration, and fish condition. The SAIL report notes the interaction with higher flows that activate accessible floodplains and secondary channels, which thereby expand the availability oflow-velocity refuge habitat. The SAIL report also identifies inundated floodplains in the Central Valley as being particularly successful habitat for fish growth because it provides optimum water temperature, lower water velocity, higher food quality and density, and reduced predator and competitor density relative to the main channel (Windell et al. 2017). 2.5.1.10 Spawning Habitat Availability During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Spawning Habitat Availability was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the spawning life stage ofthese species, in the upper reaches of their watershed of origin. Effects of the action that contribute to the Spawning Habitat Availability are likely to result in a probable change in fitness of: reduced reproductive success. One of the greatest threats to sDPS green sturgeon is the loss of spawning habitat due to the construction of darns in the Sacramento River system. Dams have limited available spawning habitats and, along with water management practices, have changed the flow and temperature profiles of the three major rivers that could be utilized by sDPS green sturgeon for spawning (i.e., Sacramento, Feather, and Yuba rivers). Generally, successful spawning for Chinook salmon occurs at water temperatures below 60°F (National Marine Fisheries Service 1997b). Reiser and Bjomn (1979) report that upper preferred water temperatures for spawning Chinook salmon range from about 55°F to 57°F. The NMFS 2004 Opinion requires water temperatures to be maintained below 56°F in the upper Sacramento River above the RBDD (National Marine Fisheries Service 2004). The 56°F temperature criterion is measured as the average daily water temperature and as such, the criterion may allow water temperatures to exceed 56°F for some periods during a day. Chinook salmon spawn in riffles or runs with water velocities ranging from 0.5 to 6.2 ft/sec (Healey 1991 , Vogel and Marine 1991). Spawning depths can range from as little as a few inches to several feet (Moyle 2002). Preferred water depths appear to range from 0.8 to 3.3 feet (Allen and Hassler 1986, Moyle 2002). Substrate is an important component of Chinook salmon spawning habitat, and generally includes a mixture of gravel and small cobbles (Moyle 2002). National Marine Fisheries Service (1997b) reports that preferred spawning substrate is composed mostly of gravels from 0.75 to 4.0 inches in diameter. Spatially, the total area of viable salrnonid spawning habitat has been significantly diminished. Physical features that are essential to the functionality of existing spawning habitat have also been degraded such as: loss of spawning gravel, and elevated water temperatures during summer months when spawning events occur (National Marine Fisheries Service 2014b). Degradation of 150 Biological Opinion for the Long-Term Operation of the CVP and SWP these features is actively mitigated through real-time temperature and flow management at Shasta and Keswick dams (National Marine Fisheries Service 2009b) as well as gravel augmentation projects in the affected area, which have been occurring under a multi-year programmatic authority (National Marine Fisheries Service 2015f). Current spawning is restricted to the mainstem and a few river tributaries in the Sacramento River (Myers et al. 1998). Naturally-spawning populations of CV spring-run Chinook salmon currently are restricted to accessible reaches of the upper Sacramento River, Antelope Creek, Battle Creek, Beegum Creek, Big Chico Creek, Butte Creek, Clear Creek, Deer Creek, Feather River, Mill Creek, and Yuba River (California Department of Fish and Wildlife 1998). The multi-agency SAIL synthesis teams also identified the relevant pathways by which Spawning Habitat Availability is likely to affect species as well as how it is likely to interact with other stressors. Specifically, Windell et al. (2017) focused on egg survival, timing, and condition as being affected by spawning habitat, specifically sedimentation and gravel quantity. For green sturgeon the loss of access to historical spawning habitat and habitat degradation have largely restricted sDPS green sturgeon to one reach of the mainstem Sacramento River and made the population vulnerable to stochastic events (National Marine Fisheries Service 2018g). 2.5.1.11 Physical Habitat Alteration During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Physical Habitat Alteration was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the spawning life stage of these species, in the upper reaches of their watershed of origin. Effects of the action that contribute to the Physical Habitat Alteration are likely to result in a probable change in fitness of: reduced reproductive success. Physical Habitat Alteration includes loss of natural river morphology and function. Flood control measures, regulated flow regimes and river bank protection measures have all had a profound effect on riparian and instream habitat in the lower Sacramento River. Levees constructed in this reach are built close to the river in order to increase streamflow, channelize the river to prevent natural meandering, and maximize the sediment carrying capacity of the river (National Marine Fisheries Service 1997b). Additionally, nearshore aquatic areas have been deepened and sloped to a uniform gradient, such that variations in water depth, velocity and direction of flow are replaced by cons istent moderate to high velocities. Gravel sources from the banks of the river and floodplain have also been substantially reduced by levee and bank protection measures. Levee and bank protection measures restrict the meandering of the river, which would normally release gravel into the river through natural erosion and deposition processes. Chinook salmon spawn in clean, loose gravel, in swift, relatively shanow riffles, or along the margins of deeper river reaches where suitable water temperatures, depths, and velocities favor redd construction and oxygenation of incubating eggs. The construction of dams and resultant controlled flows and extensive gravel mining affect spawning habitat. Chinook salmon require clean, loose gravel from 0.75 to 4.0 inches in diameter for successful spawning (National Marine Fisheries Service 1997b). Juvenile Chinook salmon prefer slow and slack water velocities for rearing and the channelization of the river has removed most of this habitat type. The 151 Biological Opinion for the Long-Term Operation of the CVP and SWP construction of dams in the upper Sacramento River has eliminated the major source of suitable gravel recruitment to reaches of the river below Keswick Dam. The threat of altered sediments to sDPS green sturgeon due to impoundments is high. The creation of upstream dams and impoundments can reduce sediment delivery to bays and estuaries. This can impact sDPS green sturgeon feeding habitat quality and quantity through changes in sediment deposition and composition and subsequent changes in prey resources or through changes in turbidity that could impact habitat use and predation by sight-predators. 2.5.1.12 Invasive Species/Food Web Disruption During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Invasive Species/Food Web Disruption was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the juvenile rearing and outmigration life stage of these species through the Delta and Bays. Effects of the action that contribute to the Invasive Species/Food Web Disruption are likely to result in a probable change in fitness of: reduced growth and/or reduced survival probability. Invasive species include both plants and animals, most ofwhich have been introduced to the Delta unintentionally through ship ballast. However, some species have been introduced intentionally by resource agencies for sportfishing or forage. Invasive aquatic plants have become established in many areas of the Delta. Establishment of invasive aquatic plants can harm or kill native aquatic species because they form dense mats that block sunlight and deplete oxygen supplies. Most of these aquatic weeds were introduced to the Delta unintentionally and include water hyacinth (Eichhornia crassipes), hydrilla (Hydrilla verticillata) and egeria (Egeria dens a). Within the Delta, the construction of levees and the conversion of adjacent riparian communities to other land uses have substantially changed the ecosystem. These changes have stressed native aquatic flora and fauna allowing infestation of invasive aquatic weeds. Invasive weeds flourish in the disturbed environment and may reduce foodweb productivity potentially harming fish and wildlife (CALFED Bay-Delta Program 2000). The majority of clams, worms and bottom dwelling invertebrates currently inhabiting the Delta are non-native species. Non-native species also comprise an increasing proportion of the zooplankton and fish communities in the Bay-Delta system. It is estimated that a new non-native species is identified in the Bay-Delta every 15 weeks (CALFED Bay-Delta Program 2000). Many fish known to prey on juvenile anadromous salmonids were introduced by resource agencies to provide sportfishing. These fish include striped bass, American shad and largemouth bass. Although introductions have increased diversity in the Bay-Delta system, this increase in diversjty has been at the expense of native species, many of which have declined precipitously or become extinct through predation and competition for resources (CALFED Bay-Delta Program 2000). At the same time, many non-native species are performing vital ecological functions such as serving as primary consumers of organic matter or as a food source for native fish and other wildlife populations (CALFED Bay-Delta Program 2000). One of the most important habitat attributes of the riverbed to listed anadromous fish species in the action area is the production of food resources for rearing and migrating juveniles, such as drifting and benthic invertebrates, forage fish, and fish eggs. Benthic invertebrates, such as oligochaetes and chironomids (dipterans), are the predominant juvenile salmonid and sDPS green sturgeon food items produced in the silty and sandy substrates of the action area. Although 152 Biological Opinion for the Long-Term Operation of the CVP and SWP specific information on food resources for green sturgeon within freshwater riverine systems is lacking, they are presumed to be generalists and opportunists that feed on similar prey to other sturgeons (Israel and Klimley 2008), such as the population of white sturgeon present and coexisting with green sturgeon in the Sacramento basin. Seasonally abundant drifting and benthic invertebrates have been shown to be the major food items of white sturgeon in the lower Columbia River (Muir et al. 2000). As sturgeons grow, they begin to feed on oligochaetes, amphipods, smaller fish, and fish eggs as represented in the diets of white sturgeon (Muir et al. 2000). Historically, the San Joaquin River has been an important source of nutrients to the Delta. Most of the San Joaquin River is now being diverted from the south Delta by CVP/SWP operations. The resultant loss in nutrients has likely contributed to an overall decrease in fertility of the Delta, limiting its ability to produce food (National Marine Fisheries Service 1997b). Additionally, pumping operations may result in a loss of zooplankton reducing their abundance in the Delta. Poor food supply may limit the rearing success of winter-run Chinook salmon. Extensive areas of the Delta are below mean high tide, but because of levees and flapgates installed throughout the Delta, these areas are no longer subject to tidal action. This effectively reduces the volume of water subject to tidal mixing and the size of the Delta floodplain. Reduced residence time of Delta water and associated nutrients restricts the development of foodweb organisms (CALFED Bay-Delta Program 2000). The multi-agency SAIL synthesis teams (Windell et al. 2017) found predation by non-native species affected egg survival, timing, and condition and juvenile survival, residence time/migration, and growth. 2.5.1.13 Predation During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Predation was identified as a primary stressor affecting the recovery of the species. This threat primarily affects the juvenile rearing and outmigration life stage of these species, from the upper reaches of their watershed of origin through the Delta and Bays. Effects of the action that contribute to Predation are likely to result in a probable change in fitness of: reduced survival probability. Predator-prey interactions can be broken down into several fundamental steps between the prey and the predator. These steps include the rates of encounters between the predator and the prey, the rate at which the predator decides to pursue and attack the prey when detected, the rate at which the predator successfully captures the prey, and, ultimately, the rate at which the prey is consumed by the predator. Each one of these steps is influenced by biological and physical factors in the surrounding environment such as prey abundance, spatial and temporal overlap of prey with the predator, habitat complexity, turbidity, and behavioral, physiological, and morphological adaptations that facilitate (predator success) or inhibit (prey avoidance) the predation process (Grossman et al. 2013, Grossman 2016). Although predation is frequently the proximate cause of mortality, the ultimate cause of mortality is often related to alterations in the physical or biological parameters of the habitat that prey occupy that enhance rate of predation. Because fish are highly adaptable, the response to habitat changes and quality are not always straightforward and linear and thus may not always be completely predictable, particularly on a shorter time scale. In general, though, habitat that is complex and offers a multitude of different 153 Biological Opinion for the Long-Term Operation of the CVP and SWP niches provides for a more diverse biological community (Grossman et al. 2013, Grossman 2016). In a stable, undisturbed, functioning habitat, multiple species can occupy the same general area by each species occupying a particular ecological niche, thereby minimizing direct competition between species and having a balanced predator-prey interaction. This is particularly true in habitats where predators and prey have co-evolved with each other. This relationship does not exist or is compromised when habitat is altered or nonnative species invade a new habitat, causing a loss of equilibrium among the species inhabiting it. The Delta and Central Valley waterways are currently highly altered and disturbed habitats. In the aquatic ecosystems of the Central Valley and Delta waterways, widespread habitat alteration has occurred over the last 150 years. Predation is a threat to winter-run Chinook salmon, especially in the Delta where there are high densities of non-native fish (e.g., small and large mouth bass, striped bass, catfish, and sculpin) that prey on outrnigrating salmon. The presence of man-made structures in the environment that alter natural conditions liikely also contributes to increased predation by altering the predator-prey dynamics often favoring predatory species. In the upper Sacramento River, rising of the gates at the RBDD reduces potential predation at the darn by pikerninnow. In the ocean, and even the Delta environment, salmon are common prey for harbor seals and sea lions. Most of the predation on juvenile Chinook salmon in the Delta likely occurs from introduced species such as striped bass, black crappie, white catfish, largemouth bass and bluegill. Native Sacramento pikerninnow and steelhead also occur in the Delta and are known to prey on juvenile salmonids. Of these non-native predatory species, striped bass are likely the most important predators because: (1) the estimated abundance of striped bass in the Sacramento-San Joaquin system greater than 18 inches in length has ranged from about 600,000 to about 1,900,000 during the period between 1969 to 2005; (2) the total number of striped bass preying upon juvenile Chinook salmon in the system is greater than these estimated population sizes because striped bass smaller than 18 inches in length feed on juvenile Chinook salmon; (3) anectodal information indicates that striped bass movements up the Sacramento River coincide with juvenile Chinook salmon emigration, resulting in a co-occupancy of habitat; and (4) striped bass are opportunistic feeders, and almost any fish or invertebrate occupying the same habitat eventually appears in their diet (Moyle 2002). The multi-agency SAIL synthesis teams also identified the relevant pathways by which Predation is likely to affect species as well as how it is likely to interact with other stressors. Windell et al. (2017) note survival across all life stages and in all geographic regions can be affected by predation, particularly within the egg to fry emergence stage, rearing to outrnigrating juveniles stage in the Upper and Middle Sacramento River and the Bay-Delta, and ocean juvenile to ocean adult stage. 2.5.1.14 Hatchery Effects During the development of the Recovery Plan for Central Valley Chinook Salmon and Steelhead (National Marine Fisheries Service 2014b), Hatchery Effects was identified as a primary stressor affecting the recovery ofthe species. This threat primarily affects the juvenile rearing and outrnigration life stage of these species, from the upper reaches of their watershed of origin through the Delta and Bays. Effects of the action that contribute to Hatchery Effects are likely to result in a probable change in fitness of: reduced growth and/or reduced survival probability. 154 Biological Opinion for the Long-Term Operation of the CVP and SWP More than 32 million fall-run Chinook salmon, 2 million spring-run Chinook salmon, 1 million late fall-run Chinook salmon, 0.25 million winter-run Chinook salmon, and 2 million steelhead are released annually from six hatcheries producing anadromous salmonids in the Central Valley. All of these facilities are currently operated to mitigate for natural habitats that have already been permanently lost as a result of dam construction. The loss of this available habitat results in dramatic reductions in natural population abundance, which is mitigated for through the operation of hatcheries. During spawning, hatchery-and natural origin salmonids may compete for habitat, and interbreeding may reduce genetic integrity. Throughout juvenile rearing and outmigration, hatchery- and natural-origin salmonids may compete for habitat and food. When larger, juvenile, hatchery-origin steelhead are released into the river, they may predate on smaller natural-origin salmonids. Recent biological opinion on the hatchery and genetic management plan for the Livingston Stone National Fish Hatchery (LSNFH) (National Marine Fisheries Service 20 17b) identified hatchery impacts to ESA-listed species in the Central Valley, which include: 1) genetic impacts due to straying of hatchery fish and the subsequent interbreeding of hatchery fish with natural-origin fish 2) high harvest-to-escapements ratios for natural stocks. California salmon fishing regulations are set according to the combined abundance of hatchery and natural stocks, which can lead to over exploitation and reduction in the abundance of wild populations that are indistinguishable and exist in the same system as hatchery populations. 3) releasing large numbers of hatchery fish can also pose a threat to wild Chinook salmon and steelhead stocks through the spread of disease, genetic impacts, competition for food and other resources between hatchery and wild fish, predation of hatchery fish on wild fish, and increased fishing pressure on wild stocks 4) in the ocean, limited marine carrying capacity has implications for naturally produced fish experiencing competition with hatchery production (Hatchery Scientific Review Group (HSRG) 2004). Increased salmonid competition in the marine environment may also decrease growth and size at maturity, and reduce fecundity, egg size, age at maturity, and survival (Bigler et al. 1996). Hatchery production may be in excess of the marine carrying capacity, placing depressed natural fish at a disadvantage by directly inhibiting tiheir opportunity to recover (Northwest Power and Conservation Council 2003). The multi-agency SAIL synthesis teams also identified some pathways by which Hatchery Effects is likely to affect species as well as how it is likely to interact with other stressors. Windell et al. (2017) state that high densities of hatchery salmon can negatively impact naturalorigin juvenile populations that may be smaller in size and numbers by causing increased competition for food. Returning adult hatchery fish can affect natural-origin adult spawners by competition for habitat or genetic introgression, reducing genetic fitness in the wild populations. 2.5.2 Upper Sacramento/Shasta Division During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, BA. Section 2.5.2.1-2.5.2.5 of the effects description below is based on the modeling associated with the February 5, 2019, PA (Appendix AI, the original PA) and associated modeling thatNMFS requested. Section 2.5.2.6 155 Biological Opinion for the Long-Term Operation of the CVP and SWP provides a supplemental effects analysis to assess the effects ofthe June 14,2019, PA revisions reflected in the final PA (Appendix A3), including a discussion of whether and how the PA revisions modify the effects analyzed in Sections 2.5.2.1-2.5.2.5. Reclamation operates the CVP Shasta Division for flood control, navigation, agricultural water supplies, municipal and industrial water supplies, fish and wildlife, hydroelectric power generation, Delta water quality, and water quality in the upper Sacramento River. Water rights, contracts, and agreements specific to the Upper Sacramento River, or that may dictate conditions therein include SWRCB Decisions 990, 90-5, 91-1, and 1641 , Settlement Contracts, Exchange Contract, and Water Service Contracts. Facilities include the Shasta Dam, Lake [4.552 Million Acre Feet (MAF) capacity], and Power Plant; Keswick Dam, Reservoir, and Power Plant; and the Shasta Temperature Control Device. The Shasta Division includes the Red BluffPumping Plant, the Coming Pumping Plant, and the Coming and Tehama-Colusa canals, for the irrigation of over 150,000 acres of land in Tehama, Glenn Colusa, andYolo counties. A description of the PA and the PA components affecting upper Sacramento River fish species is in Appendix Al. A depic6on of the deconstructed action describing how the upper Sacramento/Shasta D ivision PA components relate to each other is provided in Figure 2.5-.2-1. The primary stressors influenced by each PA component are identified in Table 2.5.2-1. A full description of each stressor, including the way in which the stressor would affect an individuars fitness, is found in Section 2.5.1 Stressors and Species Response. The exposure, risk, and response of each species to the projectrelated stressors are then analyzed in the following sections for each P A component. 156 Biological Opinion for the Long-Term Operation of the CVP and SWP Upper Sacramento/Shasta Division Cold Water Sea ronal Operations ['=·(_ ManaBement Spawning and Rearjng Habitat Tools Restoration Restoration oper.ations 1_ SummerOps. Spawning Gravel Injection lower Intakes near Wilkins Slough ShastaTCO Improvements Rice Spring Flows Decomposition Smoothins Spring Pulse ISNFH Production Flows Spring Memt. of Spawning Adult Res;cue Locations Juvenile Trap and Haul Figure 2.5.2-1. Deconstructed action describing the relation of project components in the Sacramento River. As provided in BA Table 4-6, blue action components were included in the PA as Core Operations and yellow action components were proposed as either Scheduling or subject to Collaborative Science, as stated in the BA. Table 2.5.2-1. Primary stressors influenced by each Proposed Action component. Primary stressors are from the NMFS 2014 Recovery Plan for Central Valley Salmonids and NMFS 2018 Recovery Plan for sDPS of Green Sturgeon {National Marine Fisheries Service 2014 2018). Project Component 2.5.2.3.1.1 Winter Minimum flows X X X X 157 X SmaiiScteen Prosram Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component 2.5.2.3.2.2 Spring Base Flows 2.5.2.3.2.3 Spring Pulse Flow 2.5.2.3.2.4 Spring Mgmt of Spawning Locations 2.5.2.3.3.1 Summer Cold Water Pool Management Tiers X X X X X X X X X X X X 1-4 2.5.2.3.3 Delta Smelt Summer-Fall Habitat 2.5.2.3.4.1 Fall and Winter Refill and Redd Maintenance 2.5.2.3.4.2 Rice Decomposition smoothing (fall operations) X X X X X X X 2.5.2.4 Operation of a Shasta Dam Raise9 q The PA proposes that operational criteria with the Shasta Dam Raise will be the same as operational criteria for the current dam and integrated CVP/SWP operations. Reclamation has advised NMFS that therefore the BA analyses suffice for purposes of consultation. There are no operational scenarios in the BA to evaluate to confirm beneficial or adverse effects of a raised Shasta Dam and NMFS therefore cannot further evaluate the Shasta Dam raise in this opinion. 158 Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component 2.5.2.5.1.1 Battle Creek Restoration (Cold water pool management) 2.5.2.5.1.2 Wilkins Slough Intakes (Cold water pool management) 2.5.2.5.1.3 Shasta TCD Improvements (Cold water pool management) 2.5.2.5.2.1 Spawning Gravel Injection (Spawning/rearing habitat restoration) 2.5.2.5.2.2 Side-Channel Habitat Restoration (Spawning/rearing habitat restoration) 2.5.2.3.2.3 Small Screen Program (Spawning/rearing habitat restoration) X X X X X X X X X 2.5.2.3.3.1 LSNFH Production (Tier 4 intervention) 2.5.2.5.3.3 Adult Rescue (Tier 4 intervention) X X X 2.5.2.5.3.4 Juvenile Trap and Haul (Tier4 intervention) X 159 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.2.1 Shasta Annual Operations Reclamation operates Shasta and Keswick dams year-round in coordination with the other dams and reservoirs of the CVP and SWP. Seasonal operations follow a set of objectives. During winter, Reclamation operates for flood control and building storage, considering both the channel capacity within the Sacramento River and Shasta Reservoir flood conservation space. When making flood control releases, Reclamation operates Shasta Dam to keep flows at Bend Bridge less than 100,000 cfs to protect populated areas downstream. This winter period can include significant flow fluctuations from Keswick Dam due to the flood control operations. During the winter and spring, when not operating for flood control, Shasta Dam is operated primarily to conserve storage while meeting minimum flows in the Sacramento River and to meet water quality and outflow requirements in the Delta. During the summer, Reclamation's operational considerations are mainly flows required for Delta outflows, instream demands, upstream temperature control, and exports. Fall operations attempt to maintain temperature control and provide for fish spawning habitat. Except for diversions needed for rice decomposition, downstream irrigation demands typically decrease during the fall, so during this time of year, Reclamation will operate to conserve storage and decrease Keswick releases. On May 22,2019, Reclamation met with NMFS to discuss the PA and reiterated the ir commitment to build storage in Shasta to improve overall storage relative to current operations. The P A includes several operational components, described in more detail in subsequent sections of this effects analysis, that Reclamation intends to implement to contribute to increased spring Shasta storage levels for the PA compared to recent years. These include (1) minimum late fall and winter flows, including modification of rice decomposition operations compared to the Current Operations Scenario (COS); (2) modified fall outflow requirements compared to the COS; (3) flexibility in export operations (especially in April and May) compared to the COS, and anticipated improved salinity conditions which would reduce carriage water demands; and (4) December 2018 changes to COA (which are also included in COS). Reclamation intends for these operations, as well as real-time operations, to aggregate and result in increased end of September carryover storage, which Reclamation expects to benefit the following May 1 storage in years that do not require flood control operations. Reclamation will use various operational flexibilities and/or contingency actions after May 1, potentially including adjusting initial allocations, to stay within a Tier, unless the change is caused by events outside Reclamation's control or beyond what was planned for in the temperature management plan. 2.5.2.1.1 Baseline and Without Action Considerations It is clear to NMFS that Reclamation has endeavored to provide a P A that balances the needs of species, water supply, and other operational objectives and constraints. The sections below describe the specific seasonal components of the P A, their relation to the conceptual models describing species life histories, the effects of those PA components on identified stressors, and the subsequent effects to the species in the upper Sacramento River. In these subsequent sections, NMFS' goal is to trace effects of the proposed operations at Shasta Reservoir and to consider and analyze how the proposed daily, monthly, and seasonal operational decisions to store or release water, operate the temperature control device (TCD), complete restoration actions, and integrate Shasta operations with those of the Delta and other reservoirs have effects downstream on the species. Depending on the timing, location, lifestage, and species affected, these effects can be beneficial, neutral, or adverse, or all three based on which species is being evaluated. For 160 Biological Opinion for the Long-Term Operation of the CVP and SWP example, a decision to store water in April has an adverse effect in April on CV spring-run Chinook salmon juveniles and a beneficial effect in May through October on winter-run Chinook salmon eggs and emergent fry. NMFS traces and analyzes these effects in this section of the Opinion, often in a comparative analysis relative to baseline conditions given the nature of modeling outputs and historical data. Our analysis culminates in an aggregate assessment with baseline effects in Integration and Synthesis section (Sections 2.8 and 2.9) to draw conclusions according to the ESA. As discussed in Section 2.4 Environmental Baseline, the historical effects of dam construction and operations on the species are part of the environmental baseline, in addition to the past, present impacts of all Federal, State, or private actions and other human activities in an action area. The "without action" scenario provides context for how the existence of the CVP and SWP facilities have shaped the environmental baseline, including habitat conditions for species and critical habitat in the action area. In particular, the existence of the dams, an altered hydrograph, and high water temperatures limit access to suitable spawning habitat. A comparative analysis looking at changes in hydrographs helps to highlight the significant changes in flows that species experience from these historical conditions. The pre-dam hydrograph in Figure 2.5.2-2 shows that the median monthly flows would naturally have been quite different than the regulated flows into the upper Sacramento River since 1950. Demands and contract deliveries have created a peak in the hydrograph in May through August, with nearly minimum flows through winter, spring, and the rest of fall. In contrast, the natural hydro graph peaks during winter and spring months of December through May, which coincides with periods of increased precipitation and warmerseason snowmelt that are typical of the Central Valley climate. 161 Biological Opinion for the Long-Term Operation of the CVP and SWP 18000 16000 -tl14000 ::: 12000 .2 u.. 2:: 10000 .r:: ...c 0 8000 c .!!! 6000 :::E "0 Q) 4000 :::E 2000 0 - Period 1 (1892-1937) - Period 2 (194&-1959) -Period 3 (1960-1993) Period 4 (1994-2014) Figure 2.5.2-2. Hydrognph of medi+m :monthly flowrflte in the Sfltramento RJver for different pre- flnd postdam periods. Shasta Dam commission: 1944-1945; Keswick Dam commission: 1950. From Swart (2016). As introduced in Section 2.5.1 Species Stressors and Response, water temperatures significantly affect the distribution, health, and survival of native salmonids in the California Central Valley. Since salmonids are ectotherrnic (cold-blooded), their survival is dependent on external water temperatures and they will experience adverse health effects when exposed to temperatures outside their optimal range. Salmonids have evolved and thrived under the water temperature patterns that historically existed (i.e., prior to significant anthropogenic impacts that altered temperature patterns) in California Central Valley streams and rivers. Although evidence suggests that historical water temperatures exceeded optimal conditions for salmonids at times during the summer months on some rivers, the temperature diversity in these unaltered rivers provided enough cold water during the summer to allow salmonid populations as a whole to thrive (U.S. Environmental Protection Agency 2003). Throughout year-round operations, physical processes drive relationships between flows, storage, cold water pool volume, and water temperatures (both lake and in-river). These relationships are driven by meteorology, precipitation, infiltration, runoff, and solar radiation, as well as Reclamation's actions and those of the water contractors included in the PA and all other diversions. Because of the thermal dynamics associated with seasonal stratification in Shasta Reservoir, Reclamation's decision concerning storage levels are linked to cold water pool volume availability and are primarily driven by hydrology, though meteorology also plays a role. As such, Reclamation's management of reservoir storage and operation ofthe temperature control device throughout the year impacts the availability of cold water and release 162 Biological Opinion for the Long-Term Operation of the CVP and SWP temperatures and the subsequent thermal dynamics of the mainstem Sacramento River. Before the Shasta Dam TCD was built, NMFS required that a minimum 1.9 MAF end of September (EOS) storage level be maintained to protect the cold water pool in Shasta Reservoir in case the following year was critically dry (i.e., drought year insurance). This was because a relationship exists between EOS storage and the cold water pool. Especially for drier conditions, greater EOS storage level typically influences greater storage (and presumably cold water pool) in spring of the following year. Since 1997, when the TCD became operational, Reclamation has been able to use the TCD as an additional means to manage water temperatures in the upper Sacramento River. It has also become apparent from Shasta operations in the drought years that an end of May storage requirement is a critical metric towards managing downstream temperatures during summer and early fall. While the ROC on LTO PA and communication with Reclamation (Field 2019) indicates that a minimum Shasta storage of approximately 3.66 MAF is necessary to access the upper gates of the TCD (Appendix AI, Table 4-7), Reclamation has stated (Field 2019) that a greater volume (approximately 3.9 to 4.1 MAF) is necessary to provide a high likelihood for operations to effectively blend water from the warmer upper reservoir levels and thereby reduce reliance on the more limited cold water. Figure 2.5.2-3 shows the general relationship between total storage, cold water pool storage, and summer/early fall downstream temperature that has been developed according to analysis done by Reclamation using data from 1998 through 2015 (Appendix AI, Figure 4-2). As this figure shows, an end of April storage between 3.9 and 4.3 MAF is needed to meet a daily average temperature of 53°F at the Sacramento River above Clear Creek gaging station in (CCR) May-October. This "rule of thumb" chart is used with temperature modeling of measured and forecasted conditions by Reclamation when developing temperature management plans. 163 Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Storage Vs s2•F or less Storage on May 1st with CCR Average Daily Maximum for May through October 33 3.2 31 Average Daily Temperature of less than S3'F at CCR M ay-Oct - - - - - - - - - - - - - -- -"' 3.0 29 Average Dally Temperature of 53'F at CCR May-Oct l8 27 r;; 2.6 " t 2.5 Average Dally Temperature of 54 · 56' F at CCR May-Oct - - -....._ ... 24 ! 2.3 0 (;' 2.2 g i 2.1 2.0 19 18 1.7 1 .6 1.5 !4 2 3 24 2.5 2.6 27 28 29 3.0 )I 32 3.3 34 35 3.6 3.7 3.8 39 41 42 43 44 45 46 47 4.8 Molhons of Acre Feet Dally M.. - lln•ar (Da ly Maxi Figure 2.5.2-3. Relationship between Temperature Compliance, Total Storage in Shasta Reservoir, and Cold Water Pool in Shasta Reservoir (ROC on LTO BA Figure 4-2). Recent analyses can be useful to understand effects of changing the flowrate of reservoir releases, which is a method Reclamation considers for controlling temperatures below Shasta Reservoir. NMFS Southwest Fisheries Science Center (SWFSC) has analyzed the relationship between CCR water temperature and Keswick gauge (KWK) water temperature and discharge. Using observed mean daily flow and temperature values from 1998 to 2017, a linear model was fit to estimate the monthly relationship between increasing/decreasing flow or temperature at KWK and water temperature at CCR. The model allows prediction of the effect of a change in KWK discharge on CCR temperature, assuming a constant flow for a given month. Figure 2.5.2-4 shows the estimated KWK discharge temperature required to obtain a water temperature less than or equal to 53.5°F at CCR for five KWK discharge levels. Using this relationship of temperature and flow, it is possible to estimate either the minimum flowrate or the maximum release temperature at KWK that is required to maintain 53.5°F at CCR in a particular month. 164 Biological Opinion for the Long-Term Operation of the CVP and SWP 54 53.75 - 4000 tt3 sec·' - oooo tt3 sec"' 8000 113 sec"1 53.5 53.25 u. ' a: .at'!8_ .,., 1- ll 53 52.75 52.5 E :.::: 0 E :::1 :0l!! 52.25 ":i e- 52 5 1.75 51.5 5 1.25 - Month -- Figure 2.5.2-4. Estimated KWK discharge temperature required to obtain a water temperature less than or equal to 53.5°F at CCR for five KWK discharge levels. The recent California drought provides experience to consider in summer temperature management The critically dry water year of2014 was followed by a dry 2015, which deepened the drought in California. An already low initial cold water pool (CWP) volume increased the difficulty of providing suitable cold water temperatures for successful egg and alevin incubation in 2015. In 2015, the Drought Exception Procedures ofRPA L2.3.C ofthe NMFS 2009 Opinion was triggered. Specifically, the February forecast, based on 90 percent hydrology, showed that a Clear Creek temperature compliance point or 1.9 MAF EOS storage was not achievable. During the development ofthe temperature management plan (TMP), there were regular and frequent check-ins on the status of the CWP, storage levels, and temperatures, along with a suite of operational scenarios and Keswick release schedules, which were evaluated by the Sacramento River Temperature Task Group (SRTTG) for recommendation to Reclamation. As more information was obtained about the current and developing condition, additional operational scenarios were considered and evaluated, including changes to the amount of storage gained or lost with each Keswick release option, release temperature, and flow rate necessary to meet downstream temperatures while attempting to meet downstream obligations. Figure 2.5.2-5 is a temperature landscape profile over space and time for the five scenarios under consideration in 2015 compared to 2014. 165 Biological Opinion for the Long-Term Operation of the CVP and SWP 10pct6000cfs 60 55 50 Mily Nov Sep 5 60 10 55 15 u....__...__........_.........,_ _ 50 Jul Sep Aug Ocl 10pct7000cfs 60 $5 50 Sep Ocl Nov 60 55 50 Nov Sep Aug 10pct8000cfs 60 55 50 May Jul Sep Aug Ocl Nov 2014 5 60 10 55 50 Mily Jul Sep Aug Ocl Nov Figure 2.5.2-5. Temperature landscape profiles of the upper Sa.cramento River for the five scenarios evaluated for 2015 compared to conditions of 2014. The isoline shows 57°F. The circles indicate 2014 redd timing and location. The black represents winter-run egg and alevin development time in the gravel. The green line represents the fry rearing phase. The y-axis indi.cates miles of downstream habitat suitable for rearing juvenile winter-run among the different flow scenarios. 2.5.2.1.2 Project Uncertainties NMFS has identified sources of uncertainty, which are identified in Table 2.5.2-2, that are considered in the evaluation of effects of the PA components for the upper Sacramento/Shasta division. Table 2.5.2-2 includes uncertainties related to modeling limitations, alternative analytical tools, and real-time implementation of the PA, noting the information provided by Reclamation, and the assumption we have applied in addressing the uncertainty. Table 2.5.2-3 provides a comparison of key current operations to the proposed operations of the PA to describe the differences in project components and sources of uncertainty. Reclamation identifies the PA components as being different from the current operations in terms of temperature management, spring pulse flows, fall base flows, and increased production at LSNFH. There are, however, additional changes to current operations that are part ofthe PA, but which are not explicitly identified in the BA. NMFS has identified these changes through our own evaluations of the PA modeling, review of historical information, and exchange of 166 Biological Opinion for the Long-Term Operation of the CVP and SWP information with Reclamation. We identify those changes in the table below, and we trace the extent of effect of these changes, noting the level of uncertainty regarding Reclamation's operations effects on flows, storage, and temperatures. Table 2.5.2-2. Sources of uncertainty associated with analysis of the P A oper ations of Shasta Da m a nd the upper Sacramento River. Source of Uncertainty Information from BA and Supplemental Reclamation Submissions Physical Modeling of the Proposed Action and Current The COS does not explicitly include the storage components of the RPA of the NMFS Operations Scenario 2009 Opinion due to limitations in CaiSimii model capability. Biological Modeling How NMFS Applied Assumptions to Address Uncertainty COS may not explicitly meet historical storages due to the real-time operations and short-term modifications within the entire system. The model creates shortages based on water supply including conservative forecasts of inflow. There are limitations to applying CalSimii storage results in a comparative manner to determine the expected impact of the proposed action. Years are considered to be within Tier 1 despite exceedances of 53.5°F daily average temperature in over 20 percent of modeled days; P A assumes that real-time operations will allow avoiding exceedances. NMFS considers that the biological response that fish experience may not exactly achieve 53.5°F, or as described in other tiers. NMFS assumes that Reclamation's operational flexibility will minimize the frequency and magnitude of exceedances that would compromise the objective of the given Tier (Note: pending additional analysis from Reclamation to support this conclusion). Climate change is incorporated using CMIP3 and AR3, which does not reflect best available science for temperature increases. Assumed that the provided modeling represents a scenario of limited effects of climate change to the species; NMFS layers additional qualitative evaluations onto quantitative analyses to reflect greater projected changes in temperature and sea level rise in CMIP5 modeling. Anderson (20 18) model simulates egg to hatch through life stage-dependent temperature mortality and the spatially dependent background mortality from hatch through fry stages. The Anderson model assumes that redds/eggs are most sensitive to DO conditions during the five days preceding hatch and results include mortality only for that period. In considering differences between results from the Anderson and Martin models, NMFS considers that the Anderson model could underestimate mortality by not accounting for egg mortality prior to the hatch period in the percentage mortality during the hatch period. Results for both models are considered in the effects analysis .. 167 Biological Opinion for the Long-Term Operation of the CVP and SWP Sour ce of Uncertainty Information from BA and Supplemental Reclamation Submissions Anderson model is based on previous (Rombough 1994) analyses, but has not completed a peer-review process. Uncertainty During RealTime Imple mentation of Proposed Action How NMFS Applied Assumptions to Address Uncertainty Considered external reviews and fieldtesting in discerning weight of evidence applied to methods according to categories identified in Section 2.1 Analytical Approach. Acknowledges the uncertainties and needs for additional research identified in review of Martinet at. (20 17) but also that it is a "parsimonious and realistic representation of temperature effects on eggs" (Gore et at. 2018). NMFS considers that the biological Annual and seasonal uncertainties with response that fish experience may not precipitation and runoff, air temperatures, and exactly achieve that of 53.5°F, or as cloud cover. described in other tiers. Uncertainty about forecasted TCD performance. NMFS considers that the biological response that fish experience may not exactly achieve that of 53.5°F, or as described in other tiers. NMFS considers that the biological Assumptions about operational precision, response that fish experience may not human error, and unanticipated events (e.g., exactly achieve that of 53.5°F, or as Carr fire, North American Electric Reliability described in other tiers. (NERC) testing). Assumptions about actual accretions and depletions in upper Sacramento River may not be accurat e, especially during dry hydrology/drought. NMFS considers that the biological response that fish experience may not exactly achieve that of 53.5°F, or as described in other tiers. A specific example of uncertainty related to real-time implementation of the PAis the exposure risk to temperature conditions during summer temperature management. While the BA describes an approach to summer temperature management, the PA does not include a process by which it would achieve any defined metric. NMFS must, therefore, include in our analysis the uncertainty of achieving any threshold storage level that dictates summer temperature management as defined in the BA for a specific Tier. For current operations, Reclamation takes a conservative approach to building storage that starts by targeting minimum flows in the fall and winter until either the reservoir nears the flood control elevation or another requirement, such as Delta water quality, requires increased releases of stored water. With this approach, Reclamation develops a monthly Keswick release forecast using the Shasta EOS carryover storage and various historical hydrologies. The current operations include an interagency workgroup that provides input to Reclamation on taking additional actions, including export curtailments, if necessary, to conserve storage and other protections/measures. Similarly, for the PA action component Fall and Winter Refill and Redd Maintenance (Section 2.5.2.3.4.1), Reclamation is proposing to set minimum fall flows according to Shasta EOS carryover storage. The operations of the PA intend to remove the 168 Biological Opinion for the Long-Term Operation of the CVP and SWP uncertainty that results from advisement offered by an interagency workgroup, but NMFS recognizes that winter and spring flows could be controlled by other requirements and, therefore, above the minimum flows identified to achieve adequate storage to provide cold water releases for winter-run Chinook salmon in the following year. Based on conversations during May 20-24, 2019, NMFS assumes that Reclamation will coordinate under all conditions, and seek technical assistance from NMFS and the USFWS regarding species intervention measures (Section 2.5.2.5.3 Intervention Measures) only in the driest of the four proposed Tiers (i.e., March 90 percent exceedance runoff forecast indicate May 1 Shasta storage of less than 2.5 MAF). In contrast, the existing process includes monthly consultations between NMFS and Reclamation from the February forecast through the issuance of the Sacramento River temperature management plan in May. These consultations provide NMFS with the opportunity to provide information regarding biological criteria for spring operations of Keswick Dam releas.es, with the intent of reducing negative effects of increased temperature on winter-run Chinook salmon while still accommodating other legal and delivery requirements. The only similar coordination process included in the ROC on LTO PA occurs when storage is forecasted to be below 2.5 MAF at the beginning of May. Furthermore, NMFS notes that analysis will include effects of deliveries to all CVP contractors, including implementation and performance of the north-of-Delta settlement contracts. Therefore, we evaluate the full effects of maximum water deliveries and diversions under the terms of existing contracts and agreements, including timing and allocation in this Opinion, as well as other obligations, including D-1641, refuge supplies, and exchange contractor deliveries. NMFS notes that, in comparison to current operations, the effects of which are considered part of the baseline, the PA does not include an EOS carryover storage performance measure, which would be especially helpful in providing future protections for back-to-back dry years. According to the PA, fall, winter and spring reservoir releases are based on a Shasta EOS storage; however, the PA does not propose any particular end of September storage target. NMFS has evaluated the effects of reservoir operations according to the project description and the modeling results provided in the BA. In a comparative analysis, and with regards to the characterization of operations since 2009, the COS, and the PA in the physical modeling, NMFS used Table 2.5.2-3 to better understand the comparative results of the PA versus the COS and the accuracy of COS in characterizing current operating criteria. While the COS is intended to represent the current operating criteria (i.e., operations that comply with the USFWS 2008 and NMFS 2009 opinions), the COS does not include year-specific adjustments, modified drought requirements, maintenance of facilities, facility malfunctions, or other short-term or unforeseen actions that change real-time operations. NMFS has identified ways in which the COS CalSimii modeling deviates from a description of actual current operations. There are, therefore, ways in which the COS does not fully characterize the historical operations of the last 10 years under the NMFS 2009 Opinion. Modeling for the COS does not explicitly prioritize releases from Folsom and Oroville reservoirs (rather that Shasta releases) per specific RPA elements to meet in-Delta water quality or flow requirements, though it does consider relative reservoir storage when determining releases for inDelta needs. For the purposes of comparing the PA to current operations, NMFS has assessed effects ofbuilding storage relative to coordinated use of Oroville releases. Additionally, the COS model does not reflect management options to limit Keswick releases to 7,500 cfs or less in July 169 Biological Opinion for the Long-Term Operation of the CVP and SWP of dry and critical years, and the model is not capable of characterizing particular temperature operations or the ability to change temperature targets throughout the year. All of these actions have the potential to result in increased coldwater pool iin Shasta Reservoir in the spring period. NMFS has used this information in better understanding the resulting comparisons of Shasta Reservoir storage for the PA versus the COS and placing that in context given conditions and operations in the last decade. To address uncertainty regarding these components, NMFS has developed a memorandum to the ROC on LTO administrative record that evaluates various lines of evidence, including the CalSimll modeling of Shasta storage (from the ROC on LTO BA Appendix D), historical evaluation ofKeswick flowrates, and CalSimii Modeling ofDrivers of Shasta Releases. Based on this evaluation, NMFS still has notable uncertainty that Reclamation's operations allow the ability to considerably increase the total Shasta storage on May 1 for the PA. However, we acknowledge that what may seem like a minor increase- if operations and other constraints allow for it to occur - for the PA can be valuable in augmenting available cold water pool volume ifthat increase occurs with the 1 MAF operating range of the total volume range. This increase could allow better access to the upper gates earlier in the year, which could contribute to better temperature management. Table 2.5.2-3. Comparison of the current operations to the Proposed Action for major CVP action components. Action Component Spring Actions Spring Pulse Flows Actual Current Operation NMFS RPA Action 1.2.3 February forecast; MarchMay 15 Keswick Release Schedule (Spring Actions): • Consultation prior to initial water allocations • Review of temperature modeling • Conserve storage. None. Characterization in Modeling of Current Operations Scenario (COS) Inclusion in Proposed Action (PA) None. None. None. Spring pulses if projected May 1 storage> 4 MAF: • up to 150 TAF limit • but not if it: • interferes with the ability to meet other anticipated demands on the reservoir • would cause Reclamation to drop into Tier 4. 170 Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component Summer Cold Water Pool Management ---- Fall and Winter Refill and Redd Maintenance Actual Current Operation Characterization in Modeling of Current Operations Scenario (COS) Inclusion in Proposed Action (PA) NMFS RPA Action 1.2.4: May 15 through October Keswick Release Schedule, Shasta Temperature Management, WRO 90-5 downstream temperature targets. • Recent (last 3 years) operational study of 53.5°F daily average temperature at CCR In real time, may end • after last winter-run Chinook salmon redd emerges, as advised by SRTIG. No direct temperature criteria. Temperature management based on use of Shasta cold water pool for winter-run survival, including WRO 90-5, by implementing I. of 4 tiers with provisions: • Tiers can switch within a year • Tiers are selected at the beginning of May unless the March forecast shows a potential for Tier 4. • Temperature management starts after May 15 or when there is evidence of winter-run spawning • Temperature management ends October 31, or 95 percent winter-run Chinook salmon emergence, whichever is earlier. No direct carryover storage criteria and therefore no Shasta storage performance measures are in the model. The model has a combination of water-related goals and constraints that results in a September Shasta storage frequency that approximates the 2009 performance measures. None. The CalSimll model does not include (b)(2) related logic/accounting. The high frequency of precipitous drops in the CO S Keswick releases in December do not accurately reflect current operations. Measures to reduce fall-run redd dewatering and rebuild cold water pool, e.g., when EO S storage is: 2.2 MAF, flow is 3,250 cfs; 2.8 MAF, flow is 4,000 cfs; 3.2 MAF, flow is 4,500 cfs; > 3.2 MAF, flow is 5,000 NMFS RPA Action 1.2.1: performance measures (Note: these are not prescribed targets that drive operations): • End of September carryover storage; and • Temperature compliance point locations. NMFS RPA Action 1.2.2 November through February Keswick Release Schedule: various requirements and input from interagency workgroup and Keswick releases for EOS carryover storages >2.4 MAF, 1.92.4 MAF, and drought. 171 Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ---- Conservation Hatchery Actual Current Operation Characterization in Modeling of Current Operations Scenario (COS) Inclusion in Proposed Action (PA) NMFS RPA Action 1.2.5: Winter-run passage and reintroduction program above Shasta Dam. None. None. Livingston Stone National Fish Hatchery. None. Increased use of Livingston Stone National Fish Hatchery during drou11:hts. 2.5.2.2 Conceptual Models and Stressor Linkages To link PA components to the potential effects to the species and the species life-stage, NMFS uses the SAIL conceptual models (Windell et al. 20 17), which describe the physical and biological drivers affecting the particular life-stage and life-stage transitions of winter-run Chinook salmon. The Sacramento River provides spawning, rearing, and migratory corridor habitat for winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and the sDPS green sturgeon, and similar conceptual models can apply to all of these anadromous fish species. With these models, NMFS is able to identify the PA components, the influence of those components on environmental drivers, and the habitat attributes and species response affected by changes in the environmental drivers. The environmental drivers and habitat attributes described by Windell et at. (2017) are also explicitly linked to the primary stressors affecting the species identified in the respective recovery plans (National Marine Fisheries Service 2014b, 2018g). Those stressors and their linkage to the recovery plan provide a reference for the severity of their effect on the species and how they may hinder or contribute to the recovery of the species. For the upper Sacramento River (Keswick Dam to RBDD), the first SAIL conceptual model (CMI) defines the egg incubation and alevin development stage as the duration of eggs in a redd to the emergence of fry (Windell et al. 2017). The hypothesized landscape attributes, environmental drivers, and habitat attributes affecting this life stage are described in Figure 2.5.2-6, where the stars indicate factors that are directly influenced by management actions (n.b., the Tiers in the figures from Windell et at. 2017 are not the same as the operational Tiers included in the Summer Cold Water Pool Management component of the PA; they are common in terminology only). In this case, management actions are understood to have an influence on Shasta and Trinity reservoir storage/hydrology, Keswick releases/flow, in-river fishery/trampling, and substrate size. For the life stages described in CMI, the attribute and driver of Shasta and Trinity storage/hydrology and Keswick releases likely contribute to the water temperature, flow conditions, spawning habitat availability, and predation stressors affecting recovery. The in-river fishery/trampling habitat attribute relates to the harvesting/angling impacts stressor, and the substrate size habitat attribute is a component of the spawning habitat availability stressor. 172 Biological Opinion for the Long-Term Operation of the CVP and SWP er River (Keswick Dam to RBDD) In-river Fishery/ Trampling TierJ: Habitat Attributes Disease Toxicity/ Contaminants Stranding/ Dewatering t 1 Contaminant Loading Proximity to Cont aminant Discharge l Keswick Releases/ Flows Depth Tier1: Environmental Drivers DO Bathy met ry Shasta & Trinity Storage/ Hydrology Substrate size Water Temperature tt Air Temperature Climate M obilized Substrate Erodible Sediment Supply Figure 2.5.2-6. Conceptual model (CMl) of drivers affecting the transition of winter-run Chinook salmon from egg to fry emergence in tbe Upper Sacramento River (From WindeD et al. 2017). The stars indicate factors and pathways that are hypothesized to be influenced by management actions. Also applicable to the upper Sacramento River (Keswick Dam to RBDD), the second SAIL conceptual model (CM2) defines juvenile rearing in this reach as the period from emergence as fry to juvenile migration past RBDD (Windell et al. 2017). The hypothesized landscape attributes, environmental drivers, and habitat attributes affecting this life stage transition are described in Figure 2.5.2-7, with stars indicating factors and pathways that are hypothesized to be influenced by management actions. These include Shasta and Trinity storage/hydrology, contaminant loading, fish assemblages, and Keswick release/flows and irrigation diversions. For the life stage described in CM2, the attribute and driver of Shasta and Trinity storage/hydrology and Keswick releases likely contribute to the water temperature and flow conditions stressors affecting recovery. 173 Biological Opinion for the Long-Term Operation of the CVP and SWP er River (Keswick Dam to RBDD) Stranding Cont aminants Tier3: Habitat Attributes ' Contaminant Loading Tier2: Envlronme Predation & c tT 'F on Turbidity Fish Assemblage I Refuge Availability & I' Risk water Disease Ent rainment Risk t Shallow Water Habitat Food Production & Retention Keswick Releases/ Flows Irrigation Diversions Air Temperature Drivef5 .Artificial Structures Proximity t o Cont aminant Discharge Tier 1: Erodibl e Sediment Supply Vegetat ion + Geomorphology & Bat hymet ry Shasta & -lrinity Storage/ Hydrology l Proximity to Irrigation Diversion Operat ions Climate Attributes Figure 2.5.2-7. Conceptual model (CM2) of drivers affecting th,e transition of winter-run Chinook salmon from juvenile rearing to outmigration in the Upper Sacramento River (from WindeU et aJ. 2017). The stars indicate factors and pathways that are hypothesized to be influenced by management actions. The third SAIL conceptual model (CM3) defines juvenile rearing in the middle Sacramento River (RBDD to Sacramento, including Sutter and Yolo Bypass) as the period starting with juvenile migration past RBDD until juveniles migrate past the I Street Bridge in Sacramento. The hypothesized landscape attributes, environmental drivers, and habitat attributes affecting this life stage transition are described in Figure 2.5.2-8. During this period, the factors and pathways that are hypothesized to be influenced by management actions include contaminant loading, fish assemblages, floodplain connectivity, flows/tributary reservoir releases, and water diversions/agricultural irrigation. For the life stage described in CM3, the attribute and driver of floodplain connectivity likely contributes to the loss of natural river morphology and function stressor affecting recovery. The driver of flows/tributary reservoir releases and water diversions/agricultural irrigation likely contribute to the passage impediments/barriers to migration and water temperature stressors affecting recovery. 174 Biological Opinion for the Long-Term Operation of the CVP and SWP Middle River (RBDD to Sacramento, including Sutter & Yolo Bypass) Contaminants Tier3: Habitat Attributes Predation & Competition Entrainment Risk t Contaminant Loading Tier2: Water Diversions/ Ag. Irrigation Turbidity Reservoir Air Releases Temperature Fish Assemblage Envlronmen I Drivel'$ Structures Proximity to Contaminant Discharge Tier 1: Sediment Supply Hydrology Vegetat ion +Geomorphology & Bathymetry Proximity to Water Diversion Operations Attributes Figure 2.5.2-8. Conceptual model (CM3) of drivers affecting the transition of winter-run Chinook salmon from juvenile rearing to outmigration in the Middle Sacramento River (from WindeU et al. 2017). The stars indicate factors and pathways that are hypothesized to be influenced by management actions. The sixth SAIL conceptual model (CM6) defines adult migration through the Sacramento River (San Francisco Bay to Keswick Dam) as the period starting with adult migration from the ocean to Keswick Dam in the Upper Sacramento River. The hypothesized landscape attributes, environmental drivers, and habitat attributes affecting this life stage transition are described in Figure 2.5.2-9. During this period, the factors and pathways that are hypothesized to be influenced by management actions include flood bypass weirs, Shasta and Trinity storage/hydrology, inriver fishery/poaching, and Keswick releases/Colusa Basin releases/flows. For the life stage described in CM6, the attributes and driver of Shasta and Trinity storage/hydrology, Flood Bypass Weirs, and Keswick releases/Colusa Basin Releases/Flows likely contribute to the water temperature, flow conditions, and spawning habitat availability stressors affecting recovery. The in-river fishery/poaching habitat attribute relates to the harvesting/angling impacts stressor. 175 Biological Opinion for the Long-Term Operation of the CVP and SWP l Toxicity/ Contaminants Tier3: Habitat Attributes In-river Fishery/ Poaching ------ Contaminant Loading Disease Stranding Risk Water Temperature ____,fl p....___K -.Lk +-Navigation Cues Tier2: Envlronmentol Drivers Proximity to Co ntaminant Discharge DO Flood Bypass Weirs1 Releases/ Colusa Basin Releases/ Flows Air Temperature Shasta & Trinity Storage/ Hydrology Climat e Tier 1: Landscape Attributes Figure 2.5.2-9. Conceptual model (CM6) of drivers affecting the transition of adult winter-run Chinook salmon from the ocean to the Upper Sacramento River (from Windell et al. 2017). The stars indicate factors and pathways that are hypothesized to be influenced by management actions. The last SAIL conceptual model relevant to the Upper Sacramento/Shasta Division (CM7) defines adult holding to adult spawning in the Upper Sacramento River (Keswick Dam to RBDD) as the period starting with adult migration past RBDD until spawning. The hypothesized landscape attributes, environmental drivers, and habitat attributes affecting this life stage transition are described in Figure 2.5.2-10. During this period, the factors and pathways that are hypothesized to be influenced by management actions include the hatchery broodstock program, Anderson-Cottonwood Irrigation District (ACID) Dam, Shasta and Trinity storage/hydrology, gravel quality & distribution/augmentation, Keswick releases/cold water storage/flows, and inriver fishery/poaching. For the life stage described in CM7, the attributes and driver of Shasta and Trinity storage/hydrology, TCD operations, and Keswick Releases/Cold Water Storage/Flows likely contribute to the water temperature, flow conditions, and spawning habitat availability stressors affecting recovery. ACID and Gravel Quality and Distribution/Augmentation relate to spawning habitat availability, while the in-river fishery/poaching habitat and hatchery broodstock program attributes relate to the harvesting/angling impacts and hatchery effects stressors, respectively. 176 Biological Opinion for the Long-Term Operation of the CVP and SWP l Toxicity/ Contaminants Tier3: Habitat Attributes Contaminant loading Tier2: Envlronm Drivers to/ Proximity to Contaminant Discharge Hl Competition/ lntrogression/ Broodstock Removal Spawning Habitat 1 Gravel Quality & Distribution/ Augmentation Competitors/ Mates Hatchery Broodstock Program Tier 1: Landscape Attributes Depth of Pool Disease Water Temperature Keswick Air Releases/ Cold Temperature Water Storage/ Flows r t----t-----1! Erodible Sediment ACID Geomorphic Features/ Bathymetry t Supply _j Shasta & Trinity Storage/ ' " - - - - Hydrology +-- Climate Figure 2.5.2-10. Conceptual model (CM7) of drivers affecting the transition of holding to spawning for adult winter-run Chinook salmon in the Upper Sacramento River (from WindeU et al. 2017). The stars indicate factors and pathways that are hypothesized to be influenced by management actions. Figure 2.5.2-1 shows the conceptual deconstruction of the action for the Shasta Division, which is informative in describing further the relationships between various processes and outcomes. PA components that reduce in river flows such as the Winter Minimum Flows (Section 2.5.2.3.1.1) help to build Shasta storage, which increases the likelihood ofmeeting temperature targets in-river/below dams in the summer as part of Summer Cold Water Pool Management (Section 2.5.2.3.3.1). Likewise, PA components that increase seasonal flows, such as releases to support the diversion of water supp lies under contracts (Section 2.5.2.3.2.1) and meet other requirements in the Delta, can reduce storage and the likelihood of meeting summer temperature requirements. Sometimes this relationship is explicit in the PA and BA analysis, as seen in Section 2.5.2.3.4.1 Fall and Winter Refill and Redd Maintenance, where Reclamation proposes to set the Keswick Dam fall release schedule based on Shasta EOS storage. In this case, Reclamation is proposing a range of Keswick releases and fall flows that are defined by Shasta EOS storage; higher EOS storage corresponds to higher fall flows because the need to actively build storage in the fall is relaxed. Other parts of the PA do not propose to manage to explicit metrics, such as flows or 177 Biological Opinion for the Long-Term Operation of the CVP and SWP storage targets. In these instances, for the purpose of analysis, NMFS has made conservative assumptions about the actions Reclamation may take to meet assumed operational targets (Table 2.5.2-2). We document our applied assumptions, many of which were discussed with Reclamation during technical assistance for this consultation, at appropriate points throughout our analysis. In keeping with the principle of institutionalized caution, our analysis and assumptions generally give the benefit of the doubt to the species where there iis uncertainty. 2.5.2.3 Upper Sacramento/Shasta Division Project Components Analysis 2.5.2.3.1 Shasta Winter Operations From December to February, Reclamation operates primarily for flood control and storage conservation, where the upper limit of operations is constrained by both the channel capacity within the Sacramento River and Shasta Reservoir flood conservation space. During: this season and into the spring period there are accretions (flows from unregulated creeks and other unmeasured sources) into the Sacramento River below Keswick Dam. These local accretions help to meet both instream demands and outflow requirements, minimizing the need for additional releases from Shasta and Folsom reservoirs. In wetter year types, Reclamation may be able to operate mostly to target flood control and minimum instream requirements because of the large volumes of accretions in the Sacramento River. In drier years, these accretions may be lower and, therefore, require increased releases from the upstream reservoirs to meet state permjt requirements and minimum health and safety exports in the Delta. 2.5.2.3.1.1 Winter Minimum Flows Reclamation proposes to set target base flows from Keswick Dam for the winter (December 1 through the end of February) based on Shasta Reservoir EOS storage (the PA component titled Winter-Spring Minimum Flows). These base flows consider historical performance in building Shasta Reservoir cold water pool. Table 2.5.2-4 provides Reclamation's example of possible Keswick releases based on Shasta Reservoir storage condition. Reclamation has indicated that it expects to refine this framework through future modeling efforts as part of seasonal operations planning. NMFS expects this table to reflect initial operations and has therefore analyzed effects according to this assumption. Any subsequent refinement to this schedule would require additional evaluation and potential reinitiation if effects are beyond the range evaluated in this Opinion. Table 2.5.2-4. Example of December through February Keswiek Dam Release Schedule for Various E nd of September Storages (from Table 4-9 in the ROC on LTO BA). Keswick Release (cfs) Shasta End of September Storage 3,250 :S 2.2 MAF 4,000 :S2.8 MAF 4,500 :S3.2 MAF 5,000 > 3.2 MAF 178 Biological Opinion for the Long-Term Operation of the CVP and SWP When considering effects to stressors, winter releases would most likely affect in-river Flow Conditions, Loss of Riparian Habitat and Instream Cover, and contribute to Loss ofNatural River Morphology and Function, Loss ofFloodplain Habitat, and Water Temperature. There may a[so be direct effects to redds and rearing fish. Fall-run Chinook salmon redds that are constructed during higher flows along the lateral channel margins can be dewatered as flows are reduced according to proposed operations. Likewise, juveniles rearing at the channel margin can be stranded when flows are lowered. The worst-case scenario for effects to species, in which Keswick Reservoir releases would be 3,250 cfs in December through February, would apply when EOS is less than 2.2 MAF. For the PA, CalSimll modeling indicates that Shasta end of September storage is less than 2.2 MAF in 20 percent of years. This case would result in a reduction in flows from an average September flow of 6,000 cfs below Keswick Dam to a proposed flow of 3,250 cfs in December to conserve/build storage. This is a reduction of nearly 50 percent during a time of year that is typically the start of the precipitation season. Effects of these changes to each species is identified below. Relative to the flows of the COS, CalSimii modeling of the PA shows very small differences in monthly average ·flow. For the period of December 1 to the end ofFebruary, the CalSimii modeling ofthe PA shows that Keswick releases are generally expected to provide similar or higher flows in the upper reach of the Sacramento River (ROC on LTO BA Appendix D Table 15-3) except in critical water year types, though in discussions during May 20-24, 2019, Reclamation indicated that it intends to operate to the lower flows presented in Table 2.5.2-4. 2.5.2.3.1.1.1 Winter-Run Chinook Salmon Exposure, Response, and Risk During the period of winter seasonal operations, from December 1 through the end ofFebruary, winter-run Chinook salmon fry have emerged from their redds and the majority of juveniles will have migrated past RBDD. Rotary screw trap data (University of Washington Columbia Basin Research 20 19) from the last 10 years show that 5 to 10 percent of a brood year's cohort will have yet to migrate past RBDD by December 1 (Figure 2.5.2-11), meaning there is limited potential exposure to the effects of the flow conditions and change in access to riparian habitat due to loss of natural river morphology and function in the spawning area. Flows during the juvenile rearing period (July-December) average about 9,000 cfs downstream of Keswick Dam, which poses a stranding risk to juveniles when flows are reduced. The greatest risk posed by these operations would occur when December flows are reduced to 3,250 cfs. The risk associated with tlhese operations is reflected in the proportion of years that Keswick flows in December would be no greater than 3,250 cfs. Assuming the initial operations reflected in Table 2.5.2-4, CalSimii modeling indicates that end of September storage is less than or equal to 2.2 MAF in about 20 percent of years (ROC on LTO BA Appendix D Table 3-2), and there is therefore a 20 percent probability in any year that December flows would be reduced to 3,250 cfs. Juvenile stranding generally results from reductions in flow that occur over short periods of time. The analysis uses the monthly flow results provided by CalSimii modeling ofPA operations, which is too coarse for a meaningful analysis of the short-term drivers of juvenile stranding. Though all ramping restrictions for dams on the Sacramento River and its tributaries are expected to remain the same for the PA, reservoir releases may vary from year to year in timing of flow fluctuations. There is, therefore, uncertainty to the level of effect of possible stranding on fish. For purposes of the analysis in Section 2.7 Integration and Synthesis of the combined effect of PA implementation when added to the environmental baseline and modeled climate change 179 Biological Opinion for the Long-Term Operation of the CVP and SWP impacts, the risk of flow fluctuations in the river reaches below Keswick Dam that can strand winter-run Chinook salmon is assumed to continue. The potential for juvenile stranding would also persist as operations continue to target lower reservoir releases in the fall and winter to maximize storage. For operation of the CVP, this potential stranding has been largely mitigated by maintaining flows above 3,750 cfs and by implementing gradual ramping rates pursuant to Water Rights Order 90-5. NMFS expects that stranding of at least a small proportion of winterrun Chinook salmon juveniles will continue with PA implementation and will adversely affect exposed individuals. Cumulative Distribution Frequency, Brood Years 2009- 2017 juvenile Winter Chinook Red Bluff Diversion Dam, 7/1 -6/30 Display through last 95% Date (2-10•) 0.8 c 0 - B\'2017 (591 ,066) B\'2016 (498.386) B\'201 5(324.246) B\'2014 (270,279) B\'2013 (1 .392.950) B\'2012 (1 ,1 86.248) B\'2011 (742,344) B\'201 0 0. 228.975) B\'2009 (3,274,893) Today 0.6 't: &. 2 "' 0.4 0.2 7/1 .8/1 9/1 10/1 11/ 1 1211 111 211 Based on Daily Estimat ed Passage. Preliminary dat a from USFWS Red Bluff: sub ject to revision. www.cbr.washingt on.edu/sacramento/ 27 Mar 2019 08:05:47 PDT Figure 2.5.2-11. Red Bluff Diversion Dam Juvenile Winter-run Chinook salmon passage data (2009 -2017). Winter-run Chinook salmon rearing habitat weighted usable area (WUA) analysis in the upper Sacramento River shows that for flows below 12,000 cfs, rearing habitat WUA value peaks at about 4,500 cfs for Reach 5 [Cow Creek to the ACID Dam]. For Reaches 4 (Battle Creek to Cow Creek) and 6 (ACID to Keswick Dam) with the ACID Dam boards in or out, the habitat-flow relationship remains relatively static even with increasing flow (Figure 2.5.2-12). Since the WUA value is "roughly equivalent to the carrying capacity of a stream reach, based on physical conditions" [Bovee (1978) as cited in Payne (2003)], changes in the WUA value describe the effect of flow and flow changes on the carrying capacity of a reach. A relative decrease in WUA could result in either a reduced quality of rearing or could force rearing fry and juveniles to move out of the habitat in to less ideal condition. For either case, a reduced WUA is expected to lead to reduced growth. In the case of this species, the WUA analysis shows the peak habitat carrying 180 Biological Opinion for the Long-Term Operation of the CVP and SWP capacity for all upper Sacramento River reaches combined occurs when Keswick releases are approximately 4,500 cfs. This release is within the higher end of the proposed release schedule in Table 2.5.2-4; greater habitat reductions as measured by WUA occur at flows less than or greater than 4,500 cfs and are expected to occur when operations require flows to be at those lower levels. With relation to the stressors Loss ofRiparian Habitat and Instream Cover, Loss of Natural River Morphology and Function, and Loss of Floodplain Habitat, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover in the immediate area of releases but perhaps moreso further downstream (e.g., less frequent inundation of side channels, floodplains, and overtopping of flood system weirs into the Sutter and Yolo bypasses). However, we note that the lower flows proposed in the PA during this time of year would not likely result in changes to riparian habitat, morphology and function, or floodplain habitat in the vicinity of Keswick releases. With regards to the Water Temperature stressor, NMFS notes that reduced winter flows at Keswick Dam can contribute to the ability to increase spring Shasta Reservoir storage levels for the PA relative to recent years. This is expected to increase the available CWP and, therefore, the likelihood of sustaining lower water temperatures during the summer temperature management season. The exposure, response, and risk to winter-run Chinook salmon to the Winter Minimum Flows component of the PA is summarized in Table 2.5.2-5. 181 Biological Opinion for the Long-Term Operation of the CVP and SWP Winter-run Juveniles 350000 300000 VI c: ::J <( ::J $ tlD c: 250000 200000 150000 ..... ro
  • 600000 !'0 500000 Q) ,_ <( Q) ..0 400000 !'0 1/) :::> "0 300000 Q) ....... .s:::. tl.O 200000 .a> s 100000 0 0 5000 10000 15000 20000 Flow(cfs) 6: ACID Dam boards in ........ segment 5 25000 30000 35000 6: ACID Dam boards out ........- segment 4 Figure 2.5.2-13. J uvenile fall-ru n Chinook salmon rearing WUA/Fiow relationship (Keswick Dam to Battle Creek). Reach 6 is Anderson-Cottonwood Irrigation District (ACID) Dam to Keswick Dam, Reach 5 is Cow Creek to ACID Dam, and Reach 4 is Battle Creek to Cow Creek. Information provided by Reclamation. Fall-run Chinook salmon WUA analysis is used as a surrogate for CV spring-run Chinook salmon in the upper Sacramento River (Battle Creek to Keswick Dam) (Figure 2.5.2-13). This analysis shows a decreasing spawning habitat WUA value that corresponds to decreasing flow from 6,000 cfs to 3,250 cfs for segments 5 (Cow Creek to the ACID Dam) and 6 (ACID to Keswick Dam). For segments 4 (Battle Creek to Cow Creek) and for segment 6 with the ACID Dam boards out, the habitat flow relationship peaks at the lowest studied flows (3,250 cfs). Overall, this WUA analysis shows a peak habitat carrying capacity for fall-run, and therefore, CV spring-run Chinook salmon, at flows around 5,000- 6,000 cfs, which is greater than the range proposed as example initial operations in Table 2.5.2-4. This reduced WUA is expected to lead to reduced growth. 183 Biological Opinion for the Long-Term Operation of the CVP and SWP With relation to the stressors Loss ofRiparian Habitat and Instream Cover, Loss ofNatural River Morphology and Function, and Loss of Floodplain Habitat, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover in the immediate area of releases but perhaps moreso further downstream (e.g., less frequent overtopping ofFremont Weir). However, we note that the lower flows proposed in the PA during this time of year wo11.1ld not likely result in changes to riparian habitat, morphology and function, or floodplain habitat in the vicinity of Keswick releases. The exposure, response, and risk to CV spring-run Chinook salmon to the Winter Minimum Flows component of the PA is summarized in Table 2.5.2-S. 2.5.2.3.1.1.3 CCV Steelhead Exposure, Response, and Risk CCV steelhead express a diverse array of life-history strategies including both anadromous and resident (i.e., rainbow trout) life histories. Anadromous and resident life histories can be adapted by individuals from the same sibling cohort, making determinations regarding run timing difficult. Rotary screw trap data from the last 10 years show that, generally, CCV steelhead begin their emigration from the upper Sacramento River starting in mid-March to early April. During the December-February timing of operations in the Winter Minimum Flows PA component, it is likely that many of the steelhead redds and a large proportion of steelhead juveniles will be exposed to the winter flow conditions and reduced access to riparian habitat. The greatest risk posed by these operations would occur when December flows are reduced to 3,250 cfs. The risk associated with these operations is reflected in the proportion of years that Keswick flows in December would be no greater than 3,250 cfs. Assuming the initial operations reflected in Table 2.5.2-4, CalSimii modeling indicates that end of September storage is less than or equal to 2.2 MAF in about 20 percent of years (ROC on LTO BA Appendix D Table 3-2), and there is therefore a 20 percent probability in any year that December flows would be reduced to 3,250 cfs. The species response to winter flows of 3,250 cfs in the upper Sacramento River would include redd dewatering, stranding, poorer feeding conditions, increased competition and predation related to less floodplain and side-channel habitat and reduced emigration flows. Similar to winter-run Chinook salmon, juvenile stranding generally results from reductions in flow that occur over short periods of time, and analytical planning tools cannot predict with certainty the level of effect of possible stranding on fish. For purposes of the analysis in Section 2.7 Integration and Synthesis ofthe combined effect ofPA implementation when added to the environmental baseline and modeled climate change impacts, the risk of flow fluctuations in the river reaches below Keswick Dam that can strand steelhead is expected to continue. The potential for juvenile stranding would also persist as operations continue to target lower reservoir releases in the fall and winter to maximize storage. NMFS expects that stranding of at least a small proportion of steelhead juveniles will continue with PA implementation and will adversely affect exposed individuals. With regard to CCV steelhead redds, the USFWS (2006) flow fluctuation and redd dewatering relationship indicates that a flow reduction from 8,000 cfs average flow during the spawning period to 3,250 cfs as prescribed by the end of September Shasta storage level would be expected to dewater approximately 31 percent of steelhead redds. Likewise, flow reductions from 8,000 cfs spawning flows to 4,000, 4,500 and 5,000 cfs would be expected to dewater approximately 22, 17, and 12 percent of redds, respectively. The species response to winter flows of 3,250 cfs in the upper Sacramento River would include dewatering, which could lead to increased egg mortality. 184 Biological Opinion for the Long-Term Operation of the CVP and SWP Steel head 180000 ll c => ro 160000 140000 Q) '- <( 120000 Q) ::0 100000 VI 80000 ro => "'0 ....... 60000 tlO "Qj 40000 Q) ..c 5 20000 0 0 5000 10000 15000 20000 25000 30000 35000 Flow (cfs) Segment 6: ACID Dam boards in - e -Segment 6: ACID Dam boards out ......... segmentS Figure 2.5.2-14. CCV steelhead spawning WUA/Fiow relationship (Keswick Dam to Battle Creek). Reach 6 is ACID Dam to Keswick Dam, Reach 5 is Cow Creek to ACID Dam, and Reach 4 is Battle Creek to Cow Creek. Information provided by Reclamation. Overall, CCV steelhead WUA analysis in the upper Sacramento River (Battle Creek to Keswick Dam) shows a decreasing spawning habitat WUA value that corresponds to flows greater than 3,250 cfs (Figure 2.5.2-14). For segments 5 (Cow Creek to the ACID Dam) and 4 (Battle Creek to Cow Creek), the habitat-flow relationship shows a slight increase in value for flows between 3,250 cfs and 7,000 cfs, with only a slight peak at flows around 6,000 cfs. In this case, the WUA analysis shows an optimum habitat carrying capacity at the lowest modeled flows, around 3,250 cfs. With relation to the stressors Loss ofRiparian Habitat and Instream Cover, Loss ofNatural River Morphology and Function, and Loss of Floodplain Habitat, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover in the immediate area of releases but perhaps moreso further downstream (e.g., less frequent overtopping of Fremont Weir). However, we note that the lower flows proposed in the PA during this time of year would not likely result in changes to riparian habitat, morphology and function, or floodplain habitat in the vicinity of Keswick releases. The exposure, risk, and response to steelhead to the Winter Minimum Flows component of the PA is summarized with similar information for other species in Table 2.5.2-5. 2.5.2.3.1.1.4 sDPS Green Sturgeon Exposure, Response, and Risk Because sDPS green sturgeon life history timing is such that spawning occurs from April through July with the median spawning in May (Poytress et al. 2015), it is unlikely that sDPS 185 Biological Opinion for the Long-Term Operation of the CVP and SWP green sturgeon will be present in the upper Sacramento River in the December-February period when Reclamation is managing the Winter Minimum How component of the PA. However, adult green sturgeon migrate up river in March to early April, and spawning migrations often coincide with high Delta outflow in the spring. Therefore reductions in late winter flows that affect Delta outflow in February and March could impact spawning migration cues. While changes in low flows are unlikely to influence the frequency, magnitude, or duration of the higher flows to which sturgeon respond, we consider that the managed changes in the hydrograph can reduce the strength of the seasonal spawning cues. Green sturgeon also over-summer in spawning habitats and may be triggered to outmigrate with the first high flows, which sometimes occur in December. Though the extent of this oversummering is not defined, prolonged low w inter flows could strand adult green sturgeon in spawning habitat. This was recently observed in the Feather River when green sturgeon outrnigrated after spending more than a year in the upper river. While additional water coming into the system below Keswick Dam could reduce potential effects of prolonged minimum flows. this component of operation is expected to result in reduced survival probability in the years in which it occurs. The exposure, risk, and response to green sturgeon to the Winter Minimum Flows component of the P A is summarized in Table 2.5.2-5. Table 2.5.2-5. Summary Exposure, Risk, Response table for species and life-stages affected by stressors of the Winter Minim urn Flows component of the PA. Species Lifestage Exposure Risk Stressor • Winterrun Chinook salmon Juvenile s 5%- 10% of population (Medium) • • years • • • • cv Springrun Chinook salmon Juvenile s 90-95% of population (Large) years • • 186 Water Temperature Flow Conditions Loss of Riparian Habitat and Instream Cover Loss ofNatural River Morphology and Function Loss of Floodplain Habitat Flow Conditions Loss of Riparian Habitat and Instream Cover Loss ofNatural River Morphology and Function Loss of Floodplain Habitat Response to Exposure and Risk as Expected Change in Fitness (Method Used) Decreased growth • rate (WUA analyses) • Increased survival probability (temperature analyses) • Reduced survival probability (dewatering, stranding) • Reduced growth rate Biological Opinion for the Long-Term Operation of the CVP and SWP Species Lifestage Exposure Risk Stressor • Spawnin g Steelhea Adults, d Redds, Juvenile s • • All (Large) -20%of years • • Green Sturgeo n Adults Small -20% of years • Spawning Habitat Availability Flow Conditions Loss of Riparian Habitat and Instream Cover Loss ofNatural River Morphology and Function Loss of Floodplain Habitat Loss ofNatural River Morphology and Function Response to Exposure and Risk as Expected Change in Fitness (Method Used) • • • Increased growth rate (WUA analyses) Reduced survival probability (dewatering, stranding) Reduced survival probability (stranding) 2.5.2.3.2 Shasta Spring Operations In the spring, the minimum winter reservoir releases (described in Section 2.5 .2.3 .1.1 Winter Minimum Flows) are maintained until flows are needed to support Sacramento River instream demands and Delta outflow requirements, or releases are required for flood control operations. CVP releases for Delta outflow requirements are coordinated to draw from both Shasta and Folsom reservoirs. Both reservoirs have substantial temperature control requirements, and both need to build substantial storage to be able to fully meet their respective summer temperature compliance requirements. The P A indicates that Reclamation operations intend to balance each reservoir's demands so that the filling of one limits the impact to the other. An overarching objec6ve for Reclamation when operating the CVP is to attain maximum reservoir storage by the end of the flood control season (i.e., the end of May) while still meeting all other authorized project purposes. NMFS used the modeling provided with the February 5, 2019 BA to evaluate the effects of the PA, though we consider the uncertainties and discrepancies identified in Section 2.5 .2.1 .2 Project Uncertainties in our analysis. 2.5.2.3.2.1 February Forecast Process and Contractual Water Allocations For the current operations, Reclamation targets February 20 of each year to make its initial forecast of deliverable water based on an estimate of precipitation and runoff within the Sacramento River basin using the 50 and 90 percent probabilities of exceedance. Reclamation provides this information to water users with an estimate of initial contractual water allocations so that the water users may begin their seasonal planning. Reclamation also provides this forecast to NMFS so that NMFS may determine the likelihood of achieving either a temperature compliance point at Balls Ferry during May- October and/or an EOS storage of at least 2.2 MAP 187 Biological Opinion for the Long-Term Operation of the CVP and SWP based on the 90 percent forecast. If neither objective is likely to be met, Reclamation will consult with NMFS monthly on Keswick releases. From March to May, Reclamation submits to NMFS a forecast of monthly average release schedules and proposed temperature compliance point. Based on information provided on May 20, 2019, to NMFS by the Department of the Interior regarding the ROC on LTO PA, NMFS assumes that Reclamation will use a similar conservative forecast for seasonal planning of reservoir releases for the PA (including developing initial and updated allocations) and temperature management planning. This includes monthly release forecasts and associated allocations based on a 90 percent exceedance inflow forecast through September. Reclamation may deviate from relying on the 90 percent exceedance inflow forecast in order to develop a conservative outlook. Such instances include scenarios when a wetter hydrology produces a more conservative outlook, or the actual conditions are significantly drier than the existing forecast such that a more conservative forecast is appropriate. The PA also specifies that when the March 90 percent exceedance runoff forecast and temperature projection indicate a May 1 Shasta storage ofless than 2.5 MAF, Reclamation would initiate discussions with NMFS and the USFWS regarding species intervention. Although not described in detail in the PA, a required element of the February forecast is the initial allocation of deliverable water (primarily delivered in May through October) that includes the north-of-Delta and south-of-Delta allocations (ROC on LTO BA). As described in Section 2.5.2.1 Shasta Annual Operations, releases made from Shasta and Keswick dams to contribute to meeting these allocations have an effect on Reclamation's ability to build or maintain storage, which in tum affects Reclamation's ability to provide adequate temperatures for spawning fish and incubating eggs during the summer. CalSimii modeling ofboth the COS and the PA show relatively similar delivery amounts for the north-of-Delta deliveries for the two scenarios (see Table 2.5.2-6 and Table 2.5.2-7). However, based on the PA modeling results, Reclamation does not show frequent instances of curtailing water service allocations to achieve a higher storage on May 1. While Section 2.5.2.3.3 Shasta Summer Operations describes the modeled likelihood of Reclamation operating to a particular "Tier" of summer cold water pool management, unforeseen events (e.g., reduced solar radiation from cloud or smoke cover, unusual Delta salinity conditions) can require a change of Tier within a year. In the absence of commitment in the PA to build storage to a particular storage metric during the spring, NMFS relies on the modeled characterization of May 1 storage and temperature management conditions. To address the uncertainty related to species' exposure to temperature conditions, we have used the modeling results of the PA as a boundary characterization of the frequency of exposure to temperatures in the summer. Moreover, because the P A includes full implementation and performance of northof-Delta settlement contracts and is seeking take authorization for those contracts, this Opinion analyzes the effects of Reclamation's operations to meet those contract requirements on the likelihood of attaining temperature metrics. We note that the deliveries for north-of-Delta contracts commonly begin in April, the start of the spring operations period, and that deliveries are of small magnitude during this month. Before reaching the highest demands in summer months, combined deliveries average more than 300 TAF in May, even in drier water year types (Table 2.5.2-6 and Table 2.5.2-7) .. Reclamation uses a rule of thumb relationship between storage on May 1st and achievable seasonal temperatures along with modeling based on expected available coldwater pool to select a tier. An assumption of historical deliveries is incorporated into the rule of thumb relationship and a conservative estimate of deliveries will be incorporated in the temperature modeling. For this reason, 188 Biological Opinion for the Long-Term Operation of the CVP a nd SWP Reclamation does not expect a change in tiers between May 1st and May 151h (the start of temperature management) due to expected water deliveries nor does Reclamation expect a change in tiers throughout the season due to forecasted deliveries. Because these demands are estimated when tiers are selected, the effects of these releases are assumed to be covered in the analysis of the PA and Reclamation would not anticipate a reduction in the performance of the PA due to months ofhigh deliveries. The combined modeled north-of-Delta deliveries in April, May, and June even in dry years average over 800 T AF (see rows corresponding to "'D" under "AVG BY WYT" in Table 2.5.2-6 and Table 2.5.2-7). NMFS notes that the recent experience of the extreme drought in 2014 through 2016 and associated modelling scenarios demonstrates that the volume and stability of cold water throughout the temperature management season can be adversely affected by June and early July deliveries in addition to deliveries in April and May. Table 2.5.2-6. Average north-of-Delta water service agricultural service contract deliveries by month and water-year type for both the COS 10 and PA. COS: North-of-Delta Deliver lea to CVP ACJ s.rviee contractors in TAF ------ -----AVG: MIN: MAX: AvgbyWYT W: AN: BN: 0: OCT NOV DEC JAN 4.7 0.0 14.9 0.2 0.0 1.9 0.0 0.0 0.0 PRV 6.9 5.2 4.5 3.0 PRV 0.3 0.1 0.4 0.0 0.1 PRV 0.0 0.0 0.0 0.0 0.0 ----> <··--- ----- ------ Allocat.ion/Cont.rac::t. Year FEB MAR APR 0.0 0.0 0.0 0.1 0.0 4.4 1.2 0.0 17.2 18.5 0.0 44.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.2 0.0 0.8 0.5 3.2 0.9 1.5 21.5 23.7 22.8 13.2 11.1 ------ -----AVG: MIN: MAX: AvgbyWYT W: AN: BN: 0: C: --··> Mer-Feb Allocat.ion JUN JUL AUG SEP 36.9 0.0 63.8 47.6 0.0 81.5 56.9 0.0 95.8 45.4 0.0 77.5 20.2 0.0 37.5 24.6 0.5 65.5 230.3 0.0 357.1 65% 0% 100% 50.2 50.0 38.4 24.9 12.8 68.0 65.3 43.1 30.6 17.0 81.4 77.3 52.7 35.9 20.3 65.4 61.1 41.8 28.7 16.3 30.0 27.5 16.8 12.2 7.5 27.0 28.1 32.3 20.3 15.6 324.7 308.4 223.7 149.4 88.6 91% 86% 63% 42% 25% PA: North-of-Delta Deliveriea to CVP Aq Service Contractor• <----- Fu 11 Year Oct-Apr TOT Full Year Oct-Apr Mar- F@b Allocation OCT NOV DoC JAN rse MAR APR MA'l J UN JUL AUG SSP 5.2 0.0 14.9 0.2 0.0 1.9 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.0 4.4 1.4 0.0 19.9 20.8 0.6 51.5 40.6 0.9 63.8 52.5 1.2 81.5 62.7 1.4 95.1 50.1 1.1 75.8 22.1 0.5 37.5 PRV 7.2 5.5 5.7 3.7 2.4 PRV 0.3 0.1 0.5 PRV 0.0 0.0 0.0 0.0 0.0 0.8 22.6 51.0 70.0 83.7 67.1 30.8 28.5 333.8 0.0 0.0 0.0 0.5 0.2 0.0 0.6 4.3 1.1 1.7 25.5 28.8 16.0 12.7 51.2 50.0 30.4 14.9 69.7 54.9 37.4 19.3 82.2 67.2 44.0 65.1 53.3 35.2 18.8 29.2 21.1 15.0 8.1 30.2 40.0 24.2 18.1 328.3 285.8 182.8 101.4 o.'o o.o 0.1 0.0 o.o 0.0 10 23.3 TOT 27.7 0.6 72.7 NMFS notes that the COS modeling does not reduce deliveries to agricultural service contractors, an action that is an option in annual operations. 189 PCT in TAl' ------ ------ Allocation/Contract Year TOT TOT 254.8 6.2 357.1 PCT 71% 2% 100% 93% 92% 80% 51% 28% Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.2-7. Average north-of-Delta settlement contract deliveries by month and water-year type for both the COS 11 and PA. COS: North-of-Delta Deliveriea to CVP Settle •ent Contractor• in TAF ··---- ------ ------ -----AVG: MIN: MAX: W: AN: BN: 0: ----> <----- ------ ------ Allocation/Contract Year Full Year Fraction of Oct-Apr Mar-Feb Hist Max TOT 'l'OT PCT fEB MAR APR MAY JUN JUL AUG SEP 1.4 0.0 9.0 0.6 0.0 13.6 7.1 0.0 58.6 81.0 29.1 123.7 305.9 145.5 358.8 352.0 287.4 398.9 381.6 322.0 407.7 294.3 241.0 331.1 77.1 23.5 89.7 197.1 60.2 302.1 1608.7 1388.2 1719.1 94% 81% 100% 0.8 335.8 94% OCT NOV DEC JAN 75.7 6.2 95.9 24.0 3.5 43.7 7.3 0.0 20.1 PRV PRV PRV 78.5 75.4 75.3 24.1 23.7 26.6 8.8 6.2 7.4 0.5 2.9 0.0 0.0 1.9 3.1 1.6 13.3 70.0 78.0 90.3 301.7 300.2 314.4 350.0 364.6 392.3 388.8 390.3 318.6 298.8 293.4 81.3 79.0 69.8 170.6 179.8 219.5 1617.0 1607.9 1646.4 76.9 68.3 20.8 27.3 7.6 4.5 1.7 1.8 0.9 0.9 7.3 15.3 83.2 95.5 320.3 289.8 378.9 332.8 384.4 338.4 282.8 256.6 76.8 72.9 208.6 233.4 1640.5 1504.2 94% 96% 95% 88% PA : North-of-Delta Delive riea to CVP Settle•ent Contractor• in TAl' Hist Max 'l'OT PCT JUN JUL AUG SEP 1 1 7 81 352 382 294 77 187 1599 93% 0 9 0 14 0 59 29 124 306 146 359 287 399 322 408 238 335 24 90 66 295 1372 1715 80% 100% 1 0 3 2 2 0 0 2 1 1 3 2 13 7 70 78 90 83 302 300 314 320 336 350 365 379 392 389 390 384 319 299 293 283 94% 93% 95% 95% 96 290 333 338 255 159 169 208 201 227 1607 1597 1637 1629 15 81 79 70 77 71 1498 87% MAX: 86 30 12 49 7 MIN: 60 6 0 20 PRV PRV PRV 62 60 61 59 30 29 32 27 9 6 7 8 59 33 5 0: C: Mar-Feb TOT MAY JAN BN: full rear Fraction of Oct-Apr APR DEC AN: ------ ------ Allocation/Contract Year MAR NOV W: <----- fEB OCT AVG: ----> Reclamation has stated that springtime operations of Shasta and Keswick dams are intended to support instream demands on the mainstem Sacramento River and Deha outflow requirements. In February and March 2019 conversations with NMFS, Reclamation formally stated that they agree with the interpretation of the PA that contract supply quantities will not be reduced to build storage or meet temperatures in a specific summertime operational Tier. NMFS also considers that Reclamation lacks legal ability to deliver less than the base contract amounts to the Sacramento River Settlement Contractors, and notes that the extreme drought in 2014 through 2016 and associated modelling scenarios demonstrated that the volume and stability of cold water throughout the temperature management season can be adversely affected not only by April and May deliv,eries but also by deliveries in June and early July. The combined modeled north-of-Delta deliveries for the PAin April, May, and June in dry eyars can average over 800 TAF (see rows corresponding to "D" under "AVG BY WYT" in Table 2.5.2-6 and Table 2.5 .2-7) and NMFS considers that the modeling does not capture any modifications to the timing of these deliveries to futher assist temperature management. During Shasta Critical Years, as defined under the Sacramento River Settlement Contracts, those contract quantities are reduced to 75 percent. However, the CalSimll results are the best available information for evaluating effects of spring operations for the PA and COS. NMFS has considered historical operations regarding these contracts but does not have adequate information to quantitatively or qualitatively include deviations from the modeled operations into the assessment of effects. NMFS therefore assumes that the CalSimll model results of flows below Keswick Dam in 11 NMFS notes that the COS modeling does not reduce deliveries to agricultural service contractors, an action that is an option in annual operations. 190 Biological Opinion for the Long-Term Operation of the CVP and SWP February through May provide a reasonable approximation of the effects of operational decisions, including fulfilling underlying contractual obligations, that are being made regarding spring operations for both the COS and the PA. Table 2.5.2-6 and Table 2.5.2-7 capture modeled volumes of storage draw down to meet contracts which can be considered when assessing impacts of deliveries on summertime temperature management actions. This modeling shows that from February through May, the PA is very similar to COS with PA flows below Keswick Dam a few hundred cfs higher than the COS (Table 2.5.2-8). Though it is limited in that it cannot capture all conditions or constraints on operations, the CalSimii modeling shows that in the spring, the PA would increase north-of-Delta agricultural service contract deliveries (Table 2.5.2-6), decrease Delta outflow (Table 2.5.2-9), and increase total exports (Table 2.5.2-10) compared to the COS. Table 2.5.2-8. CaiSimii modeling results of flows below Keswick, PA minus COS (excerpted from ROC on LTO BA, 15-3 of Appendix D). Proposed Action 011519 minus Current Operations 011319 IIOI1INy f -jCfSJ oct Nov Dec .J¥1 flO -3,506 -3.836 -2.657 -2.313 2.881 2.738 1.564 4 11 3.372 2.020 1.1103 .0% -62 21 I 4811 -33 2.020 140 ·2. 183 1.0011 1,345 5GY. ·112 · 1.2'1 5110 0 750 60% 58 -1.311 -272 2011 0 0 0 0 0 654 2.124 0 0 0 -25 -186 40 0 0 0 0 0 0 0 0 0 0 0 .JS -1.545 Q-40 782 3tl0 408 07 -3.522 .J.Oi!i I 2,065 1218 10 1,108 1.300 170 1,170 85 080 a.law NonnOII (IlY.J ·193 1 -7$ 1.014 Dly (U %) 151 102 370 125 222 38 ·24 sutiatic IUr Jun Sip Jill Pro!litility o1 10% 2011 JOT. 70T. 8011 goy, 1.100 1.374 1,340 0 0 -128 771 ..:W7 9CO ·122 4911 102 -99 -222 523 48 .JO -12 -87 50 114 270 135 75 119 13Q 135 530 643 -93 120 -2.501 114 249 484 -4,706 4 39 077 60 188 173 g 880 100 370 1.327 ..as 20 183 515 I 383 22 850 1.073 ·133 -120 424 -5-S 233 746 ...t66 Hl3 -56 92 5QS 402 307 187 882 0 0 0 e34 790 1133 025 049 520 0 -6.327 -3,597 .,:;3 -430 -355 -176 22 lOng""" fOVtl'tOI'Iml {16%) e or lhe .. •"""be<> po'IO1E41, 1999} cT0.:eft .... d .U "'""""'" ,,. :mJo'.d •l Ell lbfr ""'9·T.,...) OS •i> 2025 a.....oh c ''"' dml "Cc:ob"" ' 'lo! VJoll:\'0 .... .. :Po!<>'!IO ,tl.,. o-d 15"" ><• ... = ._.., Table 2.5.2-10. CaiSimll modeling results of total exports, PA minus COS (excerpted from ROC on LTO BA, Table 53-3 of Appendix D). Proposed Action 011519 minus Current Operations 011319 NOv Sblietic f tD - AfJ! lhy JUI PrOCaei.lity of a..-lo% 20% Jt% 3.461 3,638 3.215 1,9-45 2.081 2.330 1,575 1.2911 361 182 27 6 0% TU% 10% -17• 'lCW. 32 un -35 ·1st! -1.&70 533 312 31ol8 3a8 380 -773 -700 -231 496 -700 -47 -21 -118 4111 -170 -126 46 -140 ·78 -4.49 -565 4.529 4.815 4,571 4.1174 15 -359 4,4'117 4,235 213 63 4,438 4.08& 211 318 1, 145 1,225 3,8.38 3.8113 2.83& 2.211 1,401 1.3<04 1,734 2.304 2.111S 1154 877 2,971 373 nil 1,381 1.703 2.1151 393 742 680 3.062 1,7107 -521 -SO -3S4 -324 747 II 0 144 .S3 0 D -20 0 0 0 0 130 1,441 -506 -415 -783 -1 462 -&65 1126 120 151 32 1,0 1'11 747 -136 -173 -105 2.077 660 -272 149 21:5 .u -79 400 225 -sa 1,296 543 longTorm lltriod' fUD 1.3117 Wll(32leo) AI>OVO NOmlal (liY,) gg Btlow NOmoal (13%) 445 24 Dry 12•"J Cribeoi(1S'llo) • a-1 tl'le az,-u 2..645 d 2.341 258 52 -211 34 -474 -1.579 -61:5 -157 -113 312 -31 sgg 1411 1,071 737 148 110 1,371 1.7011 -SCI2 ·22S 548 1,23-4 1.535 .t b:.,d.-&-•4 t, ti-t< S.="'• llbValcy t NNO t Sep Doc Nov Date 52 50 56 54 58 Daily Average Temperature ('F) Hlndcast for Year 2015 Note: Redel dopos1hon dates are shown with wh1te Clrclos (size scaled by numbor of redds). and magenta 60 62 rupresent data hll emergence "' ..!! .."' E 0 .."' E _g E "' "'c 0 .. 0 u c .\! " i5 Feb Mar Apr May Jun Jul Aug Sep Oct Nov Date QO/o 10% 20% 30% 40% 50% 60% 70% 80% 100% ProbabilityTemperalure·Dependenl Egg SU<'61°F (Medium), 76% of days >53.5°F (Aug - Oct.) (Large) 1% of days >6 1°F (Small) 80% of days >53.5°F (Aug -Oct.) (Large) 13% of days >6 1°F (Medium) 97% of days >53.5°F (Aug -Oct.) (Large). 36% of days >61°F (Medium), 99.6% of days >53.5°F (Aug -Oct.) (Large). Stressor Response to Exposure and Risk as Expected Change in Fitness (Method Used) Water Temperature • Reduced reproductive success • Reduced survival probability 17-35% of years Water Temperature • Reduced reproductive success • Reduced survival probability 7-15% of years Water Temperature • Reduced reproductive success, • Reduced survival probability 5-7% of years Water Temperature • Reduced reproductive success, • Reduced survival probability Risk 45-68% of years 2.5.2.3.3.1.3 CCV Steelhead Exposure, Response, and Risk By the start of Summer Cold Water Pool Management, juvenile CCV steelhead will have started their migration out of the upper Sacramento River and tributaries with about 10 percent of juveniles having already passed RBDD by May 15 (University of Washington Columbia Basin Research 20 19). The remaining 90 percent of juvenile CCV steelhead still in the upper Sacramento River would experience the conditions upstream ofRBDD associated with the early temperature management season. By July, some adult CCV steelhead will have passed upstream of the RBDD with peak migration in September and October (McEwan 2001). There is limited information regarding CCV steelhead spawning locations in the Sacramento River, but since 223 Biological Opinion for the Long-Term Operation of the CVP and SWP CCV steelhead spawning and eggs/alevin incubation occurs from November through April, effects to eggs are not considered under the effects of Summer Cold Water Pool Management. Tier 1 As described for winter-run Chinook salmon, Reclamation would determine that Tier 1 operations apply as an initial early season target in approximately 68 percent of years based on the CalSimii modeling. HEC-5Q modeling of the PA indicates that during the temperature management seasons of Tier 1 years, the threshold temperature of 61 °F 7DADM for juvenile rearing, when converted to DAT, is exceeded in 23 percent of days from May 15 - October 31. For adult CCV steelhead migration, the threshold of 68°F is not exceeded during Tier 1 at RBDD during this period in Tier 1 years. Tier 2 As described for winter-run Chinook salmon, Reclamation would determine that Tier 2 operations apply as an initial early season target in approximately 17 percent of years. HEC-5Q modeling of the PA indicates that during the temperature management seasons of Tier 2 years, the threshold temperature of 61 op 7DADM for juvenile rearing, when converted to DAT, is exceeded at RBDD in 35 percent of days from May 15 - October 31. For returning adult CCV steelhead, the migration temperature threshold of 68°F is not exceeded at RBDD in Tier 2 years during this period. Tier 3 As described for winter-run Chinook salmon, Reclamation would determine that Tier 3 operations apply as an initial early season target in approximately 7 percent of years. HEC-5Q modeling of the PA indicates that during the temperature management seasons of Tier 3 years, the threshold temperature for of 61 op for juvenile rearing, when converted to DAT, is exceeded at the RBDD in 65 percent of days from May 15 -October 31. However, for returning adult CCV steelhead, the migration temperature threshold of 68°F would be exceeded in about 1 percent of days at RBDD during this period. Tier 4 As described for winter-run Chinook salmon, Reclamation would determine that Tier 4 operations apply as an initial early season target in approximately 7 percent of years. The HEC5Q modeling of the P A indicates that during the temperature management seasons of Tier 4 years, the threshold temperature of 61 °F for juvenile rearing, when converted to DAT, would be exceeded at the RBDD in about 77 percent of days from May 15 - October 31. For returning adult CCV steelhead, the migration temperature threshold of 68°F would be exceeded at RBDD in less than 15 percent of days May 15 - October 31. Temperature exceedances above the 61 op 7DADM EPA Region 10 threshold for juvenile CCV steelhead rearing could cause a competitive disadvantage with other fish, elevated disease rates and even death (Water Temperatures). For returning adult CCV steelhead, the migration temperature threshold of 68°F would be exceeded in less than 15 percent of days at RBDD during this period. Effects of this component of the P A on CCV steelhead are condensed and summarized in Table 2.5.2-16. 224 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.2-16 Summary Exposure, Risk, Response table for steelhead life-stages affected by stressors of Summer Cold Water Pool Management. Tier Life-stage Exposure Risk Response to Exposure and Risk as Expected Change in Fitness (Method Used) Stressor 1 Juvenile 12%of days >6 1°F atRBDD (Medium) 45-68% of years Water Temperature • Reduced lifetime reproductive success 2 Juvenile 17-35% of years Water Temperature • Reduced lifetime reproductive success 3 Adult (migration) , Juvenile 20%of days > 61 op at RBDD (Medium) 1% of days > 68°F at RBDD (Minor) 44%of days > 61 op at RBDD (Medium) 15% of days> 68°F at RBDD (Medium) 59% of days > 61 op at RBDD (Large) 7-15% of years Water Temperature • Reduced reproductive success, Reduced lifetime. reproductive success 4 Adult (migration) , Juvenile • 5-7% of years Water Temperature • • Reduced reproductive success, Reduced lifetime reproductive success 2.5.2.3.3.1.4 Green Sturgeon Exposure, Response, and Risk The timing of Summer Cold Water Pool Management is such that it coincides w ith the peak of egg, larval and juvenile green sturgeon presence in the upper Sacramento River. Occurring from April to July, green sturgeon spawning in the Sacramento River extends from Cottonwood Creek just downstream of Balls Ferry to Hamilton City (Poytress et al. 2015). Tier 1 As described for winter-run Chinook salmon, Reclamation would determine that Tier 1 operations apply as an initial early season target in approximately 68 percent of years based on 225 Biological Opinion for the Long-Term Operation of the CVP and SWP the CalSimii modeling. Tier 1 operations are not expected to have a lethal effect on sDPS of green sturgeon eggs based on the HEC-SQ modeling of the PA which indicates that during Tier I years, the threshold temperature of lethal effect (7l.S°F) is not exceeded at Hamilton City from May 1S - October 31. Sublethal effects would be expected in Tier 1 years; 31 percent of Tier I days exceed the threshold of 63 .S°F at Hamilton City from May IS - October 31. Tier 2 As described for winter-run Chinook salmon, Reclamation would determine that Tier 2 operations apply as an initial early season target in approximately 17 percent of years. HECSQ modeling of the PA indicate that during Tier 2 years, the threshold temperature of7l.S°F for egg mortality is not likely to be exceeded at Hamilton City during May IS - October 31. Sublethal effects would be expected in Tier 2 years; 42 percent of Tier 2 days exceed the threshold of 63 .S°F at Hamilton City from May lS -October 31. Tier 3 As described for winter-run Chinook salmon, Reclamation would determine that Tier 3 operations apply as an initial early season target in approximately 7 percent of years. HEC-SQ modeling of the PA indicate that during Tier 3 years, the threshold temperature of7l.S°F for egg mortality is exceeded in less than 1 percent of days at Hamilton City during May IS - October 31. Sublethal effects are expected in Tier 3 years; 67 percent of Tier 3 days exceed the threshold of 63 .5°F at Hamilton City from May lS -October 31. Tier 4 As described for winter-run Chinook salmon, Reclamation would determine that Tier 4 operations apply as an initial early season target in approximately 7 percent of years. HEC-SQ modeling of the PA indicate that the threshold temperature of7 l.S°F for egg mortality is exceeded in 8 percent of Tier 4 days at Hamilton City from May 1S - October 31. Sublethal effects are expected in Tier 4 years; 74 percent of Tier 4 days exceed the threshold of 63 .S°F at Hamilton City during May 1S - October 31. Based on the temperature thresholds of the early life stages of this species and the predicted range of water temperatures in the upper Sacramento River during the temperature management season, the PA would be expected to negatively affect the growth, or survival of sDPS green sturgeon eggs and alevin (Altered Water Temperature stressor). Effects of this component of the PA on green sturgeon are condensed and summarized in Table 2.5.2-17. 226 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.2-17. Summary Exposure, Risk, Response table for green sturgeon life-stages affected by stressors of Summer Cold Water Pool Management. Tier Life-stage 1 Adult (spawning), Egg, Larval 2 Adult (spawning), Egg, Larval 3 Adult (spawning), Egg, Larval 4 Adult (spawning), Egg, Larval Stressor Response to Exposure and Risk as Expected Change in Fitness (Method Used) Exposure Risk 31% of days >63.5°F at Hamilton City (Medium) 42%of days >63.5°F at Hamilton City (Medium) 67%of days >63.5°F at Hamilton City (Medium} 8% of days >71.5°F (Small) 74%of days >63.5°F at Hamilton City (Medium) 45-68% of years Water Temperature • Reduced reproductive success 17-35% of years Water Temperature • Reduced reproductive success 7-15% of years Water Temperature • Reduced reproductive success 5-7% of years Water Temperature • Reduced reproductive success Reduced survival probability • 2.5.2.3.4 Shasta Fall Operations Fall (October-November) operations are dominated by temperature control and the provision of adequate fish spawning habitat. By late fall, the remaining cold water pool in Shasta Reservoir is usually limited. This forces consideration of the operational tradeoffs of maintaining high flows in early fall; summer and fall spawning fi sh may construct redds at the edge of the river where there is an increased likelihood of dewatering when flows are reduced. However, Reclamation is limited in its ability to reduce releases and build storage because early fall Sacramento River releases are still requ ired to meet both the significant instream diversion demands between Keswick Dam and W ilkins Slough and SWRCB Delta requirements. For some actions, Reclamation may reduce releases, if it has that authority. This necessitates maintaining higher releases to support the instream demands until they decrease later in the season. After instream 227 Biological Opinion for the Long-Term Operation of the CVP and SWP demands decrease, Reclamation's objective is to decrease Keswick releases to a lower level in order to conserve storage. 2.5.2.3.4. t Fall and Winter Refill and Redd Maintenance As part of Shasta fall operations, Reclamation proposes to rebuild reservoir storage and cold water pool for the subsequent year by limiting the number of years that high fall releases are maintained. Maintaining releases to keep late-spawning winter-run Chinook salmon redds underwater may draw down storage necessary for temperature management in the subsequent year. Reclamation proposes to consider these competing needs with a risk analysis as described in their March 20,2019, amended text: "Reclamation will minimize effects with a risk analysis of the remaining winter-run Chinook salmon redds, the probability of sufficient cold water in a subsequent year, and a conservative distribution and timing of subsequent winter-run Chinook salmon redds. Ifthe combined productivity of the remaining redds plus a conservative scenario for the following year is less than the productivity of maintaining releases, Reclamation will reduce releases to rebuild storage. The conservative scenario for the following year would include a 75 percent (dry) hydrology; 75 percent (warm) climate; a median distribution for the timing ofredds, and the ability to remain within Tier 3 or higher (colder) Tiers." If, based on the above risk analysis, Reclamation determines releases need to be reduced to rebuild storage, targets for winter base flows (December 1 through end of February) from Keswick would be determined in October and would be based on the previous month's Shasta Reservoir end of September storage projection. The October and November release targets would be determined according to BA Table 4-9 and revised to improve refill capabilities for Shasta Reservoir to build cold water pool for the following year. Based on Reclamation's description of their risk analysis and the Fall and Winter Refill and Redd Maintenance P A component, NMFS is not able to determine how often October and November flows would need to be reduced to build storage, or how the effects to species will be considered. Without further clarification, NMFS assumes that the Shasta EOS and fall flows provided by the CalSirnll model results accurately capture the results of the risk analysis and operational criteria. The likelihood of Reclamation implementing a particular release schedule is reflected in the proportion of years that Shasta end of September storage is less than or equal to 2.2 MAF. For the PA, CalSimll modeling indicates that Shasta end of September storage is less than 2.2 MAF in 20 percent of years. Based on the PA, in years with the lowest Shasta storage at the end of September, Reclamation is expected to reduce flows to the greatest extent in the fall, winter, and spring to build storage. However, this action likely has a negative effect on downstream migration of juvenile salmonids. A recent assessment of mark-recapture survival models in the Sacramento mainstem revealed that of the numerous mortality factors considered, spanning multiple spatial scales, flow correlated most strongly with out-migration success (Iglesias et al. 2017). This assessment focused on hatchery-origin Chinook salmon, but it provides additional evidence that flow is one of the most important factors affecting overall survival of Chinook salmon in the Central Valley (Kjelson and Brandes 1989, Zeug et al. 2014, Michel et al. 2015). Likewise, comparison of2015 and 2016 tagging data that included both CV spring-run Chinook salmon and fall-run Chinook salmon showed faster migration times and higher survival correlated to the higher flow 228 Biological Opinion for the Long-Term Operation of the CVP and SWP conditions in 2016 (Cordoleani et al. 2018). Overall, juvenile mortality during out-migration to the ocean is considered a critical phase to overall population dynamics (Williams 2006), and recent evidence suggests that winter-run Chinook salmon outmigration survival, and the conditions that affect it, are the primary drivers of smolt-to-adult ratio (SAR) dynamics (Michel 2018). Recent conditions in the mainstem Sacramento are such that a review of coded wire tag recovery data for winter-run, late-fall-run, and fall-run Chinook salmon showed annual SAR estimates ofless than 1 percent. For winter-run Chinook salmon, the mean SAR from 1999 to 2012 was 0.64 (standard error of0.18), well below the Columbia River Basin Fish and Wildlife Program suggested minimum of 2 percent SAR required for population survival and 4 percent for population recovery for Upper Columbia River and Snake River Chinook salmon populations (Michel 20 18). Therefore, while reducing reservoir releases helps build storage for the following temperature management season, doing so also has a negative effect on downstream migration and survival. The resultant fall and winter flows for the PA are expected to be lower than what those of current operations, exacerbating winter-run Chinook salmon SAR, estimates of which are already below population survival and recovery benchmarks under baseline conditions. Effects of this component of the PA on species are summarized in Table 2.5.2-18. Table 2.5.2-18. Summary Exposure, Risk, Response table for species and life-stages affected by stressors of Fall and Winter Refill and Redd Maintenance. Species Lifestage Winterrun Chinook salmon Juveniles Exposure Risk <50% of 20% population (Medium) of years CCV steelhead • • • • cv springrun Chinook salmon Stressor Redds All (Large) 20% of years • • • Adults (migratio n, spawnmg ), Redds • All (Large) 20% of years • • • Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss ofNatural River Morphology and Function Res.ponse to Exposure a nd Risk as Expected Change in Fitness (Method Used) • Reduced survival probability • Reduced survival probability • Reduced reproductive success Reduced survival probability (re: Spawning Habitat Availabiility Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss ofNatural River Morphology and Function Spawning Habitat Availabiility Flow Conditions, Loss of Riparian Habitat and Tnstream Cover, Loss ofNatural River and Function 229 • Biological Opinion for the Long-Term Operation of the CVP a nd SWP Species Lifestage Exposure Risk sDPS green sturgeon NA NA NA Stressor NA Response to Exposure and Risk as Expected Change in Fitness (Method Used) dewatering, stranding) NA 2.5.2.3.4.1.1 Winter-Run Chinook Salmon Exposure, Response, and Risk Before the end of October, most winter-run Chinook fry will have emerged from their redds and about half of the year's cohort ofjuveniles will have migrated past RBDD. Rotary screw trap data from the last 10 years show that more than 50 percent of a brood year's cohort will have yet to migrate past RBDD by October 1 (University of Washington Columbia Basin Research 2019). The species response to the conditions associated with Fall and Winter Refill and Redd Maintenance would be related to the Flow Conditions stressor which include possible stranding, poorer feeding conditions, increased competition and predation related to less floodplain and side-channel habitat, and reduced emigration flows. The stranding risk associated with changes in operations is dependent on the physical attributes ofthe habitat and the magnitude of the change in flow. Flows during the egg incubation and initial juvenile rearing period (August to September) average approximately 8,000 cfs downstream of Keswick Dam; a stranding risk to juveniles exists when flows are reduced. The greatest risk posed by the operations proposed in the PA would occur when November flows are reduced to 3,250 cfs. For the PA, CalSimii modeling indicates that end of September storage is less than or equal to 2.2 MAF in about 20 percent of years, and therefore in those years it is expected that October and November flows would be reduced to 3,250 cfs (ROC on LTO BA Appendix D Table 3-2). Similar to effects to winter-run Chinook salmon for the Winter Minimum Flows component of the PA, juvenile stranding generally results from reductions in flow that occur over short periods of time, and analytical planning tools cannot predict with certainty the level of effect of possible stranding on fish. For purposes of the analysis in Section 2.7 Integration and Synthesis ofthe combined effect ofPA implementation when added to the environmental baseline and modeled climate change impacts, the risk of flow fluctuations in the river reaches below Keswick Dam that can strand winter-run Chinook salmon would continue. The potential for juvenile stranding would also persist as operations continue to target lower reservoir releases in the fall and winter to maximize storage. NMFS expects that stranding of at least a small proportion of winter-run juveniles will continue with PA implementation that will adversely affect exposed individuals. With relation to the stressors Loss ofRiparian Habitat and Instream Cover and Loss ofNatural River Morphology and Function, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover both in the immediate area of releases and further downstream (e.g., less frequent inundation of side channels). These changes can 230 Biological Opinion for the Long-Term Operation of the CVP and SWP reduce accessibility to habitat that may support successful outmigration survival by providing rearing areas, refuge, or increased food availability. 2.5.2.3.4.1.2 CV Spring-Run Chinook Salmon Exposure, Response, and Risk By mid-October, close to 100 percent of CV spring-run Chinook salmon will have completed spawning in the upper reaches ofthe Sacramento River (Vogel and Marine 1991). The greatest risk posed by operations from October to November would occur in approximately 20 percent of years when Shasta end of September storage is expected to be less than or equal to 2.2 MAF. The species response to fall flows that are reduced to 3,250 cfs in the upper Sacramento River would include redd dewatering, stranding, poorer feeding conditions, increased competition and predation related to less floodplain and side-channel habitat and reduced emigration flows (Flow Conditions). The dewatering risk associated with changes in operations is dependent on the physical attributes of the habitat and the magnitude of the change in flow. Flows during the CV spring-run Chinook salmon spawning period (August to October) average approximately 8,000 cfs downstream of Keswick Dam; a dewatering risk to CV spring-run Chinook salmon redds exists when flows are reduced. The greatest risk posed by the operations proposed in the P A would occur when November flows are reduced to 3,250 cfs. For the PA, CalSirnli modeling indicates that end of September storage is less than or equal to 2.2 MAF in about 20 percent of years; therefore in those years it is expected that October and November flows would be reduced to 3,250 cfs (ROC on LTO BA Appendix D Table 3-2). Similar to effects to winter-run Chinook salmon, juvenile stranding generally results from reductions in flow that occur over short periods of time, and analytical planning tools cannot predict with certainty the level of effect of possible stranding on fish. For purposes of the analysis in Section 2 .7 Integration and Synthesis of the combined effect ofPA implementation when added to the environmental baseline and modeled climate change impacts, the risk of flow fluctuations in the river reaches below Keswick Dam that can strand CV spring-run Chinook salmon would continue. The potential for juvenile stranding would also persist as operations continue to target lower reservoir releases in the fall and winter to maximize storage. NMFS expects that stranding of at least a small proportion of CV spring-run Chinook salmon juveniles will continue with PA implementation that will adversely affect exposed individuals. With regard to CV spring-run Chinook salmon redds, the USFWS (2006) flow fluctuation and redd dewatering relationship, indicates that a flow reduction from an average spawning flow of about 8,000 cfs to 3,250 cfs would be expected to dewater about 33 to 42 percent of Chinook salmon redds (depending on whether the ACID Dam boards are out or in). Likewise, flow reductions from 8,000 cfs spawning flows to 4 ,000, 4,500 and 5,000 cfs would be expected to dewater about 24 to 29 percent, 18 to 22 percent and 12 to 15 percent of Chinook salmon redds, respectively. The species response to fall flows of 3,250 cfs, in the upper Sacramento River would include dewatering, which could lead to increased mortality. With relation to the stressors Loss ofRiparian Habitat and Instream Cover and Loss ofNatural River Morphology and Function, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover both in the immediate area of releases and further downstream (e.g., less frequent inundation of side channels). These changes can 231 Biological Opinion for the Long-Term Operation of the CVP and SWP reduce accessibility to habitat that may support successful outmigration survival by providing rearing areas, refuge, or increased food availability. 2.5.2.3.4.1.3 CCV Steelhead Exposure, Response, and Risk CCV steelhead express a diverse array of life-history strategies including both anadromous and resident (i.e., rainbow trout) life histories. Anadromous and resident life histories can be adopted by individuals from the same sibling cohort, making determinations regarding run timing difficult. During the October to November timing of operations for the Fall and Winter Refill and Redd Maintenance P A component, the majority of adult CCV steelhead are migrating past RBDD (McEwan 2001). The greatest risk posed by these seasonal operations would occur during the 20 percent of years when minimum Keswick flows would be 3,250 cfs. The species response to fall flows of 3,250 cfs in the upper Sacramento River would include stranding, increased competition and reduced spawning habitat availability related to less floodplain and side-channel habitat (Flow Conditions). The dewatering risk associated with changes in operations is dependent on the physical attributes of the habitat and the magnitude of the change in flow. Flows during the steelhead spawning period (August to October) average approximately 8,000 cfs downstream of Keswick Dam; a dewatering risk to st,eelhead redds exists when flows are reduced. The greatest risk posed by the operations proposed in the PA would occur when November flows are reduced to 3,250 cfs. For the PA, CaiSimii modeling indicates that end of September storage is less than or equal to 2.2 MAF jn about 20 percent of years; therefore in those years it is expected that October and November flows would be reduced to 3,250 cfs (ROC on LTO BA Appendix D Table 3-2). Similar to effects to winter-run Chinook salmon, juvenile stranding generally results from reductions in flow that occur over short periods of time, and analytical planning tools cannot predict with certainty the level of effect of possible stranding on fish. For purposes of the analysis in Section 2. 7 Integration and Synthesis of the combined effect of PA implementation when added to the environmental baseline and modeled climate change impacts, the risk of flow fluctuations in the river reaches below Keswick Dam that can strand steelhead would continue. The potential for juvenile stranding would also persist as operations continue to target lower reservoir releases in the fall and winter to maximize storage. NMFS expects that stranding of at least a small proportion of CCV steelhead juveniles will continue with PA implementation that will adversely affect exposed individuals. With relation to the stressors Loss ofRiparian Habitat and Instream Cover and Loss ofNatural River Morphology and Function, NMFS considers that the managed changes in the hydrograph can reduce access to riparian habitat and instream cover both in the immediate area of releases and further downstream (e.g., less frequent inundation of side channels). These changes can reduce accessibility to habitat that may support successful outmigration survival by providing rearing areas, refuge, or increased food availability. 2.5.2.3.4.1.4 sDPS Green Sturgeon Exposure, Response, and Risk sDPS green sturgeon life history timing is such that it is unlikely that sDPS green sturgeon will be present in the upper Sacramento River when Reclamation is managing flows to Fall and Winter Refill and Redd Maintenance. Adult sDPS green sturgeon migrate up river in March to 232 Biological Opinion for the Long-Term Operation of the CVP and SWP early April, and spawn from April through July with the median spawning May (Poytress et al. 2015). 2.5.2.3.4.2 Rice Decomposition Smoothing Water demand changes in the upper Sacramento River throughout the fall could result in some early fall-run Chinook salmon redds being dewatered. Reclamation proposes to meet a shifting demand as upstream Sacramento Valley CVP contractors and the Sacramento River Settlement Contractors synchronize their diversions to reduce demands for peak rice decomposition. NMFS notes this action is also part of the four action components of the PA identified on May 22, 2019, that Reclamation intends to implement to contribute to increased spring Shasta storage levels compared to the COS and current operations. Based on the description of the PA component and the assessment of its effects in the BA, NMFS understands that this action has the potential to build storage, which may have a beneficial effect on the subsequent cold water pool. However, increased coordination between Reclamation and the water contractors that considers the spawning and rearing needs of species would likely provide increased awareness, if not protection, for those species. As part of the Fall and Winter Refill and Redd Maintenance PA component operations described in Section 2.5.2.3.4.1, Reclamation would assess the downstream water demands of the upstream CVP contractors and the Sacramento River Settlement Contractors. Coordinated diversions in late October and early November could provide increased reliability that target flows would be met according to the Fall and Winter Refill and Redd Maintenance operations and that Reclamation would be able to build storage during this period. NMFS assumes that the minimum flows identified in the P A for this season would be achieved, and this action component would, therefore, provide greater certainty that Reclamation would be able to reduce releases and build storage according to the Fall and Winter Refill and Redd Maintenance action component. The effects of this action are included in the analysis of Shasta Fall Operations. 2.5.2.4 Operation of a Shasta Dam Raise Under a separate ESA consultation for construction, Reclamation proposes to enlarge Shasta Dam and Reservoir by raising the dam crest 18.5 feet. The PA states tlhat the additional storage created by the 18.5-foot dam raise would be used to improve the ability to meet water temperature objectives and habitat requirements for salmonids during drought years and increase water supply reliability; however, no new operational criteria are proposed. The PA description of operational criteria with the Shasta Dam Raise will be the same as operational criteria for the current dam and integrated CVP/SWP operations. Reclamation has advised NMFS that the BA analyses suffice for purposes of consultation. There are no operational scenarios in the BA to evaluate to confirm beneficial or adverse effects of a raised Shasta Dam and NMFS therefore cannot further evaluate the Shasta Dam raise in this Opinion. However, we note that if operations with a larger dam do result in either modifications to Shasta or system-wide operations (as modeled in CalSimll) or effects to the species that are beyond the range analyzed in this Opinion (for example, changes in spring flows to build new storage), reinitiation of this Opinion would be triggered. 2.5.2.5 Conservation Measures Conservation measures are included in the PA with the intent of avoiding and minimizing or compensating for CVP and SWP project effects, including take, on listed species. 233 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.2.5.1 Cold Water Management Tools Reclamation has proposed to explore additional non-flow actions intended to extend the cold water pool. However, during a consultation meeting between Reclamation and NMFS on June 25,2019, Reclamation indicated that Reclamtion does not commit to implementing any ofthese PA components, but rather, Reclamation would consider the benefits of each as possible measures to be taken to improve cold water pool availability. These possible PA components and an assessment of their effect, to the extent possible, are included below. 2.5.2.5.1.1 Battle Creek Restoration As discussed in the Environmental Baseline section of this Opinion, pursuant to the RPA in the NMFS 2009 Opinion, Reclamation and DWR shall provide improved instream flow releases and safe fish passage to prime salmon and steelhead habitat on Battle Creek for winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead. This is also a Priority 1 NMFS recovery action (National Marine Fisheries Service 2014b). The project has been supported with Federal, State and private funding. As of2019, implementation of the Battle Creek Salmon and Steelhead Restoration Project has completed construction of phase one (of two), which included removal of one fish passage barrier (a dam) and construction ofNMFS-approved fish screens and ladders at the two remaining dams on North Fork Battle Creek. Phase two of the project has completed planning, and is currently in design phase. Although implementation has been significantly delayed, NMFS expects benefits to listed salmonids once completed. IfReclamation determines that this PA component would be a cost-effective means to extend the availability of Shasta cold water pool, Reclamation proposes that it could continue and/or accelerate implementation of the Battle Creek Salmon and Steelhead Restoration Project. This project is intended to reestablish approximately 42 miles of prime salmon and Steelhead habitat on Battle Creek, and an additional 6 miles on its tributaries. While lacking specificity, NMFS notes overall beneficial effects of this accelerated action and intends to engage with Reclamation on specific approaches in order to provide credit for this action. Winter-run Chinook salmon are currently limited to a single population that spawns in an approximately 10-mile stretch of the Sacramento River, but they are being reintroduced to Battle Creek (around 200,000 juveniles were released in Battle Creek in 20 18), and any returning adults from the release would benefit from the restoration efforts. NMFS notes that the PA is not intended to bear the responsibility of establishing viable populations, which are required for recovery of the species. However, we offer that an additional population of winter-run Chinook salmon in Battle Creek could provide strategic temperature compliance flexibility in the Sacramento River, which could alleviate constraints on Shasta operations for species protection in some conditions. The effects of parts of this project are included in the baseline conditions of the analysis for this Opinion. Because Reclamation is not commiting to the action component and the ROC on LTO PA does not include specificity in resources, timing, or defined actions by which the project would be accelerated, benefits besides those considered in the baseline condition are included in this analysis of effects at the framework level. Any influence Reclamation pursues to accelerate implementation of the restoration project is expected to result in earlier access to preferred habitat for listed salmonids. 234 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.2.5.1.2 Lower Intakes near Wilkins Slough Due to temperature requirements, Sacramento River flows at or near Wilkins Slough have decreased below the 5,000 cfs minimum navigational flow deemed by Congress. As many of the fish screens at diversions in this region were designed to operate at no less than the 5,000 cfs minimum flowrate, they may not function properly at the lower flows and, therefore, may not meet state and federal fish screening requirements during the lower flows (U.S. Bureau of Reclamation 20 19) or may cavitate and damage intake pumps. This could result in take of state and federally protected species that use this section of the river. If Reclamation determines that this PA component would be a cost-effective means to extend the availability of Shasta cold water pool Reclamation would provide grants to water users within this area to install new diversions and screens that would operate at lower flows. Reclamation expects that if this action were implemented, it would provide greater flexibility in managing Sacramento River flows and temperatures for both water users and wildlife, including listed salmonids (U.S. Bureau of Reclamation 2019). However, because the ROC on LTO PA does not include specificity in timing or defined actions, any benefits of this action are included in the analysis of effects in this Opinion at the framework level. Any influence Reclamation pursues to accelerate implementation of the project is expected to result in earlier benefits for listed salmonids. Given the framework-level programmatic nature of the Lower Intakes near Wilkins Slough action component, where further commitment and collaborative planning is necessary to identify effects and quantify a level of benefits and incidental take, but where it is still possible to estimate a general level of impact qualitatively, NMFS applies the following assumptions regarding the potential species exposure, response, and risk: • If Relamation were to implement this PA component, construction related to the Lower Intakes near Wilkins Slough PA component would be done in a manner consistent with best management practices and applicable in-water work windows, such that exposure to construction-related impacts would be minimized to the greatest extent practicable. The frequency with which species would be exposed to the construction related impacts remains uncertain as it is unknown or difficult to predict the number, timing, and location of water diversions requiring fish screen installation or remediation. NMFS assumes that a small proportion of fish may be exposed to construction-related effects such as increased turbidity, pile driving effects associated with installation of coffer dams, flow alteration around a construction site, and effects associated with handling and transport of fish isolated and rescued from behind coffer dams. • IfRelamation were to impl ement this PA component, there would be a long-term benefit associated with improving the function of existing fish screens or installing new fish screens near Wilkins Slough. This benefit would be assumed to affect juvenile fish in particular as they are most susceptible to being entrained into unscreened or poorly screened diversions. The frequency of exposure would be assumed to be high because installation or repair of fish screens would result in a semi-permanent reduction in the otherwise lethal effect of entrainment and impingement. 2.5.2.5.1.3 Shasta Temperature Control Device Improvements IfReclamation determines that this PA component would be a cost-effective means to extend the availability of Shasta cold water pool, Reclamation would study the feasibility of infrastructure 235 Biological Opinion for the Long-Term Operation of the CVP and SWP improvements to enhance TCD performance, including reducing the leakage of warm water into the structure. However, Reclamation is not committing to implementing this PA component, but rather would consider the benefits relative to other such tools identified in Section 2.5.2.5.1. Depending upon the outcome of the proposed Shasta Dam raise, the TCD would be either modified or replaced by Reclamation, as informed by updated modeling. Depending on the size of the raise, the existing TCD structure would be retrofitted to account for additional dam height and to reduce leakage of warm water into the structure, but no new structure would be needed. However, modifications to, or replacement of, the existing structure are more likely to be necessary for increasingly higher dam raises. The authority for this action is 3406(b)(6). While the resources are provided for this action and Reclamation expects that if selected for implementation that this action would provide greater flexibility in managing Sacramento River flows and temperatures, the ROC on LTO PA does not commit to its implementation nor does it include specificity in timing, performance metrics, or defined actions. Therefore any benefits of this action are included in this analysis of effects in this Opinion at the framework level. Any influence Reclamation pursues to accelerate implementation of the improvements is expected to result in earlier benefits for listed salmonids. 2.5.2.5.2 Spawning and Rearing Habitat Restoration 2.5.2.5.2.1 Spawning Gravel Injection Reclamation proposes to create additional spawning habitat by injecting 40- 55 tons of gravel into the Sacramento River by 2030, using the following sites: Salt Creek Gravel Injection Site, Keswick Dam Gravel Injection Site, South Shea Levee, Shea Levee, and Tobiasson Island Side Channel. The effects of this project are included in the baseline conditions of the analysis for this Opinion. Because the ROC on LTO PA does not include specificity in resources, timing, or defined actions by which this project would occur, any benefits of this action besides those included in the baseline are included in this analysis of effects in this Opinion at the framework level. Any influence Reclamation pursues to accelerate implementation of the restoration is expected to result in earlier benefits for habitat access listed salmonids. Given the framework-level programmatic nature of the Spawning Gravel Injection action component, as a result ofReclamation's continued support of this programmatic action, NMFS applies the following assumptions regarding species exposure, response, and risk: • Expected long-term benefit associated with increasing the quantity and quality of spawning substrate in the upper Sacramento River. This benefit is expected to affect adult fish in particular as they return to spawn. The frequency of exposure is assumed to be high because completed restoration activities would result in a semi-permanent increase in spawning habitat availability. 2.5.2.5.2.2 Side Channel Habitat Restoration Reclamation and the Sacramento River Settlement Contractors propose to create 40- 60 acres of side channel habitat at approximately 10 sites in Shasta and Tehama County by 2030, including Cypress A venue, Shea Island, Anderson River Park; South Sand Slough; Rancheria Island; Tobiasson Side Channel; and Turtle Bay. 236 Biological Opinion for the Long-Term Operation of the CVP and SWP The effects of this project are included in the baseline conditions of the analysis for this Opinion. Because the ROC on LTO PA does not include specificity in resources, timing, or defined actions by which this project would occur, any benefits of this action besides those included in the baseline are included in this analysis of effects in this Opinion at the framework level. Any influence Reclamation pursues to accelerate implementation of the restoration is expected to result in earlier access ofbeneficial habitat for listed salmonids. Given the framework-level programmatic nature of the Side Channel Habitat Restoration action component, as a result ofReclamation's continued support ofthis programmatic action, NMFS applies the following assumptions regarding species exposure, response, and risk: • Expected long-term benefit associated with increasing the quantity and access to quality side channel rearing habitat in the upper and middle Sacramento River. This benefit is expected to affect rearing and migrating juvenile fish. The frequency of exposure is assumed to be high because completed restoration activities would result in a semipermanent increase in rearing habitat availability. 2.5.2.5.2.3 Small Screen Program As part of adaptive management, Reclamation and DWR propose to continue to work within existing authorities (e.g., Anadromous Fish Screen Program) to screen small diversions throughout Central Valley CVP/SWP streams and the Bay-Delta. The beneficial effects of previous actions under this program (minimizing entrainment at a specific diversion) are included in the baseline conditions of the analysis for this Opinion. Because the ROC on LTO PA does not include specificity in resources, timing, or defined actions by which this program would occur, any benefits of new actions are included in this analysis of effects in this Opinion at the framework level. Any influence Reclamation pursues to accelerate implementation of this program is expected to result in earlier benefits for listed salmonids. Given the framework-level programmatic nature of the Small Screen Program action component, where further collaborative planning is necessary to identify effects and quantify a level of benefits and incidental take, but where it is still possible to estimate a general level of impact qualitatively, NMFS applies the following assumptions regarding species exposure, response, and risk: • That construction related to the Small Screen Program action component will be consistent with best management practices and applicable in-water work windows, which would minimize exposure to construction-related impacts to the greatest extent practicable. The frequency with which species would be exposed to the construction related impacts remains uncertain as it is unknown or difficult to predict the number, timing, and location of water diversions requiring fish screen installation or remediation. NMFS assumes that a smaEl proportion of fish may be exposed to construction-related effects such as increased turbidity, pile driving effects associated with installation of coffer dams, flow alteration around a construction site, and effects associated with handling and transport offish isolated and rescued from behind coffer dams. • That there is a long-term benefit associated with improving the function of existing fish screens or installing new fish screens in the Sacramento River. This benefit is assumed to 237 Biological Opinion for the Long-Term Operation of the CVP and SWP affect juvenile fish in particular as they are most susceptible to being entrained into unscreened or poorly screened diversions. The frequency of exposure is assumed to be high since installation or repair of fish screens would result in a semi-permanent reduction in the otherwise lethal effect of entrainment and impingement. 2.5.2.5.3 Intervention Measures In the March forecast (mid-March), if the forecasted Shasta Reservoir total storage is projected to be below 2.5 MAF at the end of May (based on the 90 percent exceedance outlook), Reclamation would initiate discussions with USFWS and NMFS on potential intervention measures in preparation for the low storage condition to continue into April and May. If total storage is less than 2.5 MAF at the beginning of May, or if Reclamation cannot meet a daily average temperature 56°F at CCR, Reclamation will attempt to operate to a less than optimal temperature target and period that is determined in real-time. Reclamation proposed to develop this alternate target with technical assistance from NMFS and USFWS. In addition, Reclamation proposes to implement intervention measures during these years (e.g., increasing hatchery intake, adult rescue, and juvenile trap and haul, as described below). These intervention measures would be considered by Reclamation only in the years identified as Tier 4 years of Summer Cold Water Pool Management. As such, the intervention measures are intended to minimize or mitigate the effects of conditions and operations associated with the Tier 4 years. 2.5.2.5.3.1 LSNFH Production (Intervention) In a Tier 4 year, Reclamation proposes to increase production of winter-run Chinook salmon at the LSNFH. As part of the increased production, Reclamation would consider New Zealand or Great Lake winter-run Chinook salmon stock for augmenting conservation hatchery stock to improve heterozygosity. Effects of increased hatchery production will depend on complex interactions between hatchery and natural-origin fish and their environment. The short-term benefit of expanded LSNFH production is that it would provide alternative (artificial) rearing and spawning habitat when the in-river environmental conditions are not suitable for egg-fry life stages. Because this PA component is only proposed for Tier 4 years, the intent is for it to offset, in part, the effects of Tier 4 operations described in Section 2.5.2.3.3.1.1 (Winter-Run Chinook Salmon Exposure, Response, and Risk). A potential long-term consequence of expanding numbers of hatchery fish is an increase of hatchery origin fish on in-river spawning grounds. In the development ofLSNFH's HGMP considerable effort has been made to minimize any adverse genetic or ecological effects to the natural population (U.S. Fish and Wildlife Service 2016b). For example, winter-run Chinook salmon are collected and spawned throughout the duration of run timing to maintain phenotypic and genetic variability. A factorial-type spawning scheme is used to increase the effective population size of hatchery-produced winter-run Chinook salmon. Phenotypic and genetic broodstock selection criteria are used to ensure that the potential for genetic bottlenecks do not occur in the hatchery. Further, limits have been established for the collection of natural-origin winter-run Chinook salmon broodstock; the annual limit for broodstock collection is 60 females and up to 120 males, totaling up to 180 adult natural-origin winter-run Chinook salmon. These 238 Biological Opinion for the Long-Term Operation of the CVP and SWP limits guard against removing too many fish from the naturally-spawning population and increase the effective population size ofthe hatchery component of the population. In fact, increasing production at LSNFH is already considered as part ofthe hatchery's HGMP, where during emergencies, such as the extreme drought of2014 and 2015, production ofwinterrun Chinook salmon may be increased above the standard production levels to partially mitigate for extremely poor environmental conditions. The temporary expansion of winter-run Chinook salmon propagation activities during the 2014-2015 was based on the anticipation of temperatures unfavorable for successful natural spawning in the Sacramento River. During those years when environmental conditions result in the need for increased hatchery production (limited to a maximum of 400 adult winter-run Chinook salmon for use as broodstock), broodstock collection targets are determined collaboratively by USFWS, NMFS, and CDFW. Factors such as expected adult escapement, expected environmental conditions, expected juvenile survival, and the number of tagged juveniles available for fishery assessments will be considered when determining whether program expansion is warranted (U.S. Fish and Wildlife Service 2016b). Also, as described in the Section 2.4 Environmental Baseline section of this Opinion and in the ROC on LTO BA Appendix C, the USFWS has been engaged in efforts regarding LSNFH. During the drought in 2014 and 2015, and at the request ofNMFS and CDFW, LSNFH increased production of winter-run Chinook salmon to compensate for expected high temperature-dependent mortality in the Sacramento River and re-instated the captive broodstock program. Reclamation also funded the rental of two commercial-size chillers to ensure adequate water temperatures for adult holding, egg incubation, and juvenile rearing. Those chillers were rented during the summer and fall and used on a just few occasions. Subsequently, Reclamation has funded a small permanent chiller to ensure temperatures for egg incubation only. Reclamation also supports USFWS efforts for coded-wire tagging, acoustic tagging, and associated monitoring of national fish hatchery-produced w inter-run Chinook salmon under long-term operational funding agreements that have a long history of renewal. NMFS anticipates that additional improvements will be necessary to support the proposed intervention measure, including securing an emergency or alternate water supply when Shasta and Keswick reservoirs reach elevations below the current penstock, acquiring water chillers to ensure that adequate water temperatures are provided during critical winter-run Chinook salmon life stages, acquiring more physical space to adequately rear increased production to help the population withstand the drought and to successfully operate the captive broodstock program, making modifications or improvements to Keswick Dam Fish Trap, making improvements to the water treatment facility, and possibly making modifications/improvements to the ACID fish trap. These improvements are described in detail in ROC on LTO BA Appendix C and generally summarized below: • Current ideas for improving water supply include: (1) replacing and upgrading valves, controllers, and alarms to ensure the water supply is more secure and staff are better able to respond to water alarms; and (2) connecting Penstock 5 (which is lower than the other penstocks) to the hatchery water system to allow greater flexibility to provide more cold water during low lake levels and during penstock 239 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • maintenance outages. Replacing and upgrading valves, controllers, and alarms would improve biosecurity and efficiency at the hatchery under all conditions. Installing chillers at critical times during drought conditions for adult holding and juvenile rearing is essential to ensure that the increased demand can be met during drought years. In 2016, a multi-agency work team concluded LSNFH would need to expand by 8 to 10 circular tanks to raise an additional 350,000 fish if the hatchery were to engage in the same drought operations they did in the recent drought. Increasing the capacity ofLSNFH would require expanding to the west side ofthe hatchery road, additional piping to that side of the property, and additional water. An investigation to to evaluate improvements to the fish trap and elevator to reduce the likelihood of injuring or killing fish during fish transfer. USFWS is planning to discuss the potential need for improvements with Reclamation, and if improvements are necessary, is confident that the agencies can identify the funds necessary to implement the improvements. The USFWS has recently begun to discuss the potential need for a drum screen to remove solids in the hatchery's effluent. The drum screen could allow the USFWS more flexibility in the use of medicated feed to prevent and treat disease. With little description ofthis action component, how it may differ from the existing HGMP or how it may affect the species, there is insufficient information available to assess the effects, and how those may differ from effects analyzed in the HGMP, which is part of the baseline. In order to provide enough certainty regarding how and when the PA component would be implemented, and to assess its effects, the expanded production at LSNFH will need to be developed further. Generally, a commitment to assess and eventually incorporate the expanded production at LSNFH would be expected to have beneficial effects decreasing the potential negative effects of environmental conditions and water operations during a Tier 4 year, but additional facility improvements or expanded use of the captive broodstock program may be necessary to accommodate this Tier 4 action. NMFS is also uncertain of the viability of using of New Zealand or Great Lakes winter-run Chinook salmon stock for augmenting conservation hatchery stock to improve heterozygosity, and there are potential negative consequences to the species of introducing an outside stock. Additional science is necessary to begin consideration of those stocks. Uncertainty regarding the effects of the PA component could be addressed, and the mechanism for incorporating the PA component in to operations would be described and understood through implementation of this Collaborative Planning Action. 2.5.2.5.3.2 Adult Rescues (Intervention) Reclamation proposes to trap and haul adult salmonids and sturgeon from Yolo and Sutter bypasses during droughts and after periods of bypass flooding, when flows from the bypasses are most likely to attract upstream migrating adults, and move them up the Sacramento River to spawning grounds. This trap and haul is in addition to weir fish passage projects that are part of the PA elsewhere. This could improve survival of the adults, leading to increased juvenile production in the following year and more flexibility with salvage. Because the ROC on LTO PA does not include details on these rescue actions (e.g., process for identifying the need, process for rescue and return, evaluation of return success or definition of performance metrics, definition of 240 Biological Opinion for the Long-Term Operation of the CVP and SWP reporting tasks), NMFS considers this a programmatic action. Effects are considered but exemption for take associated with this action is not provided in this Opinion. 2.5.2.5.3.3 Juvenile Trap and Haul (Intervention) lfRec1amation projects Tier 4 operations for an upcoming summer (i.e., less than 2.5 MAF of Shasta storage at the beginning ofMay), the PA includes that Reclamation will propose implementation of a downstream trap and haul strategy for the capture and transport ofjuvenile Chinook salmon and steelhead in the Sacramento River watershed. This is proposed for drought years when low flows and resulting high water temperatures are unsuitable for volitional downstream salmonid migration and survival. Reclamation proposes to place temporary juvenile collection weirs at key feasible locations downstream of spawning areas in the Sacramento River. Reclamation would transport collected fish to a safe release location or locations in the Delta upstream of Chipps Island. Juvenile trap and haul activities would occur from December 1 through May 31, consistent with the migration period for juvenile Chinook salmon and steelhead (National Marine Fisheries Service 2014a), depending on hydrologic conditions. In the event of high river flows or potential flooding, the fish weirs would be removed. The benefits ofthis component is uncertain, even for years of extremely low storage. Because the ROC on LTO PA does not include details on these trap and haul actions (e.g. , process for identifying the need, process for trapping and return, evaluation of return success or definition of performance metrics, defmition of reporting tasks), NMFS considers this a programmatic action. Exemption for take associated with this action is not provided in this Opinion. 2.5.2.6 Supplemental Analysis of June 14, 2019, Final PA During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, BA that was used for the majority of the analysis in this Opinion. It was not possible to include these revisions in any modeling due to the White House memorandum that mandated issuance of final biological opinions within 135 days of January 31, 2019 (June 17, 2019, and subsequently extended to July 1, 2019). The effects description above (Section 2.5.2.1-2.5.2.5) was based on the modeling associated with the February 5, 2019 PA (Appendix A1 , the original PA) and associated modeling that NMFS requested. The following subsection provides a supplemental effects analysis ofthe June 14, 2019 PA revisions reflected in the final PA (Appendix A3), including a discussion ofwhether and how the PA revisions modify the effects analyzed above. Also during the consultation for this Opinion, the Sacramento River Settlement Contractors (SRSC) drafted for adoption a resolution that includes three key actions that are integrated into the February 5, 2019, description ofthe proposed action and analyzed in this Opinion (Appendix A3): 4. The SRSC intend to meet and confer with Reclamation, NMFS, and other appropriate agencies in connection with Reclamation 's operational decision-making for Shasta Reservoir annual operations during drier water years when operational conditions are designated as Tier 3 and Tier 4 scenarios. 5. The SRSC intend to continue to participate in, and act as project champions for, similar types of future Recovery Program projects, subject to the availability of funding, regulatory approvals, and acceptable regulatory assurances. 6. The SRSC are committed to continue their active engagement and leadership in the 241 Biological Opinion for the Long-Term Operation of the CVP and SWP ongoing collaborative Sacramento River Science Partnership effort. The actions described in the draft SRSC resolution are qualitatively factored into the analysis of this Opinion. 2.5.2.6.1 Revisions to the PA Relevant to the Shasta/Upper Sacramento Division As a result of discussions, the Upper Sacramento River (Section 4.1 0.1) and Governance (Section 4.12) sections of the BA included notable changes and clarification (Appendix A3). These sections are noted in the discussion of each below. 2.5.2.6.1.1 Summer Cold Water Pool Management (BA Section 4.10.1.3.1) Revisions to the Summer Cold Water Pool Management section of the BA (Section 4.10.1.3.1) include a description of the process for development of an annual temperature management plan, including use of conservative forecasts and NMFS participation through the SRTTG. Compared to the previous analysis., this revision decreases the uncertainty of operations being able to stay within the determined Tier for the duration of the temperature management season. With this change, we consider our previous analysis of the modeled outcomes of temperature management- which, due to limitations of the models, do not explicitly mimic the process of developing a temperature management plan by projecting stream temperatures through summer for various management scenarios -to be more accurate in characterizing the likelihood of maintaining the determined Tier of projected and expected operations. That is, given the commitment to develop a temperature management plan based on conservative meteorology, hydrology, and inflows, we consider it more likely that the operations will stay within the determined Tier throughout the season, which is what is reflected in the modeling and analysis. We do not have quantitative support to indicate exactly how any results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management would change in response to this revision. However, we consider that the temperature management plan may reduce the likelihood of exceeding the temperature target, which is used in the characterization of exposure to increased temperatures in the previous analysis. Given the inability to quantify this reduction and NMFS' adherence to the principle of institutionalized caution, we still consider the results in Section 2.5.2.3.3.1 Summer Cold Water Pool Management as the best quantitative characterization of the exposure of the species to the stressor of increased water temperature and the risk based on the expected long-term proportion of years in each Tier type. 2.5.2.6.1.2 Commitment to Cold Water Management Tiers (BA Section 4.10.1.3.2) The addition of the Commitment to Cold Water Management Tiers section of the final PA (Section 4.10.1.3.2) includes definition of commitments to the cold water management tier identified at the beginning of the temperature management season and actions required if a change in Tier is required. Compared to the previous analysis., this revision decreases the uncertainty of operations moving to a different Cold Water Management Tier during the temperature management season. With this change, we consider our previous analysis of the modeled outcomes of temperature management - which do not incorporate mid-season changes to a different Tier - to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management will not change quantitatively, as this 242 Biological Opinion for the Long-Term Operation of the CVP and SWP commitment to maintaining the determined Tier and required actions upon changes in Tier do not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. The PA revisions include the action of chartering an independent panel in the case that Reclamation moves to a warmer Tier during the temperature management season. While this is greatly informative in increasing the understanding of what conditions or operations contributed to the need to change Tiers, it is a post-hoc evaluation that in and of itself does not afford additional protections to the species or alter the quantitative analysis already completed based on the modeling results. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management will not change quantitatively, as this evaluation of the need to change Tier does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. 2.5.2.6.1.3 Upper Sacramento Performance Metrics {BA Section 4.10.1.3.3) Revisions to the Cold Water Pool Management section of the final PA includes the addition of Section 4.10.1.3.3 Upper Sacramento Performance Metrics. The objective of these performance metrics is to ensure that the conditions that manifest as a result of operations within a tier reflect the modeled range, and show a tendency towards performing at least as well as the distribution produced by the simulation modeling of the PA. It includes tracking of both TDM and egg-to-fry survival over time with the objective of completing annual and multi-year hindcast evaluations of the ability to meet the survival objectives and of the expectation that hydrology will occur as identified by the probabilities in the modeling. The metrics also include identification of expected improvement of egg-to-fry survival from habitat restoration projects recently completed, currently underway, or proposed to be completed by year 2030 (the duration of the PA). The additions identify drought and dry year actions and annual reporting, along with hindcast analysis of survival to identify if results are within the central tendency of modeled and analyzed results. The text also describes the process for chartering independent reviews, including established timelines, triggers, and focus topics. Compared to the previous analysis., this addition to the Cold Water Pool Management section contributes to increasing the certainty that the central tendency of the analyzed results is what the species will experience when these operations are implemented. That is, the analysis characterized exposure and risk based on the central statistics of modeled TDM for each Tier type and the long-term projected likelihood of occurrence of each year type. However, the TDM results included a broad range for each Tier due to the variability of conditions included in each Tier type. With this change, we consider our previous analysis of the modeled outcomes of temperature management- which is based on the central tendency to capture the most likely conditions- to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management will not change quantitatively, as this commitment to assess cold water management does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. 243 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.2.6.1.4 Conservation Measures (BA Section 4.10.1.4.2) Revisions to the Conservation Measures section of the final PA (Section 4.1 0.1.4.2) include introduction of measures to avoid and minimize or compensate for CVP and SWP project effects on species. The recent revisions have added measures related to Shasta reservoir temperature modeling, improvements to LSNFH, and actions required to protect winter-run Chinook salmon during and after high mortality years. The Temperature Modeling Platform PA component that Reclamation is proposing to consider as a possible Cold Water Manamgment Tool would advance a tool that could provide a more accurate characterization of reservoir temperature conditions and contribute to more efficient use of available cold water pool, improved temperature conditions, and likely increased species protections. However, Reclamation is not committing to implementing this PA component, but rather would consider the benefits, as a cost-effective means to extend the availability of Shasta cold water pool, relative to other such tools identified in Section 2.5.2.5.1. In addition, the final PA has added a conservation measure intended to protect the third cohort of winter-run Chinook salmon after two consecutive years of poor survival. This measure increases the likelihood that protections will be afforded to maximize the egg-to-fry survival of the year class immediately following two brood years of low egg-to-fry survival. This measure is intended to allow opportunities for actions to be implemented to protect species despite the probability ofyear types that may occur. While the PA modeling based on a historic 82-year sample set indicates a 68 percent likelihood that a year would be in Tier 1 operations, the complex dynamics of the historic hydrologic timeseries in California suggests that it is prudent to prepare for multiple years of drier-than-normal conditions, even if the summary statistics of conditions in the model period do not capture these sequential years of extended wet or extended dry periods. Compared to the previous analysis., these revisions and additions to the conservation measures contribute to decreasing the uncertainty of the characterization of the volume of cold water pool available, and therefore the likelihood of achieving the target temperature of the determined cold water management Tier. This would be the case for the Temperature Modeling Platform, which if Reclamation determines that this PA component is a cost-effective means to extend Shasta cold water pool, it would be expected to improve the ability to predict summer operations by providing a more accurate characterization of cold water pool volume and reservoir temperature dynamics. However, the benefits of this measure are uncertain as Reclamation has only committed to consider it and those benefits will not be immediately realized, as the modeling would not be available for implementation. Compared to the previous analysis, the addition of the conservation measure to protect the third cohort after two years of poor survival decreases the uncertainty associated with high mortality values modeled for Tier 3 and Tier 4 years. NMFS expects that because of any actions taken in this instance, the resulting mortality value would be in the middle range of the broad range that results from the modeling (e.g., 5-77 percent in Tier 3 years), especia11y after two consecutive years of low survival. With this change, we consider our previous analysis of the modeled outcomes oftemperature management to still apply as a conservative characterization of projected and expected operations. Based on factoring in a 32 percent background (i.e., nontemperature dependent) mortality to the modeled temperature dependent mortality for each year, the 82-year modeled dataset includes three intervals in which this type of intervention may have 244 Biological Opinion for the Long-Term Operation of the CVP and SWP been warranted (1931-1934, 1976-1977, and 1991-1992). The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management could slightly over-represent a third year of high mortality, however, the results of the modeling would not notably change the exposure of the species to the stressor of increased water temperature, or the risk based on the expected longterm proportion of years in each Tier type. 2.5.2.6.1.5 Drought and Dry Year Actions (BA Section 4.12.5) Revisions to the Governance section ofthe PA includes the addition of Section 4.12.5 Drought and Dry Year Actions to develop a toolkit of actions to be taken in drought conditions, and a process by which early warnings of drought conditions may allow for clear and swift development of a drought contingency plan. Compared to the previous analysis, the addition of the dlrought and dry year actions decreases the uncertainty associated with high mortality values modeled for Tier 3 and Tier 4 years. NMFS expects that any actions taken in this instance would increase the likelihood that resulting mortality values would be minimized to the extent possible. With this change, we consider our previous analysis of the modeled outcomes of temperature management to still apply as a conservative characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management could slightly over-represent a high mortality event that could be prevented by this Drought and Dry Year Action; however, the results of the modeling would not notably change the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. 2.5.2.6.1.6 Chartering of Independent Panels (BA Section 4.12.6) and Four Year Reviews (BA Section 4.12.7) Revisions to the Governance section ofthe PA include the addition of Section 4.12.6 Chartering oflndependent Panels and Section 4.12.7 Four-Year Reviews to charter reviews either at set dates or as triggered. The review topics are expected to include the Upper Sacramento Performance Metrics and associated topics in that section. While the reviews will be greatly informative in increasing the understanding of effects of temperature conditions and operational decisions on species response, they are post-hoc evaluations that alone do not afford additional protections to the species or alter the quantitative analysis already completed based on the modeling results. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management will not change quantitatively, as this commitment to assessing the performance of the PA does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. 2.5.2.6.1.7 SRSC Meet and Confer During Tier 3 and Tier 4 Scenarios The commitment from the SRSC to meet and confer during Tier 3 and Tier 4 years, as requested, further decreases the uncertainty associated with high mortality values modeled for Tier 3 and Tier 4 years. NMFS expects that any actions taken would increase the likelihood that resulting mortality values would be minimized to the extent practicable, particularly for winter-run Chinook salmon. Additionally, delayed diversions for rice decomposition during the fall months 245 Biological Opinion for the Long-Term Operation of the CVP and SWP could provide increased reliability that target flows would be met according to the Fall and Winter Refill and Redd Maintenance operations for buiMing storage and reducing the effects of flow fluctuations. 2.5.2.6.1.8 SRSC Recovery Program The SRSC have carried out 41 Salmon Recovery Program actions since 2000, including 29 fish screen installation projects that avoid and minimize juvenile salmonid and sDPS green sturgeon injury and death at agricultural diversions, four fish passage projects tlhat improve fish passage to upstream spawning habitat and reduce straying into the Colusa Basin, and eight spawning and rearing habitat improvement projects that contribute to increased production and improved growth and survival of juvenile salmonids and sDPS green sturgeon. The continuation of these actions are expected to result in long-term benefits to winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, sDPS green sturgeon, and their designated critical habitats. The actions would also benefit fall-run Chinook salmon (which would provide benefits to southern resident killer whale by improving prey availability). The anticipated long-term benefit associated with increasing the quantity and quality of spawning substrate in the upper Sacramento River will affect adult salmonids in particular as they return to spawn and may result in increased production over time. The frequency of exposure is assumed to be high because completed restoration activities would result in a semipermanent increase in spawning habitat availability. The benefits associated with increasing the quantity and access to quality side-channel and inchannel rearing habitat in the upper and middle Sacramento River will affect rearing and migrating juvenile salmonids and sDPS green sturgeon. The frequency of exposure is assumed to be high because completed restoration activities would result in a semi-permanent increase in rearing habitat availability. The benefits associated with modifications to existing man-made structures from Keswick downstream to Verona will affect adult migrant and rearing and migrating juvenile salmonids and sDPS green sturgeon. The frequency of exposure is assumed to be high because completed restoration activities would result in a semi-permanent increase in rearing habitat availability. 2.5.2.6.1.9 SRSC Commitment to the Sacramento River Science Partnership The Sacramento River Science Partnership (Partnership) will establish a general agreement, understanding, and framework for the establishment and implementation of the Mainstem Sacramento River Integrated Water and Fish Science and Monitoring Partnership between the The scope, mission, and objectives of this Partnership are expected to improve the science that is used to protect and support the recovery of winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead. The Partnership is also expected to provide benefits to sDPS green sturgeon and fall-run Chinook salmon and to result in benefits to SRKW since Chinook salmon are such an important prey base. 2.5.3 Trinity River Division (Clear Creek and Spring Creek Debris Dam) During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, biological assessment. 246 Biological Opinion for the Long-Term Operation of the CVP and SWP Sections 2.5.3.1-4, and 2.6.3.1 of the effects description below is based on the modeling associated with the February 5, 2019 PA (Appendix AI) and associated modeling that NMFS requested, and the April 30, 2019 PA (Appendix A2). Section 2.5.3.3 provides an effects analysis to assess the effects of the June 14, 2019 PA revisions reflected in the final PA (Appendix A3). Reclamation operates the Trinity River Division to divert water to the Sacramento River system, and to ensure necessary flow releases into the Trinity-Klamath Basin. Operations are in coordination with the Shasta Division to: (1) support water supply and hydroelectric power generation for the CVP, (2) manage flood control, and (3) meet minimum flow and water temperature objectives within the Trinity River, Clear Creek, and Sacramento River. PA components for the Trinity Division include (1) Whiskeytown Reservoir Operations, (2) Clear Creek Minimum Flows, (3) Clear Creek Channel Maintenance and Spring Attraction Pulse Flows, and (4) Spring Creek Debris Dam (ROC on LTO BA Table 4-6 [ROC on LTO BA]). A depiction of the de constructed action describing how the PA components relate to each other is provided in Figure 2.5.3-1. The primary stressors influenced by each PA component are identified in Table 2 .5 .3-1. A full description of each stressor is found in the Stressor Introduction Section 2.5.1. The temporal and spatial occurrence of the listed species life stages is described in 2.5.3.1. The exposure, risk and response of each species to the project-related stressors are analyzed in the following sections for each PA component. 247 Biological Opinion for the Long-Term Operation of the CVP and SWP Trinity Seasonal Operations Spring Creek Debris Dam Clear Creek Water Temperature ManagemcntSununcr Water Temperature ManagementFall Minimum lnstrcam Base Flows Spring Attraction Pulse Flows Channel Maintenance Pulse Flows Figure 2.5.3-1. Deconst ructed action describing the relation of PA components in the Trinity Division. Table 2.5.3-1. Primary stressors influenced by the P A components covered in the Trinity River Division effects analysis. Project Component Spring Creek Debris Dam X X X Water Temperature ManagementSummer X X 248 Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component Water Temperature Management Fall Minimum Instream Base Flows Spring Attraction Pulse Flows Channel Maintenance Pulse Flows X X X X X X X X X X X X X X X X X X X 2.5.3.1 Temporal and Spatial Occurrence of Listed Salmonids in Clear Creek 2.5.3.1.1 CV Spring-run Chinook Salmon Adult CV spring-run Chinook salmon migrate into Clear Creek from April to August, and peak passage occurs in May and June (Giovannetti and Brown 2013, Clear Creek Technical Team 2018). Adults distribute throughout Clear Creek and hold in deep pools throughout the summer from Whiskeytown Dam (RM 18.3) as far downstream as RM 4. Whiskeytown Dam precludes historical access of CV spring-run Chinook salmon to the upper Clear Creek watershed, and there is not complete spatial or temporal separation between fall-run Chinook salmon and CV spring-run Chinook salmon during spawning (Giovannetti and Brown 2013). CV spring-run Chinook salmon migrate into Clear Creek several months before fall-run Chinook salmon migration begins. A large portion of the CV spring-run Chinook salmon typically moves to the upstream I 0 miles of the creek, to hold in the colder water of the canyon. Before the arrival of fall run Chinook salmon, and just prior to the onset of CV spring-run Chinook salmon spawning, the USFWS installs and operates a temporary weir each year to physically separate the two runs during spawning to minimize hybridization and redd superimposition. The segregation weir is placed at RM 7.5 or 8.2 in late August and left in place until early November after the peak of fall-run Chinook salmon spawning when there is no chance of hybridization, and risk of redd superimposition is very low. The weir location and timing were determined to protect the most CV spring-run Chinook salmon, while minimizing effects to other salmonids (Giovannetti and Brown 2013). Any CV spring-run Chinook salmon downstream of the weir are likely to hybridize with fall-run Chinook salmon, or redds would be subject to redd superimposition. 249 Biological Opinion for the Long-Term Operation of the CVP and SWP Spawning occurs from early September through October, and peaks in late-September (Giovannetti and Brown 2013). Egg incubation occurs from September to early February based on redd timing. Based on juvenile passage indices from the USFWS rotary screw trap (RM 8.4), fry emergence begins in early November, peak passage occurs from mid-November through January, and a small number of juveniles and smolts are captured throughout the remainder of the monitoring season, which generally ends on July 1 annually (Earley et al. 2009, Schraml et al. 20 18). While the majority of juvenile CV spring-run Chinook salmon outmigrate as fry, a portion rears in Clear Creek through the spring and summer, and emigrate as sub-yearlings. Juvenile CV spring-run Chinook salmon have been observed during snorkel surveys in the spring and summer months (U.S. Fish and Wildlife Service 2007). 2.5.3.1.2 CCV Steelhead Adult CCV steelhead migration into Clear Creek begins in late-August and continues through April. CCV steelhead spawning begins in mid-December and continues through April, with peak spawn timing occurring from mid-December through early February. Spawning is distributed throughout the creek, with the majority of redds located downstream of RM 6 in recent years (Schaefer et al. 2019). Egg and alevins are present in redds from mid-December through June. Emergent fry are first observed in the rotary screw traps beginning in mid-January, and juvenile CCV steelhead are captured during all months of monitoring, which occurs from November through June (Schraml et al. 20 18). Underwater observational surveys for various studies and fish rescue operations during restoration work by the USFWS have also documented the presence of juvenile CCV steelhead in the summer and fall months. Juvenile CCV steelhead rear in fresh water from one to three years. Multiple year classes of juvenile CCV steelhead rear in Clear Creek year round, and are distributed throughout the entire length of the creek. Based on rotary screw trap catch, smolts account for a low proportion of the juvenile passage indices. For example, in 2012, smolts accounted for 1.4 percent passage and were observed January through May (Schrarnl et al. 2018). However, larger-sized juveniles and smolts more easily avoid capture in the rotary screw traps, and passage estimates may underestimate these life stages. 2.5.3.1.3 Sacramento River Winter-run Chinook Salmon On occasion, the USFWS has observed adult winter-run Chinook salmon and evidence of spawning in Clear Creek during monitoring since surveys began in 1999 (Newton and Brown 2004, Killam and Mache 2018). Video monitoring data at the mouth of Clear Creek has documented adults passing upstream, and although rare and intermittent, a few carcasses and redds !have been reported over the years. Most recently, in July 2017, one redd was observed and three hatchery-tagged winter-run Chinook salmon carcasses were recovered (Clear Creek Technical Team 2019). Observations of winter-run Chinook salmon have only been made in the lower 6 miles of Clear Creek. 2.5.3.2 Seasonal Operations and Whiskeytown Reservoir Operations The Trinity Reservoir supply and operations are in coordination with the Shasta Division to support water supply and hydroelectric power generation for the CVP, manage flood control, and meet minimum flow and water temperature objectives w ithin the Trinity River, Sacramento River, and Clear Creek. The Department of the Interior's 2000 Trinity River Mainstem Fishery Restoration Record of Decision (2000 ROD) seasonally regulates trans-basin diversions to 55 250 Biological Opinion for the Long-Term Operation of the CVP and SWP percent of the approximately 1.2 MAF annual inflow on a 10-year average basis, which impacts Reclamation's temperature operations and CVP deliveries on the Sacramento River. Water diversions from the Trinity Division to the Shasta Division have averaged about 650,000 T AF per year from 2001-2018 (Trinity River Restoration Program). Trinity River water is diverted from Lewiston Reservoir to Whiskeytown Reservoir through the Clear Creek Tunnel and Carr Power Plant. The diverted water flows through Whiskeytown Reservoir, and is diverted either into Spring Creek Tunnel, through Spring Creek Power Plant, and into Keswick Reservoir where it is released into the upper Sacramento River; or is released from Whiskeytown Dam into Clear Creek. The Whiskeytown Reservoir Operations PA component includes: (1) regulation of inflows for power generation and recreation; (2) support of upper Sacramento River temperature objectives; and (3) providing releases to Clear Creek to meet water temperature objectives for CV spring-run and CCV steelhead. Whiskeytown Reservoir has a capacity of 241 TAF at the 1,21 0 feet reservoir surface elevation, and current operations build storage in the spring. It is drawn down by approximately 35 TAF from November through April to regulate wet-season runoff for winter and spring flood management. Heavy rainfall events and flood control management occasionally result in glory hole spillway discharges into Clear Creek. Although Whiskeytown Reservoir is primarily used as a conveyance system for trans-basin dliversions, Reclamation operates both Carr and Spring Creek Power plants to generate electricity and maintain lake elevations for recreation. Hydroelectric power is also generated at the City of Redding power plant, located immediately downstream from Whiskeytown Dam. Whiskeytown Reservoir also supplies domestic water to the Clear Creek Community Services District. The volume of water moving through Lewiston and Whiskeytown reservoirs affects Sacramento River and Clear Creek water temperatures. There are two temperature control curtains located in Whiskeytown Reservoir, designed to work in tandem to reduce mixing of cold water inflows and warm surface waters, and to enhance cold water availability to the Whiskeytown Reservoir outlets at Spring Creek Tunnel (1,085 ft. elevation) and Whiskeytown Dam (Vermeyen 1997, Clear Creek Technical Team 2018). The Oak Bottom Temperature Control Curtain (replaced in May 2016) is located at the Carr Powerplant Tailrace, and the Spring Creek Temperature Control Curtain (replaced in 2011) is located at the Spring Creek Tunnel intake (Clear Creek Technical Team 2018). The outlet works at Whiskeytown Dam has two intakes (the upper one at 1,100 ft. elevation, and the lower one at 972ft. elevation) to release water into Clear Creek. Reclamation evaluates thermal profiles of Whiskeytown Reservoir throughout the year, and thermal stratification typically begins around April. The outlets access different water temperature zones in the stratified reservoir and can be operated to help manage downstream temperatures and conserve the cold-water pool. Reclamation proposes to continue providing temperature profile measurements for Whiskeytown and Trinity Reservoirs to support operational decisions for water temperature management. While Trinity Seasonal Operations were included as a PA component, Reclamation did not specifY any operational actions beyond water availability in Whiskeytown Reservoir. Whiskeytown Reservoir Operations related to Clear Creek releases include water temperature management, minimum instream base flows, and spring attraction and channel maintenance flows described in Section 2.5.3.4. 251 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.3.3 Spring Creek Debris Dam After a consultation meeting on May 21, 2019, Reclamation provided an updated description of the Spring Creek Debris Dam PA component (Caramanian 2019), and a final PA on June 14, 2019 (Appendix A3), which included additional details that are summarized here. Because Reclamation did not provide an effects analysis of this P A component, we included some assumptions to determine effects to species and habitat. Spring Creek Debris Dam was constructed to regulate runoff containing debris and acid mine drainage from Spring Creek, a tributary to the Sacramento River that enters Keswick Reservoir. Runoff containing acid mine drainage from Iron Mountain Mine is stored in Spring Creek Reservoir. In January 1980, Reclamation, CDFW, and SWRCB exectl!ted a memorandum of understanding (MOU) to implement actions that protect the Sacramento River system from heavy metal pollution from acid mine drainage in Spring Creek and adjacent watersheds. Since 1990, concentrations oftoxic metals have been reduced by approximately 95 percent from what historically emptied into the Sacramento River (Caramanian 20 19). This reduction was due to significant remedial actions by the EPA including the completion of (1) Minnesota Flats Iron Mountain Mine Acid Mine Drainage Treatment Plant in 1994, (2) Slickrock Creek Retention Reservoir in 2004 and, (3) dredging of contaminated sediments from the Spring Creek arm of Keswick Reservoir in 2009-2010. Due to improvements in water quality, operation of the Spring Creek Debris Dam and Shasta Dam have deviated from the I 980 MOU, and as a result, Reclamation CDFW, SWRGB and EPA are progressing towards a revised MOU with similar guideI ines to what Reclamation is proposing for interim operations as part of this PA. Reclamation is proposing to implement operational actions involving water releases at Spring Creek Debris Dam, Spring Creek Power Plant, and Keswick Reservoir, that result in meeting water quality criteria standards for concentrations of copper and zinc from acid mine drainage pollution from Spring Creek at a compliance point in the Sacramento River, to protect aquatic life. Reclamation proposes to conduct water quality monitoring, and with increased frequency during Spring Creek Debris Dam spillway releases, or when there are drops below the minimum elevation threshold in Spring Creek Reservoir. The operation described herein is also dependent on the water treatment capabilities afforded by EPA. Storage elevation levels in Spring Creek Reservoir determine the operational action used to maintain water quality criteria in the Sacramento River. Actions include (1) undiluted controlled releases when storage is between 720 and 795 feet, typically December through June, (2) dilution releases through the spillway, combined with increased releases from Keswick Dam, when storage exceeds 795 feet, and (3) no releases from the reservoir when storage is below 720 feet, and instead a minimum dilution flow of 250 cfs from Spring Creek Power Plant. Reclamation operates to maintain Spring Creek Reservoir storage elevation between 720 and 795 feet, and Reclamation assumes operational scenarios for levels above or below this range would occur very infrequently. In the unlikely situation when the Spring Creek Debris Dam spillway is used, Reclamation anticipates an "emergency" relaxation ofEPA's criteria for a 50 percent increase in the objective concentrations of copper and zinc. Although the general operational goal is to avoid use of the Spring Creek Debris Dam spillway, some storm events or series of events are unavoidable. The spillway operation typically occurs during a large storm or series of events, January through April, and are coincident with large flood management flows released from Keswick Dam. In 252 Biological Opinion for the Long-Term Operation of the CVP and SWP recent years EPA, Reclamation, CDFW, and the RWQCB have agreed not to use the emergency criteria until a spill is imminent. During significant rain events Spring Creek Debris Dam releases may target a dilution ratio with Keswick releases to achieve an acceptable water quality below Keswick Dam. Spring Creek Reservoir spillway dilution flows from Keswick are expected to be coincident with large flood management flows and are not expected to impact water supply or cold-water pool resources. Reclamation also does not plan to operate Spring Creek Reservoir below 720 feet elevation to avoid potentially significant degraded water quality when reservoir soils are exposed, and assumes this would only occur in a very rare situation. Any time dilution flows are necessary, Reclamation's objective is to minimize the build-11.1p of toxic metals in the Spring Creek arm of Keswick Reservoir. To accomplish this, the releases from the debris dam are coordinated with releases from Spring Creek Powerplant (Spring Creek Power Plant draws water from Whiskeytown Reservoir) to keep the metals in circulation within the main body of Keswick Reservoir. 2.5.3.3.1 Sacramento River Winter-run, CV Spring-Run Chinook Salmon, CCV Steelhead, and Green Sturgeon Exposure, Response, and Risk In conjunction with the EPA remedial actions, the proposed operation of Spring Creek Debris Dam will be operated to decrease concentration levels of zinc and copper entering the Sacramento River, and minimize adverse physiological effects to listed salmonids and green sturgeon. Spring Creek Debris Dam spillway releases will likely only occur during large storms from January through April when the Spring Creek Reservoir is over 795 feet, resulting in higher flows into the Sacramento River. In addition, higher Keswick releases will be needed to dilute contaminants being spilled from the Spring Creek Debris Dam, and achieve the water quality criteria level below Keswick Dam. Increased Keswick releases during these months, may result in a decrease of Shasta Reservoir storage, and have the potential to impact water supply and cold-water pool resources reserved for summer and fall months for the Sacramento River. Warmer releases into the Sacramento River may occur resulting in exposure to unsuitable water temperatures for CV spring run and Sacramento River w inter-run Chinook salmon, spawning, and egg incubation. Because Spring Creek Reservoir spillway dilution flows from Keswick are expected to coincide with large flood management flows, they are not expected to impact water supply or cold-water pool resources. Flow changes in the Sacramento River between January and June have the potential to impact CCV steelhead spawning and juvenile CV steelhead, Sacramento River winter-run, and CV spring-run Chinook salmon rearing. Large increases may expose salmonid embryos in redds. to risk of scour and fine sediment infiltration, and flow decreases may strand or isolate juvenile salmonids in side channels downstream of Keswick Dam. On the rare occasion when Spring Creek Reservoir is below 720 feet storage elevation and increased releases from Spring Creek Powerplant are needed for dilution flows, additional water draw from Whiskeytown Reservoir may impact cold-water pool resources. Warmer releases from the reservoir into Clear Creek during CV spring-run Chinook salmon holding, spawning, and egg incubation could result in decreased egg survival. In any operational scenario, NMFS expects contaminants to remain within standards and physiological effects of contaminants on listed fish are not expected to occur. Reclamation will 253 Biological Opinion for the Long-Term Operation of the CVP and SWP monitor water quality in the Sacramento River as described in the 1980 MOU, and w ith increased sampling frequency during dilution flows, and altered operations if necessary to ensure levels of contaminants are within standards. Reclamation expects to maintain reservoir levels, such that dilution flow operations are not expected to occur. As the EPA treatment plant is the first defense to keeping acid mine pollution within water quality standards in the Sacramento River, NMFS adopts Reclamation 's assumption regarding proposed operation of Spring Creek Debris Dam. Therefore, exposure to Sacramento River flow, water temperature, or contaminant stressor effects in Clear Creek are not expected to occur to extents that would result in impacts to listed species. 2.5.3.4 Clear Creek This section addresses the portion of Trinity River Division water that is diverted into Whiskeytown Reservoir and becomes part of Clear Creek releases. Reclamation proposes to provide releases from Whiskeytown Dam into Clear Creek to: (1) to meet water temperature objectives for CV spring-run and CCV steelhead, (2) provide minimum instream base flows, and (3) create pulse flows for both attraction of adult CV spring-run Chinook salmon and channel maintenance. In years when channel maintenance flows do not occur, Reclamation proposes to use mechanical methods to mobilize gravel or shape the channel, if needed, to meet biological objectjves. Each PA component and their effects on listed species in Clear Creek are described below. 2.5.3.4.1 Clear Creek Temperature Management Reclamation proposes to manage Whiskeytown Dam releases to meet a daily average water temperature of(l) 60°F from June 1 through September 14, and (2) 56°F or less from September 15 to October 31 at the U.S. Geological Survey Igo stream gaging station (IGO), located at RM 11.0 on Clear Creek (U.S. Geological Survey 2019). In Critical or Dry water year types (based on the Sacramento Valley 40-30-30 Index Water Year Hydrologic Classification [California Data Exchange Center (Department of Water Resources 2019)], Reclamation will operate to as close to these temperatures as possible, but acknowledges temperature criteria may not be met. During the water temperature management period, Reclamation proposes to increase minimum instream base flows when needed to meet criteria. Water temperature criteria in the P A are the same as current operations, which were developed to reduce thermal stress to CV spring-run Chinook salmon during holding, spawning, and embryo incubation, and over-summering CCV steelhead. The amount of cold-water pool available depends on carry-over storage, reservoir water temperature, and the amount, timing, and water temperature of inflows from Trinity Reservoir through Whiskeytown Reservoir to Keswick Reservoir and Clear Creek. Since the Trinity River 2000 ROD flows were first implemented in 2005, temperature compliance of 56°F or less during the September 15 to October 31 spawning period (as discussed below) has been more difficult to meet due to changes in water diversion patterns that have resulted in longer residency time and warming in Whiskeytown Reservoir. By September, the cold-water pool in Whiskeytown becomes limited, and in some cases may result in less cold water available for Clear Creek during the CV spring-run Chinook salmon spawning period. Operational strategies that have been used to offset this limited cold water availability have included early recognition to use 254 Biological Opinion for the Long-Term Operation of the CVP and SWP different outlet configurations at Whiskeytown Dam to conserve and access colder water during periods of thermal stress (He and Marcinkevage 20 16). Additional operational strategies that have been used in the summer to conserve cold water for the CV spring-run Chinook salmon spawning period include reducing Clear Creek releases in July, and avoiding full power peaking operations at Trinity, Carr and Spring Creek powerhouses (Clear Creek Technical Team 2013). The recent replacement of the tom temperature control curtains in Whiskeytown Reservoir are expected to help to provide more cold water, and Reclamation's Technical Service Center is currently evaluating of the performance ofboth temperature curtains, with a final report expected in 2019. For the Clear Creek analysis, Reclamation used the HEC-5Q model, to simulate temperature conditions on the rivers affected by CVP and SWP operations, using CalSimii output for Whiskeytown Reservoir. Output was provided for three locations: Whiskeytown Dam (RM 18), IGO temperature compliance point (RM 11 ), and the confluence of Clear Creek and the Sacramento River. The current operating scenario (COS) refers to the current modeling representation of project operations at the time of consultation. Because the proposed temperature management is the same as current operations, the P A and COS modeling results are similar. To evaluate thermal conditions for adult and juvenile salmonids in Clear Creek, exceedance plots of monthly mean water temperatures were examined with consideration of the temperature criteria under various water year types (Figure 2.5.3-2). While monthly exceedance plots are useful for assessing the conditions that the PA component will provide monthly, they do not reflect the daily water temperature that occurs. In addition, because the temperature criterion changes on September 15, it is difficult to compare monthly temperatures to the different criterion period. HEC-5Q modeling results showed that water temperature objectives are met at IGO each month under the PA component, except in Critical water year types, which are expected to occur in 15 percent of years (Table 2.5.3-2). In Critical water year types, monthly average temperatures exceeding 56°F are expected to occur approximately 7 percent of the time in September and October (Figure 2.5.3-2). 255 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.3-2. HEC-5Q modeling results at the IGO gaging station temperature criteria compliance point for the proposed action. Results include monthly average water temperatures and probability of exceedance, and mean monthly water temperature under the different water year types (source: ROC on LTO BA, Appendix D, Attachment 3-4, Table 3-3). Statistic Probability of Exceedance 10% Oct Dec Jan Monthl)! Tem(!!rature (OEG-F) Feb Mar Ma)! Jun Jul Aug Se!! 46.3 46.1 47.3 49.1 56.6 56.6 55.6 48.2 47.1 45.6 45.2 45.6 45.2 46.9 46.5 48.6 48.1 50.3 49.9 49.4 53.1 54.2 53.8 52.2 51.8 51.1 48.7 20% 30% 40% 50% 52.5 51.9 56.0 55.4 56.2 55.7 54.7 54.3 53.4 53.0 50.9 50.6 46.8 46.5 44.9 44.6 45.0 44.8 46.1 45.9 47.9 47.6 49.2 48.9 51.6 51.2 55.2 55.0 55.6 55.3 54.0 53.5 60% 70% 52.4 51.8 51.2 50.4 50.2 49.8 46.3 46.1 45.9 44.3 44.1 43.9 44.5 44.2 44.0 45.7 45.5 45 .3 47.4 47.2 46.9 48.6 48.4 48.1 50.9 50.7 50.3 54.6 54.5 54.2 55.2 54.9 54.5 53.1 52.9 52.4 50.7 49.4 45.5 43.6 43.8 44 .8 46.4 47.4 49.6 53.8 54.0 52.1 53.0 50.8 46.9 44.8 44.9 46.0 47.7 48.9 51.4 55.0 55.3 53.8 Wet (32%) Above Normal (16%) Bel'ow Normal (13%) 51 .4 50.1 46.5 44.5 44.5 54.9 55.0 52.8 47.4 47.6 51.1 52.3 45.1 46.0 46.3 47.2 47.9 48.9 48.9 50.1 50.9 50.9 51.3 53.4 54.8 55.0 53.6 56.3 44.6 44.2 45.0 45.7 44.6 44.5 Ory (24%) Critical (1 5%) 46.4 46.8 47.2 47.5 48.6 48.7 48.5 50.9 50.1 51.0 45.5 45 .7 45.9 47.2 51.9 53.1 54.9 55.2 55.7 56.2 52.7 53.5 54.2 56.7 80% 90% 55.0 Nov l ong Term 1 Full Simulation Period Water Year Typesb,c 55.0 55.5 • Based on the 82-year Ca!Simii simulation period. bAs defined by the Sacramento Valley 40-30-30 Tndex Water Year Hydrologic Classificat ion (SWRCB D-I 64 I, I999). c These results are displayed with calendar year type sorting. 256 Biological Opinion for the Long-Term Operation of the CVP and SWP septemb er Clear C re ek at 64 go Te mperature - 62 60 ) ) ' 58 56 54 52 so r -- - ------ - ----- 46 44 10 0% 90% 80% 70% 60% SO% 40% 30"4 20% 10% 0% Probability of Exceedence - - - COS6 - - PA5(wo\ISA) 0 etob er Cl ear C ree k at go Temperature - 64 I 62 I I 60 I rf 58 -- 56 54 52 so 46 44 100% 90% 80% 70% 60% SO% 40% 30% 20% 10% 0% Probability of Exceedence - - - COS6 - - PA5(wo\ISA) Figure 2.5.3-2. HEC-5Q modeling result exceedance plots based on the 82-year CaiSimll simulation period, in September and October at the IGO gaging station temperature compliance point. Plots compare the Current Operating Scenario (COS6) to the Proposed Action (PA5woVSA), and the probability that monthly average water temperatures (degrees Fahrenheit) will occur. Because the temperature criteria changes on September 15, it is difficult to compare monthly temperatures to the different criteria periods (source: ROC on LTO BA, Appendix D, Attachment 3-4, Figure 3-7 and Figure 318). The water temperature criteria as proposed, have been in place in Clear Creek since 1999. Since 1999, daily average water temperatures have generally been below 60°F at IGO during the summer holding period (Figure 2.5.3-3). However, water temperatures have exceeded 56°F 257 Biological Opinion for the Long-Term Operation of the CVP and SWP during the spawning period, and exceedance occurs more frequently in drier water year types (Figure 2.5.3-4, Figure 2.5.3-4). In general, exceedance occurs when the cold-water pool is depleted in Whiskeytown Reservoir. 65 • • • • HEC-5Q mean monthly (V/et) --- HEC-5Q mean monthly (Critical) Criteria ,-.. 60 0 ... '-' -§ Q) i:l "' 55 Q) Q) 6L Q) .. Q .• . ............... 50 6/1 6/15 6/29 7/13 7/27 8/ 10 8/24 917 9/21 10/5 10/19 Date Figure 2.5.3-3. Daily average water temperatures during the water temperature management season. (Criterion=60 °F from June 1-Sept 14; and :S56°F September IS-October 31) at the U.S. Geological Survey IGO, located at RM 11.0 on Clear Creek, 1999-2018. The PA HEC-SQ monthly water temperature modeling results during Sacramento Valley Index water year type Critical and Wet are shown for comparison. 258 Biological Opinion for the Long-Term Operation of the CVP and SWP 100% -- 9096 -- 801999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 -- 50percent of period met ?temperature criteria minimum DAT maximum DAT Figure 2.5.3-4. Minimum and maximum daily average water temperatures (DAT) during the fall water temperature management period (Sept 15-Oct 31) for CV spring-run Chinook salmon spawning, when DAT at the U.S. Geological Survey Igo stream gaging station (IGO), located at RM 11.0 on Clear Creek, are managed to 1999-2018. Bars correspond to the axis on the right, and represent the percent of days DAT were met within the period, and indicate the Sacramento Valley Index water year type (W=wet; AN=above normal; BN=below normal; D=dry; and C=critical). The mouth of Clear Creek is the extent of juvenile rearing habitat and outmigration of CV spring-run Chinook salmon and CCV steelhead, and (2) CCV steelhead spawning habitat. Water temperatures at the mouth during the temperature management season generally represent the warmest temperatures in Clear Creek. The mouth is also the entry point of upstream adult migration where water temperatures are ?rst experienced. Daily average water 259 Biological Opinion for the Long-Term Operation of the CVP and SWP temperature measurements near the mouth of Clear Creek from 1999 1to 2018 ( 75 - - HEC-5Q mean monthly (Critical) ····· HEC-5Q mean monthly (Wet) 70 !;"< .._.. 65 ....... . Ci) II> -a j:I., "' 60 II> II> SJ II> Q 55 6/ 1 6/ 15 6/29 7/ 13 7/27 8/ 10 8/ 24 Date 917 9/21 10/5 10/ 19 Figure 2.5.3-5), range above HEC-5Q monthly modeled temperatures during the temperature compliance period (Table 2.5.3-3, Figure 2.5.3-5). The discrepancy between actual and modeled temperatures may be due to differences in locations. Particularly in the summer months when the Sacramento River releases are high, flows create backwater into Clear Creek and cool the mouth, which may be influencing the model results. 260 Biological Opinion for the Long-Term Operation of the CVP and SWP 75 - - HEC-5Q mean monthly (Critical) ····· HEC-5Q mean monthly (Wet) 70 !;"< .._.. 65 ....... . Ci) II> -a j:I., "' II> II> 60 SJ II> Q 55 6/1 6/ 15 6/29 7/13 7/27 8/ 10 8/ 24 Date 917 9/21 10/5 10/ 19 Figure 2.5.3-5. Daily average water temperatures during the temperature compliance period near the mouth of Clear Creek for the years 1999-2018 (Chamberlain 2019c). The PA HEC-SQ monthly water temperature modeling results during Sacramento Valley Index water year type Critical and Wet are shown for comparison. 261 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.3-3. HEC-5Q modeling results at the mouth of Clear Creek for the proposed action. Results include monthly average water temperatures and probability of exceedance, and mean monthly water temperature under the different water year types (source: ROC on LTO BA, Appendix D, Attachment 3-4, Table 4-3). !DEG·F! Sta!istic Probab'llity of Exceedance 10% 20% 30% 40% 50% 60% 70% 80% 90% Oct 56.0 55.1 54.6 54.2 53.9 53.1 52.7 Nov Dec 48.9 48.3 47.4 47.0 46.8 52.2 51 .8 52.6 52.1 51.6 51.2 50.9 50.7 50.5 50.1 49.7 53.9 52.4 52.8 53.9 54.5 57.5 Jan Feb Mar 46.6 46.3 45.9 45.8 45.5 48.4 48.2 47.9 47.4 47.0 46.5 46.3 46.6 45.9 45.5 45.3 44.9 44.7 44.3 45.2 45.0 46.1 45.6 44.1 43.9 51.1 47.0 50.4 50.4 51.3 51.4 52.7 Jun 52.1 51.8 51.3 50.9 50.7 56.9 55.5 54.9 54.5 54.1 46.9 46.6 50.9 50.3 49.8 49.5 49.2 49 1 48.9 50.5 50.2 44.7 44.5 46.4 45.9 48.5 48.1 45.1 45.6 47.2 49.4 46.7 44.9 45.0 44.5 45.2 46.0 45.2 45.3 452 45.8 46.8 46.6 46.6 47.0 47.4 47.6 46.9 47.0 47.5 48.5 Jul Aug 53.8 53.4 62.2 61.7 61.1 60.8 60.6 60.4 60.1 61.4 61 .0 60.7 60.5 60.2 60.1 59.8 49.9 49.1 53.1 52.5 59.9 59.5 59.4 59.1 57.7 56.9 56.6 56.3 55.8 55.4 55.2 54.8 54.4 50.8 54.5 60.7 60.2 56.1 48.8 504 490 49.4 49.6 50.9 506 50.3 50.7 52.3 53.7 53.8 53.8 54.3 57.9 60.6 60.5 60.6 60.7 61.3 60.0 59.8 60.0 60.6 60.8 55.2 55.0 55.7 56.4 59.1 Long Term Full Simulation Water Year Typesb,c Wet (32%) Above Normal (16%) Below Normal (13%) Dry (24%) Critical !15%) • Based on the 82-year CalSimn simulation period. bAs defi ned by the Sacramento Valley 40-30-30 Index Water Year Hydrologic Classification (SWRCB D-1641 , 1999). c These results are displayed with calendar year type sorting. 2.5.3.4.1.1 CV Spring-Run Chinook Salmon Exposure, Response, and Risk The water temperature management season encompasses the CV spring-run Chinook salmon adult holding, spawning, and egg incubation!alevin development life stages, and ends just prior juvenile emergence. A small number of sub-yearling juveniles are present during the temperature management season. The PA HEC-5Q monthly water temperature modeling results during the summer water temperature management period (60°F at IGO from June !-September 14) show average monthly water temperatures well below the 60°F criterion from June-August in all water year types (Table 2.5.3-3 and Figure 2.5.3-3). Under current operations, daily average water temperatures at IGO from 1999-2018 were consistently warmer than what was modeled for the PA (Table 2.5.33 and Figure 2.5.3-3). Daily average water temperatures have only exceeded 60°F at IGO for a few days in some years under current operations (except in 2000, when flow releases were low to accommodate the removal of Saeltzer Dam). Under current operations, average monthly summer base flows in July and August have ranged between 50 cfs and 180 cfs. Base flows greater than 150 cfs have been released in Critical water year types under current operations to meet water temperature criterion in the summer, and will likely be needed under the PA. Use of higher base flows in the summer may degrade the cold-water pool in Whiskeytown Reservoir, decreasing the ability to meet fall spawning water temperature criterion. 262 Biological Opinion for the Long-Term Operation of the CVP and SWP At the mouth of Clear Creek from June through August, water temperatures greater than 68°F create a passage impediment, lowering adult returns. Adult CV spring-run Chinook salmon migration into Clear Creek continues through the temperature management period, with approximately 35 percent of the population index passing in June, and very low numbers passing in July and August. Daily average water temperatures near the mouth of Clear Creek from 1999 to 2018 were generally within optimal ranges for adult migration in June; suboptimal (>68°F) during some periods in July and August; and occasionally over 70°F (when migration generally stops) in July (Figure 2.5.3-5). The low rate of migration in July and August is likely due to life history characteristics of CV spring-run Chinook salmon in the Upper Sacramento tributaries, and temperature-related migration barriers associated with warmer water at the confluence of Clear Creek. Temperature and low flow barriers at riffles and cascades may inhibit access to the upper watershed in the summer. Daily average water temperatures are likely to continue to remain below 60°F upstream of the IGO compliance point under the PA based on HEC-5Q temperature modeling results, and observed daily average water temperature data under current operations (Figure 2.5.3-3). However, monitoring from 2003-2016 has shown that, annually, an average 49 percent (range = 25 to 73 percent) of the adult CV spring-run Chinook salmon population index is located downstream of the IGO temperature compliance point at RM 11.0 (Figure 2.5.3-6); these fish are therefore more likely to be exposed to water temperatures greater than 60°F. In addition, after the segregation weir is installed in late August, an average of 20 percent (range 1 to 36 percent) of the population index is located downstream of the segregation weir at RM 8.2 or 7.5 (Figure 2.5.3-6) and as far downstream as RM 4, where in some years, daily average water temperatures reach over 65oF (Clear Creek Technical Team 2016). The CV spring-run Chinook salmon adults downstream of the segregation weir are also subject to hybridization with fall-run Chinook salmon, and their incubating eggs would be exposed to impacts from suboptimal temperatures, and redd superimposition by fall-run Chinook salmon. 263 Biological Opinion for the Long-Term Operation of the CVP and SWP 0.8 0.7 n 0.6 0.5 200 0.4 0.2 0.1 0 25 29 68 r 11 0.3 n 120 98 45 21 nn 659 95 77 u 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 DDowustream oflgo (RM 11.0) •Downstream of Segregation \Veir (RM 7.5 or 8.2) Figure 2.5.3-6. Annual proportion of the CV spring-run Chinook salmon population index located downstream of the IGO temperature compliance point (RM 11), and downstream of the segregation weir (RM 7.5 or 8.2), in Clear Creek, 2003-2016. Label at each stacked bar represents the annual population indlex (Chamberlain 2019b). Cumulative exposure to stressful water temperatures can lead to increased risk of disease, decreased fecundity, prespawn mortality, and decreased reproductive success in adult CV springrun Chinook salmon . While daily average water temperatures are likely to remain below 60°F upstream of the IGO compliance point under the PA and to provide suitable holding habitat during the summer water temperature management period, the current adult CV spring-run Chinook salmon holding distribution pattern will likely continue under the PA, and therefore a high percentage of the population will be exposed to suboptimal water temperatures each year. During the fall water temperature management period (::S56°F at IGO from September ISOctober 31) the PA HEC-5Q monthly water temperature modeling shows difficulty meeting temperatures in Critical water year types, which are expected to occur in 15 percent of years. The P A states that meeting temperatures in Dry water year types may be difficult as well. From 1999 to 2018, the temperature criterion has been exceeded during the spawning period in 14 of 19 years (excluding 2000) at IGO, and exceedance has not been limited to Dry and Critical water year types (Figure 2.5.3-4). The temperature criterion was exceeded during the entire spawning period in 2005, 2014, and 2015 (Figure 2.5.3-4). Additionally, in 4 years (2009, 2014-2016) 264 Biological Opinion for the Long-Term Operation of the CVP and SWP average daily water temperatures continued to be above 56°F at the Whiskeytown Dam outlet, and at IGO, through mid-November. From 2003-2016, results from monitoring data have shown an average of 42 percent (range=30 to 64 percent) of the CV spring-run Chinook salmon redd index (redd count from Whiskeytown Dam to the segregation weir at RM 7.5 or 8.2) was located downstream of the temperature compliance point at IGO (Figure 2.5.3 7). In addition, an average of 8 percent (range = 0 to 26 percent) of the CV spring-run Chinook salmon annual redd index begins before September 15 (Provins 20 19a), which would be exposed to the 60°F summer water temperature management period. 0.8 0.7 0.6 0.5 0.4 22 0.3 37 0.2 53 86 82 52 64 53 10 28 25 142 0.1 0 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 1:1Redds Figure 2.5.3-7. Annual proportion ofCV spring-run Chinook salmon redd index located downstream of the IGO temperature compliance point (RM 11) in Clear Creek, 2003-2016. Labels at each bar represent the annual redd index (redd count between Whiskeytown Dam (RM 18.3) and the segregation weir at RM 7.5 or 8.2) (Chamberlain 2019b). Spawning gravel additions have created suitable spawning habitat in a 1-mile reach downstream of IGO, and a large portion of redds are located here each spawning season. Incubating eggs are exposed to different water temperatures depending on redd location. In general, redds located further upstream experience colder water temperatures in Clear Creek, especially during the earliest stages of incubation. In an evaluation of water temperature exposure at Clear Creek CV 265 Biological Opinion for the Long-Term Operation of the CVP and SWP spring-run Chinook salmon redd locations, from 2008-2018, eggs experienced mean daily temperatures over 56°F for approximately 25 percent of incubation days (Figure 2.5 . 3- C) 65°F) and for smoltification (>66.2°F), increasing their susceptibility to stress, disease, predation, and mortality. However, based on the typical CV spring-run Chinook juvenile outmigration period, a very small number are expected to be present in summer months, and even less would be located in the lower three miles where water temperatures are suboptimal. Water temperature management under the PAis not expected to affect survival of rearing and outmigrating juveniles. 267 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.3.4.1.2 Sacramento River Winter-run Chinook Salmon Exposure, Response, and Risk Winter-run Chinook salmon adults, carcasses and redds have been observed intermittently in the lower six miles of Clear Creek during monitoring surveys. Based on their spawn timing from May through August, redds located downstream of the IGO temperature compliance point under the PA would be exposed to suboptimal and lethal water temperatures, resulting in high rates of temperature-dependent mortality during the egg incubation period. In some years since 2000, water temperatures in Clear Creek within the first mile downstream of Whiskeytown Dam were suitable during the winter-run Chinook salmon egg incubation period; this would also likely occur under the P A. However, based on the very small number of adult winter-run Chinook salmon that are expected to spawn in Clear Creek, and the likelihood that spawning will occur downstream ofRM 6, any redds that are constructed are expected to be exposed to warm water temperatures, and successful egg incubation is unlikely. Juvenile winter-run Chinook salmon from the Sacramento River may rear in Clear Creek downstream of the Anderson-Cottonwood Irrigation Diversion (ACID) crossing at approximately RM 1.5. Non-natal rearing is limited to this location because the sheet pile dam protects the ACID irrigation pipe that crosses Clear Creek, creates an upstream migration barrier for juvenile salmonids. Water temperatures during fall water temperature management would provide additional suitable juvenile rearing habitat outside of the Sacramento River, increasing survival. 2.5.3.4.1.3 CCV Steelhead Exposure, Response, and Risk Migrating adults and rearing juveniles from various year classes would be present in Clear Creek during the temperature management period. Various age-classes of juvenile CCV steelhead are distributed throughout Clear Creek year-round. The warmest water temperatures occur during the summer months with potential negative impacts to the returning adults, and rearing juveniles. Depending on the length of exposure, suboptimal water temperatures can affect growth rates, increase risk of predation and susceptibility to disease, inhibit smoltification, and cause direct mortality in all life stages of CCV steelhead (U.S. Environmental Protection Agency 2003). Specifically for adults, exposure to suboptimal temperatures prior to spawning inhibit migration, increase susceptibility to disease, reduce egg viability, and increase rates ofprespawn mortality. Water temperatures may be suboptimal for adult CCV steelhead during the earliest migration and holding period. Within the temperature management period, based on preliminary adult passage data from the video monitoring station located at the mouth of Clear Creek from 2014 to 2018, an average of 40 percent (range 12-71 percent) of adult CCV steelhead migrated into Clear Creek from mid-August through October (Cook 2019, Killam 2019). Only a small portion (average 6 percent) enter Clear Creek before September 15, before flow releases increase and the temperature criterion is reduced to 56°F. Daily average water temperatures near the mouth of Clear Creek generally range from 60-70°F from mid-August to September 15, and are below 60°F consistently beginning in October (Figure 2.5.3-5). Based on a literature review of salmonid water temperature criteria, Richter and Kolmes (2005) summarized that water temperatures near 700F block steelhead migration, and recommended 60.8°F weekly mean daily temperature and 64.4°F 7DADM as criterion for adult salmonid migration. The EPA recommends migration temperatures between 18oC (64.4 oF) and 268 Biological Opinion for the Long-Term Operation of the CVP and SWP 20°C (68°F) 7DADM for Chinook salmon and steelhead to prevent migration blockage and increased risk of disease (U.S. Environmental Protection Agency 2003). Because daily average water temperatures at the mouth are generally below 60°F during the majority of the CCV steelhead migration period, and only a small proportion ofthe annual return occurs before mid-September when water temperatures exceed optimal ranges, impacts to migrating adult CCV steelhead are not expected during the water temperature management period. In addition, migration timing often corresponds to the evening hours, when water temperatures are cooler. CCV steelhead adults hold in Clear Creek until spawning begins in midDecember, and are restricted downstream of the segregation weir until early November when it is removed. Water temperatures are generally adequate for holding during this time, and therefore not expected to reduce egg viability or survival of adult CCV steelhead. Due to the winter spawn timing, the CCV steelhead egg/alevin life stages would not be exposed to the PA summer or fall temperature management regimes. In addition to protection for holding adult CV spring-run Chinook salmon, summer temperature management was designed to protect over-summering rearing juvenile CCV steelhead. Richter and Kolmes (2005) reported ideal conditions for CCV steelhead juvenile growth to be below l9°C (66.2°F), and optimal at 14-]5°C (57.2-59°F). Frequency ofanadromy in the early freshwater life stages of 0. mykiss may be influenced by environmental factors, including stream temperatures, genetic factors, and individual condition (Kendall et al. 2014). Sloat and Reeves (20 14) found significantly increased rates of anadromy in juvenile 0. mykiss reared i.n warmer temperatures (seasonally adjusted temperatures between 6 and l8°C [42.8-64.4°F], compared to 6 and 13°C [42.8-55.4°F]). During July and August, historically months with the warmest water temperatures observed in Clear Creek, the PA HEC-5Q modeling results at IGO and the mouth showed monthly average water temperatures are generally within optimal ranges for juvenile CCV steelhead rearing and growth (Table 2.5.3-2 and Table 2.5.3-3). Daily average water temperatures from 1999 to 2018 ranged from approximately 55°F to 60°F in July and August at IGO (Figure 2.5.3-3), but generally ranged from approximately 6SOF to 70°F near the mouth at the lowest extent of rearing habitat (Figure 2.5.3-5). The highest density of CCV steelhead spawning occurs in the lower 6 miles of Clear Creek. Any juveniles rearing in the furthest downstream 3 miles of Clear Creek during the summer water temperature management period would likely be exposed to suboptimal temperatures, increasing their susceptibility to stress, disease, predation, and mortality. However, CCV steelhead juvenile outmigration generally does not occur in the summer so they would not be exposed to the warmest water temperatures at the mouth, and rearing juveniles would access upstream habitat with suitable water temperatures. Based on fresh-water rearing life history of juvenile CCV steelhead, which is l-3 years, a large portion are expected to be present in Clear Creek during the summer months. However, the majority are expected to access rearing habitat with suitable water t,emperatures, and therefore exposure to suboptimal water temperatures would be limited to a small number of individuals. Although this exposure is expected to result in sublethal and lethal effects, some levels of exposure to warmer water temperatures may also be beneficial and a contributing factor influencing rates of anadromy (Sloat and Reeves 20 14). 269 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.3.4.2 Clear Creek Flow Releases Reclamation proposes to release a minimum instream base flow of 200 cfs from October I through the end of May and 150 cfs from June through September in Clear Creek, in all water year-types except Critical, when flows may be reduced based on available water from Trinity Reservoir. Additional flows may be required for fall temperature management. Base flows determine the amount of aquatic habitat available for most of the year based on the current channel configuration. Reclamation also proposes to create ( 1) spring attraction pulse flows to attract and encourage upstream movement of adult CV spring-run Chinook salmon into Clear Creek, and (2) channel maintenance pulse flows to provide sediment transport and geomorphic benefit. Up to 10 TAF for each type of pulse flow would be available annually. As described in the Appendix C ofthe ROC on LTO BA, the Clear Creek Implementation Team will provide pulse flow shaping and scheduling recommendations in coordination with Reclamation. CalSimll is a reservoir-river basin model used to simulate the coordinated operation of the CVP and SWP over a range of hydrologic conditions. CalSimii modeling assumptions included projected climate change, and sea level rise assumptions corresponding to Year 2030. Despite detailed model inputs and assumptions, the CalSimll results differ from real-time operations under stressed water supply conditions. Reclamation proposes to adjust operations when necessary, depending on conditions and constraints, to meet legal and contractual obligations. Assumptions: • Modeled runs assumed 200 cfs base flow from October through May, and 10 TAF for spring attraction pulse flows in May and June, in all but Critical water year types. While 150 cfs releases are propos,ed from June through September (Harrison 20 19b), 85 cfs is modeled in July and August in all water year types (Table 2.5.3-4). For this analysis, it was unclear if Reclamation's modeling results showing releases lower than 150 cfs in July and August was an inconsistency resulting from changes from an earlier version of the PA, or if it was a result of competing objectives for CalSimll model inputs. Reclamation clarified that the PA is 150 cfs in July and August (Harrison 20 19b), but is not simulated in the modeL Therefore, the assumption for this analysis is that the PA is what will occur, and the values in the model for these months are an underestimate, and in error. Under current operations, Clear Creek releases in July and August from 20002018 have generally been lower than 150 cfs in most years to conserve cold water pool in Whiskeytown Reservoir for fall water temperature management, except in 2014 and 2015 when base flows higher than 150 cfs were needed to meet water temperature requirements (Figure 2.5.3-9). • In Critical water year types, the proposed reduction in minimum instream base flows was not quantified. CaiSimll modeling results (Table 2.5.3 4) indicate releases would be approximately 40-75 cfs less than proposed base flows. In Critical water year types, the minimum flow releases could be as low 50 cfs from January 1-0ctober 31, and 70 cfs November-December as specified in the MOA under the 1960 minimum flow requirements (amended in 2000 under the lnstream Flow Preservation Agreement by and among U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service and California Department ofFish and Game, August 11, 2000), and under the April15, 2002 SWRCB 270 Biological Opinion for the Long-Term Operation of the CVP and SWP permit. NMFS assumes flows specified in the MOA would be the lowest minimum instream base flow releases that would occur in Critical water year types. • While the 10 TAF for channel maintenance pulse flows proposed to occur from January through April were not modeled, discussions with Reclamation clarified that this volume of water would not change model outputs significantly (Harrison 2019a). • While ramping rates during flow decreases of controlled releases from Whiskeytown Reservoir were not proposed in the PA, during technical assistance meetings between Reclamation and NMFS on May 24, 2019, Reclamation proposed rates of 15-25 cfs per hour. This range would decrease stranding risks to juvenile salmonids, and fit within the precision of the constraints of the operation of the outlets. Table 2.5.3-4. Monthly CaiSimll outputs for Clear Creek at IGO for the proposed action for all water yeartypes based on the Sacramento Valley Index (source: ROC on LTO BA, Appendix D, Attachment 32, Table 14-2). . . -,.- - - - -- .. - .. - .. - . - - - - Statistic Probability of Exceedance 10% 20% 30% 40,. 50% 60% 70% 80% 90% Long Term Full Simulation Perloi Water Year Typesb,c Wet (32%) Above Normal (16%) Below Normal (13%) Dry (24%) Criticalj15'•l Oct 200 200 200 Nov 200 200 200 Dec 200 200 200 Jan Feb 200 200 200 200 200 200 Mar Flow jCFS) Aer 200 200 200 Mal Jun Jul Aus see 200 200 200 277 277 277 200 200 200 85 85 85 85 85 85 150 150 150 200 200 200 200 200 200 200 277 200 85 85 150 200 200 200 200 150 200 200 200 200 150 200 200 200 200 150 200 200 200 200 150 200 200 200 200 150 200 200 200 200 150 200 200 200 200 150 277 277 277 277 237 200 200 200 150 150 85 85 85 85 85 85 85 85 85 85 150 150 150 150 150 187 188 190 225 207 194 191 265 181 85 86 148 200 200 195 188 133 200 200 195 188 141 200 200 195 188 154 309 192 195 190 167 249 196 195 190 167 207 196 195 190 167 200 196 195 190 167 277 277 274 267 214 200 200 191 183 111 85 85 85 85 85 85 85 85 85 94 150 150 150 150 133 • Based on the 82-year CalSimii simulation period. bAs defined by the Sacramento Valley 40-30-30 Index Water Year Hydrologic Classification (SWRCB D-1641 , 1999). c These results are displayed with calendar year- year type sorting. 271 Biological Opinion for the Long-Term Operation of the CVP and SWP July - August 200 175 {i2 150 u '-" 125 0 100 75 50 Figure 2.5.3-9. Mean monthly flows [cubic feet per second (cfs)] in July and August at the Igo gaging station (RM 11.0) from 2000-18, Clear Creek, California. Data source: SacPAS: Central Valley Prediction & Assessment of Salmon website (University of Washington Columbia Basin Research 2019). 2.5.3.4.2.1 Minimum Instream Base Flows Under the PA, minimum instream base flows are 200 cfs from October through May, and 150 cfs from June through September. Increased minimum flows of 150 cfs were first provided in the fall of 1995 for adult fall-run Chinook salmon (Brown 1996) and were based on recommendations for salmon and steelhead summarized in the Clear Creek Fishery study (Department of Water Resources 1986, Newton and Brown 2004). This flow schedule was incorporated into the CVPIA Anadromous Fisheries Restoration Program: Release 200 cfs October 1 to June 1from Whiskeytown Dam for spring-, fall-, and late fall-run chinook salmon spawning, egg incubation, emigration, gravel restoration, spring flushing and channel maintenance; release 150 cfs, or less, from July through September to maintain 60oF temperatures in stream sections utilized by spring-run Chinook salmon (U.S Fish and Wildlife Service 2001). Reclamation has integrated temperature control and minimum base flow requirements into operations since 1995, which initially led to increased returns of fall-run Chinook salmon. During the summer of 1999, Reclamation first made releases from Whiskeytown Dam to support juvenile steelhead rearing downstream of Saeltzer Dam (prior to its removal in 2000), and increased releases in the fall to reduce water temperatures for CV spring-run Chinook salmon spawning. The proposed minimum instream base flows are the same as what were established in 272 Biological Opinion for the Long-Term Operation of the CVP a nd SWP the NMFS 2009 Opinion, and therefore COS CalSimli modeling outputs and flow conditions under current opera6ons are expected to be similar under the PA. 2.5.3.4.2.1.1 CV Spring-Run Chinook Salmon Exposure, Response, and Risk Adult CV spring-run Chinook salmon migration into Clear Creek continues during the summer base flow period, with very low rates of passage in July and August (Figure 2.5.3-). From 20132016, approximately 35 percent ofCV spring-run Chinook salmon passage occurred in June, which also coincided with spring attraction pulse flows. Lowering base flows from 200 cfs to 150 cfs on June 1 would likely create a passage impediment at the confluence due to warm water temperatures, and result in decreased adult migration rates and lower returns of CV spring-run Chinook salmon to Clear Creek. I() 0 "' ---r-- 0 ' . I _...__ ..., 0 I ---.--I I ''' 0 0 __.__ .''' C'i .... EJ .. .. ---r-- 0 --r-- : _..._ 0 0 March Apnl May JI.JM! July = August Figure 2.5.3-10. Proportion of annual CV spring-run Chinook salmon passage by month at the Clear Creek Video Station from 2013 to 2016. Pulse flows have occurred all years. Lines in boxes are sample medians, box-ends are upper or lower quartiles, whiskers are minimum and maximum (Clear Creek Technical Team 2018). The low rate of migration in July and August is likely due to the timing of CV spring-run Chinook salmon in the Upper Sacramento tributaries, and temperature-related migration barriers associated with warmer water at the confluence. While summer base flows would not limit adult holding habitat or passage in the deep pools of canyon reaches, they may restrict upstream 273 Biological Opinion for the Long-Term Operation of the CVP and SWP passage from the lower alluvial reaches by creating temperature and low flow barriers at riffles and cascades. The USFWS has (1) developed rearing and spawning flow-habitat relationship curves for CV spring-run Chinook salmon, CCV steelhead, and fall-run Chinook salmon for Clear Creek; (2) compared habitat available to habitat needed to support population recovery; and (3) provided recommendations for creek flows and habitat needs for a range of population sizes (U.S. Fish and Wildlife Service 2015a). Weighted usable area (WUA) provides a metric ofCV spring-run Chinook salmon spawning and rearing habitat availability based on water depth, flow velocity, and substrate. To estimate spawning and rearing WUA available under the PA, Reclamation performed modeled runs using flow-habitat relationship curves with mean monthly CalSirnii flow estimates (Unger 2019). Differences in spawning and rearing WUA in the modeled scenarios and exceedance curves were similar for the P A and COS minimum instream base flows in all water year types. When comparing the PA WUA values to flow-habitat relationships in U.S. Fish and Wildlife Service (20 15a), the proposed minimum flows provided adequate rearing habitat for fry and juveniles, but not enough spawning habitat (Figure 2.5.3-1 ). Low estimates of spawning WUA in the modeled runs are likely due to the use of outdated WUA curves. New WUA curves were developed after gravel supplementation projects increased available spawning habitat in Clear Creek (U.S. Fish and Wildlife Service 2015a). Under the updated curves, the proposed flows provide 50,000-60,000 sq. ft. ofWUA. (Figure 2.5.3-). 274 Biological Opinion for the Long-Term Operation of the CVP and SWP Spring-run Spawning, All Years .... 9,000 1.1) c 8,000 :J ro 7,000 <( 6,000 Q) .._ Q) _o ro :J 5,000 1.1) 4,000 "0 3,000 .... .c. Q) Q() - coss - PA20 2,000 1,000 0 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Probablility of Exceedance 120000 100000 -Original Habitat Availability - 80000 Habitat Needs Ul 40,000 "'0 30,000 20,000 Q) ..c 0£) 'Q) s 10,000 - - COSS - 1 0 100% 90% 80% 70% 60% 50% 40% 30% PA20 20% 10% Probablility of Exceeda nee Figure 2.5.3-12. Weighted usable area (WUA) modeling results for CCV steelhead juvenile rearing (top) and spawning habitat (bottom) in Clear Creek under the proposed action (PA20) and current operation scenario (COSS) (Unger 2019). While the WUA results show adequate habitat, increased water temperatures associated with lowered base flows in Critical water year types and warm air temperatures in the summer may reduce the actual amount of rearing habitat available in the lower watershed. Daily average water temperatures can range from 65°F to 70°F in July and August in the most downstream three miles of the creek, which may restrict the total available habitat for rearing (Figure 2.5.3-5). In Critical water year types (15 percent of years), base flows may be reduced to approximately 150 cfs during CCV steelhead spawning, and redds may be susceptible to dewatering and egg mortality, depending on when flow decreases occur. Water year type forecasting begins February and type is determined in May. In addition, under current operations, flows greater than 200 cfs have been needed to meet water temperature criterion for CV spring-run Chinook salmon egg incubation though October 3 1. In those years, flow redU!ctions back to 200 cfs (or less in Critical 277 Biological Opinion for the Long-Term Operation of the CVP and SWP water year types) that occur after the onset of CCV steelhead spawning in mid-December would expose redds to dewatering. Any flow reductions from mid-December through April would expose a large portion of CCV steelhead redds to dewatering. In an evaluation estimating fall-run Chinook salmon redd dewatering rates in Clear Creek, flow decreases from 275 cfs to 200 cfs dewatered 6.1 percent of redds; 200 cfs to 150 cfs dewatered 11 percent of redds; and 275 cfs to 150 cfs dewatered 29 percent ofredds (USFWS 2015). We expect these rates to be similar for CCV steelhead under flow reductions that would occur under the P A. However, the proportion of CCV steelhead redds dewatered would likely more variable than fall-run Chinook salmon, due to the longer spawning season, and depending on when flow decreases occur. Based on redd dewatering rates, and the low occurrence of Critical water year types, a small amount of reduced egg-to-fry survival of CCV steelhead is expected during minimum base flow decreases. While an adequate amount of suitable spawning and juvenile rearing habitat is available based on WUA curves, the flat-lined, steady flow regime may not provide the dynamics needed to create habitat variability that supports diversity of life stages essential for survival of CCV steelhead. Steady base flows, together with reduced occurrence and magnitude of channel forming flows has resulted in the stabilization of gravel bars, riparian vegetation encroachment, and decreased habitat complexity in Clear Creek (McBain and Trush 2001, Graham Matthews & Associates 2011 ). The PA provides some flow variability to improve connectivity and channel processes that improve habitat, create migration cues, and improve downstream passage, which is discussed under the Spring Attraction and Channel Maintenance pulse flow components below. 2.5.3.4.2.2 Spring Attraction Pulse Flows Reclamation is proposing to allocate 10 T AF to create spring attraction pulse flows, with a daily release up to the safe release capacity (approximately 900 cfs, depending on reservoir elevation and downstream capacity). Pulse flows would occur in all water year types, but restricted to a 3day single event in Critical water year types. The frequency, duration, and timing would be developed by the Clear Creek Implementation Technical Team, as described in Appendix C of the ROC on L TO BA. The goal of spring attraction flows is to create hydrologic, temperature, and turbidity cues to encourage adult CV spring-run Chinook salmon to Clear Creek from the Sacramento River, and attract them to the furthest upstream habitats for holding and spawning where they can access colder water temperatures, large and remote holding pools, and newly provided, clean spawning gravel. Proposed spring attraction pulse flows may reduce stressors related to water operations by improving flow conditions and water temperature, and increase passage over impediments and improving natural river morphology and function. Spring attraction pulse flows have been implemented since 2010, and timed to coincide with the CV spring-run Chinook salmon migration period. The Clear Creek Technical team has developed the pulse flow schedule annually using an adaptive approach, by varying the timing, magnitude, and duration of releases based on monitoring results (e.g.,Clear Creek Technical Team 2016). Attraction flows are intended to mimic natural hydrologic cues, which include cooler water temperatures and increased turbidity. In years when the adult CV spring-run Chinook salmon population size is. large enough to detect, snorkel survey and video monitoring data have shown that pulse flow releases have been successful (Chamberlain 2019a). 278 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.3.4.2.2.1 Spring-Run Chinook Salmon Exposure, Response, amd Risk The proposed spring attraction pulse flows are intended to encourage entry to Clear Creek by coinciding with the adult CV spring-run Chinook salmon migration in Clear Creek, which spans from April through August, and peaks in May and June. Exposure of adult CV spring-run Chinook salmon to pulse flow conditions is dependent on both the timing of scheduled releases and adult returns. Increased flow releases of this magnitude in the spring, when base flows are decreasing and water temperatures are warming, create migration cues for adult CV spring-run Chinook salmon and improve passage conditions by cooling water temperatures, creating turbidity, and increasing passage routes. Improved passage and migratory cues would likely increase numbers of adult CV spring-run Chinook salmon into Clear Creek, and encourage upstream migration to holding pools in the coldest habitat, which would likely increase reproductive success. Spring attraction pulse flows have been implemented on Clear Creek annually since 2010, and monitoring has indicated some success. Pulse flows events have increased turbidity, decreased water temperatures, and successfully attracted CV spring-run Chinook salmon into Clear Creek at higher rates than the periods without pulse flows in some years (Clear Creek Technical Team 2016, 20 18). Monitoring data has shown that a change in distribution upstream of holding CV spring-run Chinook salmon in Clear Creek before and after pulse flows has occurred less frequently (Clear Creek Technical Team 20 19). Due to the nature of CV spring-run Chinook salmon in Clear Creek, individuals that migrate in during the pulse flows may stage and hold in the lower reaches rather than migrating upstream, and be susceptible to negative effects from warmer water and introgression with fall-run. Continued implementation of spring attraction flows in the PA in June is expected to provide increased opportunity for adult passage during the lower base flow period. Spring attraction pulse flows would not occur during CV spring-run Chinook salmon spawning and egg incubation, and therefore, this life stage would not be exposed to the effects of the pulse flows. Rotary screw trap data have shown that 97 percent ofjuvenile CV spring-run Chinook salmon emigrate as fry, with peak migration in November and December (Earley et al. 2013, Schram) et al. 2018). The remaining cohort rearing in Clear Creek would be exposed to the effects of spring attraction pulse flows annually. Rearing juvenile CV spring-run Chinook salmon have been observed in Clear Creek throughout the spring and summer months during snorkel surveys. While this life history variation appears to represent a small fraction of rotary screw trap passage estimates, these individuals may contribute significantly to the returning adult populations. In the Stanislaus River, outrnigrating juvenile Chinook salmon contributed to the returning adult spawning population in different proportion depending on their migratory strategy and flow regime (Sturrock et al. 2015). Spring attraction pulse flows are expected to benefit juvenile CV spring-run Chinook salmon by improving downstream passage. Pulse flows increase turbidity and velocity, cool water temperatures, and cr,eate cues for outmigration. Improved outmigration conditions is expected to reduce stress, disease, predation rates, and thereby improve survival. Pulse flows temporarily provide access to juvenile rearing habitat within floodplains and side channels, which may increase food availability and growth rates. Spring attraction pulse flows may also djsplace juveniles downstream into warmer water habitat, which may increase risk of predation, disease, and mortality. During spring attraction pulse flow ramp down, juveniles may also become 279 Biological Opinion for the Long-Term Operation of the CVP and SWP stranded and isolated from the creek, and succumb to predation or desiccation. Down-ramping rates will be implemented, which w ill reduce stranding risk and minimize negative impacts on survival from flow decreases. However, a low proportion of juveniles are still expected to become stranded or isolated. Each year during spring attraction pulse flows, we expect benefits to a low proportion of juveniles expected to outrnigrate, decreased survival to a low proportion of displaced juveniles of a low proportion of juveniles subject that remain in the lower reaches, and decreased to stranding. 2.5.3.4.2.2.2 Sacramento River Winter-run Exposure, Response, and Risk In some years, video monitoring data have shown winter-run Chinook salmon migrating into Clear Creek during pulse flows (Clear Creek Technical Team 2016). Winter-run adults, carcasses and redds have been observed in Clear Creek during post pulse flow surveys. Pulse flows may attract adult winter-run Chinook salmon into Clear Creek, but spawning in the lower alluvial reaches would likely be unsuccessful due to high rates of temperature-dependent mortality during the summer egg incubation period. 2.5.3.4.2.2.3 CCV Steelhead Exposure, Response, and Risk Some CCV steelhead embryos would still be incubating from April through June. However, because approximately 90 percent of the annual CCV steelhead redd count occurs by midFebruary (Schaefer et al. 20 19), a small proportion of the redds would be exposed to scour and fine sediment infiltration, increasing the risk of mortality of incubating embryos. Rearing juvenile CCV steelhead are present throughout Clear Creek during the spring attraction pulse flows. Multiple year classes of juv,enile CCV steel head rear in Clear Creek year round, and are distributed throughout the entire length of the creek. Juvenile CCV steelhead rear in fresh water from 1 to 3 years. Spring attraction pulse flows occur during a time when smolts have been observed outrnigrating in Clear Creek. Exposure to pulse flows would give CCV steelhead access to temporary rearing habitat within side channels, potentially increasing food availability resulting in increased growth rates. Increased flows and turbidity and cooler water temperatures create migration cues, improve downstream passage conditions, reduce predation, and increase survival of smolts. Available rearing habitat (WUA) for juvenile CCV steelhead increases from approximately 200,000 sq ft. at base flows to 700,000 sq ft when flows are nearing 900 cfs (U.S. Fish and Wildlife Service 2015a). T hough short lived, the pulses may provide opportunity for new food sources, and improved growth and survival. Conversely, juvenile CCV steelhead may be displaced downstream during attraction pulse flows and after flows decrease, remain in unsuitable habitat, which would likely be warmer and at risk of increased predation, disease, and mortality. During spring attraction pulse flow ramp down, juveniles may also become stranded and isolated from the creek, and succumb to predation or desiccation. Down-ramping rates will be implemented, which will reduce stranding risk and minimize negative impacts on survival from flow decreases. However, a low proportion of juveniles are still expected to become stranded or isolated. Therefore, we expect increased survival and fitness of a high proportion of CCV steelhead rearing juveniles and outrnigrating smolts, in addition to decreased survival to a low proportion of juveniles that remain in the lower reaches after spring-pulse flows. A small proportion of juveniles would also be subject to stranding during the pulse flows. 280 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.3.4.2.3 Channel Maintenance Pulse Flows Reclamation is proposing to allocate I 0 TAF channel maintenance puRse flows each water year, up to the safe release capacity (approximately 900 cfs, depending on reservoir elevation and downstream capacity), except in Dry (24 percent) and Critical (15 percent) water year types. Reclamation will reduce the volume and occurrence of the proposed channel maintenance pulse flows if storm events create natural spills through the Whiskeytown Glory Hole of sufficient duration and magnitude, which include (1) for each storm event that results in a spill of at least 3,000 cfs for 3 days, channel maintenance flow volume for that year or the following year will be reduced by 5,000 acre-feet, and (2) if two spills of at least 3,000 cfs for 3 days each occur, additional channel maintenance pulse flows would not be released that year. Each new water year, channel maintenance pulse flows would not occur until after January 1, such that Reclamation would have enough information to make initial assessments and assumptions of water year type and available storage, and determine what restrictions on occurrence and amount of water may be needed for planning the flows. Given the parameters identified in the PA, NMFS expects that one to four channel maintenance pulse flows would occur from January through April. To maximize the magnitude of the flow and thereby the geomorphic benefit, NMFS also assumes that flows would be scheduled to occur during natural rain events. The goal of the PA channel maintenance flows is to provide high flow events that will benefit geomorphic processes in the channel and improve salmonid habitat for spawning and rearing. While the magnitude is significantly less than the 3,000-4,000 cfs recommended for sediment transport and floodplain inundation, and the 4,000-6,000 cfs for channel formation (U.S. Bureau of Reclamation and ESSA Technologies Ltd 2008), flows would provide some benefit to sediment transport and improving salmonid habitat. In an evaluation of sediment transport in Clear Creek, Graham Matthews & Associates (2013) findings showed that recent spring attraction pulse flows near 1,000 cfs mobilized supplemental spawning gravel (injection gravel), and have had some value for channel maintenance. Whiskeytown Dam blocks coarse sediment transport, and average annual peak flows and flooding frequency have been reduced downstream of the dam. All but the highest flows that pass as a spill were eliminated. This has led to channel simplification, riparian encroachment, and loss of quality and quantity spawning habitat. High flows are important to form and maintain channel and floodplain morphologies, maintain connectivity, and necessary to sustain previous and current restoration activities, including spawning gravel routing. Injection gravel has been added annually to Clear Creek since 1996 (approximately 176,000 tons) and is dependent on high creek flows for transport downstream. Peak flows resulting from tributary run-off have little effect in the upper 2 miles of the creek so flow releases from Whiskeytown Dam are especially important in this section for injection gravel mobilization (Graham Matthews & Associates 2011). The controlled operation of flows downstream of Whiskeytown Dam have reduced the frequency of high flows that historically existed, which are necessary to achieve ecological function of Clear Creek. The 2004 Environmental Water Program (EWP) proposal set release targets based on sediment transport modeling, and bed mobility studies that suggested flow magnitudes should range from 4,000 to 6,000 cfs, over two days, at a rate of 3 per 10 years based on the 40-year historical dataset of inflow upstream of the reservoir (U.S. Bureau of Reclamation and ESSA Technologies Ltd 2008). Upon further evaluation, it was determined that 3,250 cfs could also 281 Biological Opinion for the Long-Term Operation of the CVP and SWP provide significant geomorphic benefit, and this target discharge was used to evaluate the feasibility ofthe implementation of the reoperation of Whiskeytown Dam to provide flood flows to Clear Creek through the Glory Hole (Reclamation and ESSA 2008). To determine the frequency of occurrence of the PA channel maintenance flows, NMFS used historic records of Glory Hole spills, and Reclamation's model results for the proportion of Dry and Critical water year types that would occur under the PA. Channel maintenance pulse flows would not occur in approximately 40 percent of years, based on the frequency of occurrence of Dry (24 percent) and Critical (15 percent) water year types. From 1965-2005, there were 13 Glory Hole flow spill events that occurred above 3,250 cfs or greater for one day or more, with gaps ofup to 12 years apart (U.S. Bureau ofReclamation and ESSA Technologies Ltd 2008). Based on the historical record, Glory Hole spills of magnitude that would reduce the need for channel maintenance pulse flows would occur in approximately 30 percent of years under the PA. Scheduled channel maintenance pulse flow releases through the outlet would likely occur in approximately 30 percent of years. Therefore, NMFS expects that scheduled channel maintenance pulse flows would occur between 30 to 60 percent of years, depending on the number of uncontrolled spills that occur through the Glory Hole spillway. In Dry and Critical water year types when channel maintenance pulse flows would not occur, Reclamation proposes to use mechanical methods to mobilize gravel or shape the channel, if needed, to meet biological objectives. Mechanical gravel mobilization or channel re-forming would be based on a plan developed by an interagency team that inclU!des USFWS and NMFS. Frequency, magnitude, and duration would be as needed to mobilize gravel equivalent to the channel maintenance pulse flows proposed in the PA. Mechanical gravel mobilization was not described in the P A jn adequate detail in order for NMFS to analyze their effects to species. However, we assume that any mechanical methods wotl!ld results in additional effects. Likely short-term effects are increased turbidity, and potential injury or mortality of fish if present during in-water work. Therefore, we analyzed this action at the framework level. Once there is sufficient information to provide enough detail in order analyze level of effect, Reclamation would need to consult separately on this action if it is determined additional effects would occur. While mechanical methods may provide some geomorphic benefit, it is unlikely that this benefit will be equivalent to channel maintenance pulse flow releases. 2.5.3.4.2.3.1 CV Spring-Run Chinook Salmon Exposure, Response, and Risk Based on migration timing data, less than 10 percent of the returning adult CV spring-run Chinook salmon population will be present in Clear Creek during channel maintenance pulse flows and, therefore, exposed to its conditions. High flow and turbidity conditions associated with channel maintenance pulse flows may attract migrating adult CV spring-run Chinook salmon into Clear Creek, if releases occur in March or April. Attraction of earlier arriving adult CV spring-run Chinook salmon to Clear Creek could increase retums, encourage movement to the preferred upstream reaches, and result in a larger spawning population and increased genetic diversjty. Channel maintenance pulse flows are expected provide long-term benefits, improving spawning habitat by mobilizing and dispersing gravel, and reducing fine sediment. During spawning, channel maintenance pulse flows may cause scour or fine sediment infiltration of CV spring-run Chinook salmon redds through early February. The proposed channel maintenance flows (unless 282 Biological Opinion for the Long-Term Operation of the CVP and SWP coupled with storm events) are low enough in magnitude, and not likely to cause high rates of redd scour. Temperature based egg-to-fry emergence data, and rotary screw trap monitoring data, have shown the majority of CV spring-run Chinook salmon fry emerge and begin to migrate downstream in November and December in Clear Creek. However, based on temperature-based emergence dates, a low percentage of redds are expected to contain incubating eggs/preemergent fry after January 1, and therefore a low proportion are expected to result in mortality in years when channel maintenance pulse flows occur (approximately every 3-6 years; 1-2 times per year). The majority of juvenile CV spring-run Chinook salmon emigrate by February. Depending on the timing of channel maintenance pulse flows, a low to medium portion of the rearing juveniles are expected to be present. Channel maintenance pulse flows may displace juveniles, make them susceptible to isolation and stranding following down-ramping, and cause mortality. Downramping rates will be implemented, which will reduce stranding risk and minimize negative impacts on survival from flow decreases. However, a low proportion of juveniles are still expected to become stranded or isolated. High flow releases are expected to benefit juveniles by providing temporary access to additional rearing habitat that provides shelter and access to food, increasing growth and survival. While juvenile CV spring-run Chinook salmon rearing habitat is not limited based on habitat suitability results, at this time ofthe year, juvenile fall-run Chinook salmon are also pres·ent in much larger numbers and compete for rearing habitat. Flows of the proposed magnitude also provide outmigration cues, increased passage routes, and increased protection from predators due to increased turbidity. While the portion of rearing juvenile CV spring-run Chinook salmon is low to medium in years when channel maintenance pulse flows occur (approximately every 3-6 years; 1-4 times per year), channel maintenance flows are expected to provide benefits to rearing and outmigrating juveniles. Additional long term expected benefits of this action to CV spring-run Chinook salmon include increased survival of eggs, and increased production due to improved spawning habitat. 2.5.3.4.2.3.2 CCV Steelhead Exposure, Response, and Risk Given the timing of the channel maintenance pulse flows contemporaneous with peak storm flows ·from January through April, and life history of CCV steelhead in Clear Creek, all life stages and the majority of the overall population, including migrating adults, incubating embryos in redds, and rearing and out-migrating juveniles would be exposed to the effects of channel maintenance pulse flows. Channel maintenance pulses flows would occur during adult CCV steelhead migration and spawning. Because the timing of CCV steelhead migration occurs over a long period, from midDecember through April, and timing may be variable based on in-river conditions, the proportion of passage that occurs after January 1 is variable annually. Based on 5 years of preliminary video monitoring passage data at the mouth of Clear Creek, 24-88 percent (average 46 percent) of steelhead migrate into Clear Creek by January 1. Based on the variability on the timing, frequency and magnitude of channel maintenance pulse flows annually (approximately every 3-6 years; 1-4 times per year), and the range of migration timing, effects to the species migration would be variable each year. For the migration life stage of CCV stedhead, channel maintenance pulse flows would be beneficial, creating cues to encourage migration from the Sacramento River and improve migration conditions by creating more passage routes. Pulse flows would likely help to increase overall population size in Clear Creek. 283 Biological Opinion for the Long-Term Operation of the CVP and SWP Channel maintenance pulse flows are expected to improve spawning habitat by mobilizing and dispersing gravel, and reducing fine sediment. CCV steelhead egg incubation occurs from midDecember through June, with peak spawning in January. Redds are located throughout the creek, with the majority distributed downstream ofRM 6. Based on spawn timing, the majority of CCV steelhead redds would be exposed to channel maintenance pulse flows, and subject to scour or infiltration of fines that cause mortality to incubating embryos. CCV steelhead may also choose spawning locations at the higher flows, and redds may be dewatered after flow releases are decreased. However, flows of this magnitude normally occurs during CCV steelhead spawning, when winter storms would likely increase creek flows, and therefore the impacts of the channel maintenance pulse flows would not be that different from natural flows. Under most circumstances, approximately 900 cfs would be released, unless it was coupled with flows from a storm event, which are generally not scouring magnitude flows. Emergent CCV steelhead fry are first observed in the rotary screw traps beginning in midJanuary. Juvenile CCV steelhead rear in fresh water from 1 to 3 years, and therefore multiple year classes are pres,e nt and distributed throughout Clear Creek year round, which includes channel maintenance pulse flow period. Exposure to channel maintenance pulse flows would give CCV steelhead access to temporary rearing habitat within floodplains and side channels, potentially increasing food availability, resulting in increased growth rates. Flows of the proposed magnitude also provide outmigration cues, increased passage routes, and increased protection from predators due to increased turbidity. Available rearing habitat (WUA) for juvenile CCV steelhead increases from approximately 200,000 sq ft. at base flows to 700,000 sq ft when flows are nearing 900 cfs (U.S. Fish and Wildlife Service 2015a). Though short lived, the channel maintenance pulse flows would allow for some overbank flow to temporarily create side channel and (and potentially floodplain connectivity if releases are coupled with storm flows) and support juvenile growth and survival. A large proportion of juveniles would be susceptible to stranding and isolation from the creek during down-ramping. However, down-ramping rates will be implemented that reduce stranding risk and minimize negative impacts on survival from flow decreases. A low proportion of juveniles are still expected to become stranded or isolated. The proportion of rearing juvenile CCV steelhead between January and April is high, and in years when they occur (approximately every 3-6 years; 1-4 times per year), channel maintenance flows are expected to provide benefits to rearing juveniles and outrnigrating smolts. Additional long term expected benefits of this action to CCV steelhead include increased survival of eggs, and increased production due to improved spawning habitat. 2.5.3.4.2.3.3 Trinity River Division - Clear Creek Effects Analysis Summary The effects analysis results suggest that water temperatures will be a high magnitude stressor on Clear Creek CV spring-run Chinook salmon during spawning. Exposure, response, and change in fitness for each action component and life stage are described in Table 2.5.3-5 for CV spring-run Chinook salmon, and 2.5.3-6 for and CCV steelhead. 284 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.3-5. Exposure and summary of responses of Clear Creek CV spring-run Chinook salmon to the proposed actio n. Action Component Life Stage (Location) Water temperature management: Summer Adults holding creek-wide Water temperature management: Summer Adults migrating creek-wide Water temperature management: Summer and Fall Egg/alevins creek-wide. Water temperature management: Summer Juveniles/ smolts creek-wide. Minimum instream base flows Adults migrating creek-wide Minimum instream base flows Eggs/alevins creek-wide Life Stage (Timio2) Stressor Response Pro bable Change in Fitness Jun-midSept Water Temperature Adults are exposed to >60•F, which may cause stress, disease, reduced fecundity, and prespawn mortality. Jun-Aug Water Temperature; Passage Impediments Warm water temperatures >65°F may block or inhibit upstream migration. Reduced survival and reproductive success. Sept-Oct Water Temperature; Spawning Habitat Availability R edds are exposed to water temperatures >56°F, resulting in temperature dependent mortality of eggs and embryos. Even meeting the propo:;ed water temperature criterion of 56°F is expected to result in temperature dependent mortality. Reduced survival and reproductive :;ucce:;s. Jun-Sept Water Temperature Temperatures may be >65°F decreasing optimal growth, and increasing stress, risk of predation, and disease. Reduced growth and survival. Jun-Aug Flow Conditions; Passage Impediments Low flow barriers at riffles and cascades may inhibit access to holding locations. Reduced survival and reproductive success. Flow conditions Base flow reductions in Critical water year types, and/or after the fall water temperature managment period will dewater redds. Eggs and alevins will be exposed to effects of dewatering and reduced hyporheic flow. Reduced survival. Nov-Jan 285 Reduced survival and reproductive success. Biological Opinion for the Long-Term Operation of the CVP and SWP Action Life Stage Component (Location) Spring attraction pulse flows Spring attraction pulse flows Spring attraction pulse flows Channel maintenance pulse flows Channel maintenance pulse flows Channel maintenance pulse flows Adults migrating and holding creek-wide Juveniles/smolts creek-wide Juveniles/smolts creek-wide Adults migrating creek-wide Juveniles/smolts creek-wide Juveniles/smolts creek-wide Life Stage (Timine;) Stressor Response Probable Change in Fitness May-Jun Flow Conditions; Loss of Natural River Morphology and Function; Passage Impediments/ Barriers Pulse flows create migration cues, increase turbidity, decrease water temperatures, and improving passage to the most upstream holding locations. Increased survival and reproductive success. May-Jun Flow Conditions; Loss of Natural River Morphology and Function; Passage Impediments/ Barriers Pulse flows improve downstream passage by creating migration cues, increasing turbidity, and increasing passage routes. High flows provide temporary access to rearing habitat. Increased growth and life history diversity. Improved survival. Flow Conditions Flow decreases following pulse flows cause isolation and stranding. Downramping rates will reduce magnitude of effect. Reduced survival. Flow Conditions, Loss of Natural River Morphology and Function, Passage Impediments/ Barriers Increased flows create migration cues by increasing turbidity, decreasing water temperatures, and improving passage of physical barriers to the most upstream reaches for holding. Flow Conditions, Loss of Natural River Morphology and Function, Passage Impediments/ Barriers Increased flows create migration cues and improve downstream passage by decreasing water temperatures, increasing turbidity and reducing predation risk. Provide temporary access to additional rearing habitat. Increased growth and life history diversity. Improved survival. Flow Conditions Flow decreases following pulse flows cause isolation and stranding. Downramping rates will reduce magnitude of effect. Reduced survival. May-Jun Mar-Apr Jan-Apr Jan-Apr 286 Increased reproductive success and survival. Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.3-6. Exposure and summary of responses of Clear Creek CCV steel head to the proposed action. Action Component Life Stage (Location) Water temperature management: summer and fall Adults migrating/ holding downstream segregation weir Water temperature management: summer Juveniles/ smolts creek-wide Minimum instream base flows Eggs/alevins creek-wide Minimum instream base flows Juveniles/ smolts creek-wide Spring attraction pulse flows Juveniles/ smolts creek-wide Spring attraction pulse flows Juveniles/ smolts creek-wide Channel maintenance pulse flows Adults migrating/ holding creek-wide Life Stage (Timing) Response Probable Change in Fitness Water Temperature Suboptimal water temperatures >70•F delay migration timing, and >65•F increase stress and susceptibility to disease, leading to reduced fecundity, and increased pre-spawn mortality. Reduced survival and reproductive success. Water Temperature Suboptimal temperatures >60•F cause stress and reduced growth, and susceptibility to disease and predation, and mortality. Reduced growth. Reduced survival. Dec-Mar Flow Conditions Base flow reductions in Critical water year types, and/or after the fall water temperature management period ends, will dewater redds. Eggs and alevins will be exposed to effects of dewatering and reduced hyporheic flow. Reduced survival and reproductive success. Year round Flow conditions; Loss of Natural River Morphology and Function Static flow regime restricts access to rearing habitat and refugia, and does not provide migratory cues. Reduced growth, survival, and life history diversity. Apr-Jun Flow Conditions; Water temperatures; Loss of Natural River Morphology and Function; Passage Impediments/Barriers Apr-Jun Flow Conditions Increased flows create migration cues and improve downstream passage by decreasing water temperatures, increasing turbidity. Provide temporary access to additional rearing habitat. Flow decreases following pulse flows cause isolation and stranding. D ownramping rates will reduce magnitude of effect. Jan-Apr Flow Conditions; Loss of Natural River Morphology and Function Aug-Oct Jul-Aug Stressor 287 Pulse flows create migration cues, increase turbidity, and increase passage routes. Increased growth, and life history diversity. Improved survival. Reduced survival. Increased life history diversity. Improved survival. Biological Opinion for the Long-Term Operation of the CVP and SWP Action C omponent Life Stage (Location ) Channel maintenance pulse flows Eggs/a Ievins creek-wide Channel maintenance pulse flows Channel maintenance pulse flows 2.5.4 Life Stage (Timing) Stressor Resp,onse Jan-Apr Flow Conditions; Loss of Natural River Morphology and Function Juveniles/ smolts creek-wide Jan-Apr Flow Conditions; Loss of Natural River Morphology and Function Juveniles/ smolts creek-wide Jan-Apr Flow Conditions Pulse flows transport sediment that can expose redds to scour and infiltration of fine sediment. Pulse flows improve downstream passage by creating migration cues, increasing turbiidity, and increasing passage routes. High flows provide temporary access to rearing habitat. Flow decreases following pulse flows cause isolation and stranding, resulting in mortality. Down-ramping rates will reduce magnitude of effect. Probable C hange in Fitness Reduced survival. Increased growth and life history diversity. Improved survival. Reduced survival. American River Division During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 201 9, biological assessment. Unless otherwise stated, Sections 2.5.4.1-2.5.4.5 ofthe effects description below are based on the modeling associated with the February 5, 2019 PA (Appendix Al , the original PA) and associated modeling that NMFS requested. There were no revisions in the June 14,2019 PA (Appendix A3) that required supplemental analysis to these sections. The main components of the PA for the American River Division covered in this effects analysis fall into a few major categories: water temperature management, flow management, the Nimbus Fish Hatchery Steelhead Program, and Conservation Measures. Both water temperature management and flow management include several sub-categories. The stressors covered in the main categories are identified in Table 2.5.4-1. 288 00 \0 N ft:J • Pl . e; - · ::s Pl () 0 ::s . a (1) w .. < a ---3 .j>.(/)0"' I I > Pl z ..., - · "' s:: 8 -· 3 :::rt:r[g-0" C1> I I I I I ::s Pl 'Tj ,...::1_ ---- Pl 0 sag :;: I I I I >-l§w g e;a .v. .!» p. :0... I I > n'"CI Q --o Passage Impediments/Barriers Harvest/Angling Impacts Water Temperature Water Quality Flow Conditions Loss ofRiparian Habitat and Instream Cover Loss ofNatural River Morphology and Function Loss ofFloodplain Habitat Loss of Tidal Marsh Habitat Spawning Habitat Availability Physical Habitat Alteration Invasive Species/Food Web Changes Entrainment Predation Hatchery Effects !:to) --3 !:to) -· Q 0 ;;' IJQ C" N I = -- Q Q "0 -·., "' "CC f") = --· 0 -·-·== 0 ., - "0 = n> = =- t') 0 tl> "'0.. > 3 n Q (J'el :t. Q Q tl> !:to) 0 0: = n> ., "CC 0 3 I = ..... = n>., "' tl> = 0.. .,.....00 "'"'0., "' n Q =- n> 0= _, ..... tl> tl> 0.. .,< Cl -= 00 Q. < :;- tl> ::r - -= = = > !:to) tl> .,3r;· = ::0 tl> .,<" 0 <" (i)• s· ::I t') ..... "' Biological Opinion for the Long-Term Operation of the CVP and SWP American River Adaptive Management 2017 Flow Seuonal Operations Not Consulted On o ,. No Discretion Releues and •Ptannlna M1n1mum• Minimum flow Power Generation Power Bypass (Drought Declaration) Winter Ops. Spawning and Rearing Habitat Restoration Spring Ops. "Planning M inimum• (TBD 2019?) SummerOps. Fall Ops. Flood Control Flood Control Delta wa (D-1641) Delta WQ (D-1641) Limited releases >4,000 cfs Limited releases >4,000 cfs Temperature Management Temperature Management Chinook Redd dewatering (JanFeb) Steelhead Redd dewatering (FebMay) Drought Temperature Management Redd Dewatering Spring Pulse Flow (Mar-April) Spring Pulse flow (reshaping) Figure 2.5.4-1 Deconstructed action describing the relation of project components in the American Division This introduction section is intended to describe how we have deconstructed the PA into stressors that affect CCV steelhead, the only ESA-listedl species that spawns within the American River, and describe how we have assessed steelhead exposure and response to PA-related stressors. Naturally-produced CCV steelhead in the lower American River are affected by many different stressors, which, for the purpose of this analysis, are categorized into two groups based on whether they do, or do not, result from CVP operations. The Environmental Baseline section characterizes those stressors which are not the result of CVP operations, although CVP operations may exacerbate the effect of the stressor. An example of a stressor that is exacerbated by CVP operations is predation. Steelhead co-evolved with predators such as pikeminnow (Ptychocheilus grandis), but exposure to both elevated water temperatures and limited flowdependent habitat availability resulting from CVP operations make juvenile stcclhcad more susceptible to predation (Bratovich et al. 2005, Water Forum 2005). 290 Biological Opinion for the Long-Term Operation of the CVP and SWP For the purposes of this analysis, "exposure" is defined as the temporal and spatial co-occurrence of a natural origin steelhead life stage and the stressors associated with the PA. A few steps are involved in assessing steelhead exposure. In the first step, the steelhead life stages and associated timings are identified. Adult steelhead immigration in the American River generally occurs from September through April with a peak occurring from December through March (Surface Water Resources Inc. 2001). Spawning reportedly occurs in late December to early April, with the peak occurring in late February to early March (Hannon and Deason 2008). The embryo incubation life stage begins with the onset of spawning in late December and generally extends through May, although, in some years incubation can occur into June (Surface Water Resources Inc. 2001). Juvenile steelhead typically rear in the American River for a year or more before emigrating as smolts from January through June (Surface Water Resources Inc. 2001). The second step in assessing steelhead exposure is to identify the spatial distribution of each life stage. The steelhead immigration life stage occurs throU!ghout the entire lower American River with adults holding from approximately RM 5 to Nimbus Dam at RM 23 (Hannon and Deason 2008). Approximately 90 percent of spawning occurs upstream ofthe Watt Avenue Bridge area located at about RM 9.4 (Hannon and Deason 2008). The juvenile life stage occurs throughout the entire river, with rearing generally occurring in the vicinity of the upstream areas used for spawning. Most juvenile steelhead are believed to migrate through the lower sections of the American River into the Sacramento River as smolts. The last step in assessing steelhead exposure is to overlay the temporal and spatial distributions ofPA-related stressors on top of the temporal and spatial distributions of lower American River steelhead. This overlay represents the completed exposure analysis and is described in the first three columns of Table 2.5.4-3. Unless otherwise specified in Table 2.5.4-3, the temporal and spatial distributions ofPA-related stressors are the same as the temporal and spatial distributions of steelhead life stages as specified in Table 2.5.4-3. Now that the exposure of lower American River steelhead to the PA has been described, the next step is to assess how these fish are likely to respond to the PA-related stressors. In general, responses to stressors fall on a continuum from slight behavioral modifications to certain death. Life stage-specific responses to specific stressors related to the P A are described in detail in the following sections and are summarized in Table 2.5.4-3. There may be other project stressors acting on lower American River steelhead than those identified in Table 2.5.4-3. However, this effects analysis intends to identify and describe the most important project-related stressors to these fish. The stressors from the project components were identified based on a comprehensive literature review, which included the following documents: • • • • • • Lower American River State of the River Report (Water Forum 2005); Aquatic Resources of the Lower American River: Baseline Report (Surface Water Resources Inc. 2001); Impacts on the Lower American River Salmonids and Recommendations Associated with Folsom Reservoir Operations To Meet Delta Water Quality Objectives and Demands (Bratovich et al. 2005); American River Steelhead Spawning 2001 - 2007 (Hannon and Deason 2008); Steelhead Restoration and Management Plan for California (McEwan and Jackson 1996); Evaluation of Effects ofFlow Fluctuations on the Anadromous Fish Populations in the Lower American River (Snider et al. 2001); 291 Biological Opinion for the Long-Term Operation of the CVP and SWP • • NMFS 2009 Opinion (National Marine Fisheries Service 2009b); and ROC on LTO BA (U.S. Bureau of Reclamation 2019) 2.5.4.1 Lower American River Water Temperature Management Releases from Nimbus Dam to the American River affect the quantity and quality of steelhead habitat (Snider et al. 2001, Water Forum 2005), water quality, and water temperature (State Water Resources Control Board 1999, Kimmerer and Nobriga 2008). Water temperature is perhaps the physical factor with the greatest influence on American River steelhead. Water temperature directly affects survival, growth rates, distribution, and developmental rates. Water temperature also indirectly affects growth rates, disease incidence, predation, and long-term survival (Myrick and Cech Jr 2001). Water temperatures in the lower American River are a function of the timing, volume, and temperature of water being released from Folsom and Nimbus dams, river distance, and environmental heat flux (Bartholow 2000). Thus, water temperatures in the lower American River are influenced by PA operations. Indirectly, water temperatures in the lower American River can be influenced by the effect of precipitation patterns and climate on storage volume and water temperatures in Folsom Reservoir. This analysis relies on both modeled water temperature results and recent water temperature data. As for other Division analyses, NMFS used modeled temperatures provided in the BA to evaluate the suitability of water temperature conditions for salmonids under the PA. Recent water temperature data from the lower American River are used to provide context for temperature scenarios that steelhead could be exposed to under the PA. Recent water temperature data from the lower American River are assumed to be in the same general range water temperatures as those expected to occur under the PA, and may be a better indicator of the daily temperature patterns that steelhead will be exposed to under the PA than the modeled water temperature results, which have a monthly time-step. Embryo Incubation Myrick and Cech Jr (200 1) examined the effects of water temperature on steelhead (and Chinook salmon) with a specific focus on Central Valley populations and reported that steelhead egg survival declines as water temperature increases past 50°F. In a summary of technical literature examining the physiological effects of temperature on anadromous salmonids in the Pacific Northwest, U.S. Environmental Protection Agency (2001) reported that steelhead egg and alevin survival would decline with exposure to constant water temperatures above 53.6°F. Rombough ( 1988) as cited in (200 1) found less than four percent embryonic mortality of steelhead incubated at 42.8, 48.2, and 53.6°F, but noted an increase to 15 percent mortality at 59°F. In this same study, alevin mortality was less than five percent at all temperatures tested, but alevins hatching at 59°F were considerably smaller and appeared less well developed than those incubated at the lower test temperatures. In a laboratory study examining survival and development of steelhead eggs incubated at either 46.4°F or 64.4°F, Turner et al. (2007) found that eggs incubated at the higher temperature experienced higher mortality, with 100 percent mortality of eggs from one of three treatments at the higher temperature. Also, those fish incubated at the higher temperature that did survive exhibited greater structural asymmetry than fish incubated at the lower temperature. Similar to Turner et al. (2007), Myrick and Cech Jr (2001) reported an increase in physical deformities in steelhead that were incubated at higher water temperatures. Structural asymmetry has been 292 Biological Opinion for the Long-Term Operation of the CVP and SWP negatively correlated with fitness in rainbow trout (Leary et al. 1984). Overall, the literature indicates that steelhead egg mortality increases at and above a range of 54°F to 57°F (Myrick and Cech Jr 2001, U.S. Environmental Protection Agency 2001, Bratovich et al. 2012). Given that the literature results are from laboratory studies, steelhead eggs incubating in the redds in the river may need even colder temperatures than 54°F to have high survival. Martinet al. (2017) found strong evidence that significant thermal mortality occurred during tihe embryonic stage in Chinook salmon in some years due to a >5°F reduction in thermal tolerance in the field compared to laboratory studies. Martin et al. (20 17) used a biophysical model of oxygen supply and demand to demonstrate that such discrepancies in thermal tolerance could arise to differences in oxygen supply in lab and field contexts. Because oxygen diffuses slowly in water, as embryos consume oxygen they deplete the concentration of oxygen in the surrounding water, reducing their rate of oxygen supply. This is exacerbated in warm waters because oxygen demand increases exponentially with temperature. Flowing water replenishes oxygen through convective transfer, and thereby increases oxygen supply. Thus, higher flows deliver more oxygen to embryos than low flows allowing for higher thermal tolerance. The Chinook salmon egg survival temperature relationships found in laboratory studies likely overestimate thermal tolerance of eggs developing in the river by roughly 3°C because those studies typically take place at relatively high flows compared to flows experienced by eggs in spawning gravels in the river (Martin et al. 2017). This issue likely applies to what is known about the relationship between thermal tolerance and steelhead survival given that, like Chinook salmon, steelhead eggs incubate under the water column in spawning gravels. The limits of thermal tolerance are set by oxygen supply and demand. As steelhead eggs are smaller than Chinook salmon eggs, it may be expected that their oxygen needs are lower. However, a study using brown trout (Salmo trutta) and Atlantic salmon (S. salar) eggs found that oxygen consumption increases relatively slowly with increasing egg mass (Einum et al. 2002). Therefore, the effects of increased water temperature associated with decreased oxygen supply are expected to be similar for steelhead eggs and Chinook salmon eggs. Based on the thermal relationships. reported above and the temporal distribution of steelhead egg incubation (i.e. , late December through May), some level of egg mortality and/or reduced fitness of those individuals that survive is expected with exposure to the water temperatures that are expected to occur with implementation of the PA For example, mean water temperatures at Watt Avenue from 1999 through 2018 ranged from about 48°F to over 55°F in March, 50°F to over 60°F in April, and 54°F to over 65°F in May (Figure 2.5.4-2). Those data indicate that steelhead egg mortality is expected to occur for at least a small proportion of the population in most years during April and May under the PA. Higher egg mortality and increased fitness consequences would occur for steelhead eggs and alevins that were spawned later in the spawning season (e.g., spawned in March or April rather than January). This selective pressure towards earlier spawning and incubation under the PA would continue to constrain the temporal distribution of spawning, resulting in a decrease in population diversity, and consequently a likely decrease in abundance. 293 Biological Opinion for the Long-Term Operation of the CVP a nd SWP 75 error bars = 1 standard deviation 70 u:-; ...:::s 65 ...co 0 E - G1 55 50 45 March April May 0 1999 • 2000 0 2001 0 2002 • 2003 0 2004 • 2005 • 2006 • 2007 • 2008 • 2009 • 2010 0 2011 • 2012 0 2013 0 2014 C2015 0 2016 • 2017 • 2018 Figure 2.5.4-2 Lower American River water temperature during March, April, and May from 1999 through 2018 represented as the mean of the daily average at the Watt Avenue gage (Original data were obtained from the CDEC website.) Modeled water temperatures also demonstrate that steelhead eggs will be exposed to stressful conditions with implementation ofthe PA. Exceedance plots ofwater temperatures below Nimbus Dam are expected to be over 54°F for about 60 and 100 percent of the cumulative water temperature distribution during April and May, respectively; water temperatures are expected to be above 57°F for about 10 percent of the distribution in April and 70 percent in May (Figure 2.5.4-3 and Figure 2.5.4-4). The frequency of temperatures above 56°F has been reduced in the PA modeling as compared to the COS. During the warmest 20 percent of the cumulative water temperature distribution during May, water temperatures are expected to exceed 62°F in both the PA and COS modeling. 294 Biological Opinion for the Long-Term Operation of the CVP and SWP 62 - - Current Operations - - Proposed A ction -LL' :I n; L. (I) (I) .... L. (I) 54 .2:- £c: 52 0 1OOo/o 90% 80% 70% 60% 50% 40% 30% 20% 10% Oo/o Probability of Exceedence Figure 2.5.4-3 Exceedance plot of modeled water temperatures in the lower American River directly below Nimbus Dam during April (HEC-5Q Temperature Model results, 2019). 295 Biological Opinion for the Long-Term Operation of the CVP and SWP 68 - - Current Operations - - Proposed Action 66 -LL' 64 J_ / _::7 Cl) '- :J 62 f tl 'Cl) a. E Cl) ....'- - 60 58 _.../ Cl) f tl - >:2 c 56 ..-/' 54 0 ::!: 52 50 48 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% Oo/o Probability of Exceedence Figure 2.5.4-4 Exceedance plot of modeled water temperatures in the lower American River directly below Nimbus Dam d uring May (HEC-5Q Temperature Model results, 2019). Water temperatures at or above the 54°F to 57°F range during the steelhead egg incubation period would occur more frequently downstream than at Nimbus Dam, as shown in the April and May exceedance plots at Watt Avenue (Figure 2.5.4-5 and Figure 2.5.4-6). Water temperatures exceeding 57°F occur about 50 percent of the years in April (Figure 2.5.4-5) and 90 percent of the years in May (Figure 2.5.4-6) under the PA.The frequency of temperatures at Watt Ave above 60°F in Apri I and 66°F in May are reduced under the P A. The frequency of temperatures between 57°F to 60°F in April and between 62°F and 66°F in May have slight increases under the PA as compared to the COS. 296 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - -Proposed Action 01 '1519 Current Operations 011319 68 66 64 u:0w Q. 62 e ::> e 8. 60 ------------------------------- .,----------,----------...-------------------------------" I E £ I I 58 --------- 8 ... ------------------ -1---------- ' ... --------- ·-,...------------------ --------------------- : I I I ::;: 56 54 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Exceedance Probability *All scenarios are simulated at ELT (Early l ong-Term) QS with 2025 climate change and 15 em sea level r ise. *These are draft results meant f•o r qualitative analysis and are subject to revision. Figure 2.5.4-5 Exceedance plots of modeled water temperat ures in t he lower American River near Watt Avenue during April (HEC-5Q Temperature Model results, 2019). 297 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - Current Operations 011319 Proposed Action 01 '1519 74 72 lL C> w Q. "'5 8. E "' t- -s 8 ::. 70 ' --------- -r--------------------- .., ----- -----..,.----------... ----------... ----------.,..__ - ------- ... ---------....------ - 1 - 68 --------- -r-- --------.---------- -,----------,----------- ----------- -------------- ------- --------- ,. ,. ,. ' ' 66 --------- : ' ---------------------------t---------.I.------------------------- 64 --------- ------- 62 - - - - - - - - - - - - - - - - - - - - -.- - - - - - - - - - -,- - - - - - - - - - 1' -..::- - - - ... ----------"''----------"' -----..-- ,.,..,._ , - -------- .,.._---------...-------------------- - - - - - - - - - - - - - - - - - - - - - - - -- - -- -- - -- - - - - - - - -- - - - - - - - - - - - - - - 60 58 ----- ---- - - -- ..,.. 100% 90% ---- 80% 'i----- -----.,.---------' T----------..,..----------.,..--- ------- - ------------ ---- ---- 70% 60% 50% 40% 30% 20% 10% 0% Exceedance Probability • All scenarios are simulated at ELT (Early Long-Term) Q5 with 2025 climate change and 15 em sea level rise. *These are draft results meant for qualitative analysis and are subject to revision. Figure 2.5.4-6 Exceedance plots of modeled water temperatures in the lower American River near Watt Avenue during May (HEC-SQ Temperature Model results, 2019). 2.5.4.1.1 Juvenile Rearing Water temperatures in the lower American River often reach and exceed levels that are stressful to juvenile rearing steelhead, particularly during the summer and early fall. Assessing the response of American River steelhead juveniles to water temperatures is challenging due partly to a historical paucity of published primary literature (Myrick and Cech 2004). Though there has been a recent increase in studies and modeling of growth and anadromy patterns using temperature as a variable (Satterthwaite et al. 2010, Sogard et al. 2012, Beakes et al. 2014), there remains a fairly substantial knowledge gap in relation to the effects of temperature on juvenile CCV steelhead. The available information suggests that American River steelhead may be more tolerant to high temperatures than steelhead from regions further north (Myrick and Cech 2004). Cech Jr and Myrick (1999) reported that when American River steelhead were fed to satiation at constant temperatures of 51.8°F, 59.0°F, and 66.2°F, growth rates increased with temperature, whereas Wurtsbaugh and Davis (1977) found that maximal growth ofjuvenile steelhead from North Santiam River in Oregon occurred at a cooler temperature (i.e., 62.6°F). Furthermore, Beakes et al. (2014) found that steelhead sourced from Coleman National Fish Hatchery and reared at 68°F maintained an average growth rate above 0.6 mm/day, but only when a daily food ration equal to 6 percent of the total wet fish biomass was fed. All of these studies were conducted in a 298 Biological Opinion for the Long-Term Operation of the CVP and SWP controlled laboratory setting with unlimited, or relatively high, food availability. Under more variable conditions, such as those experienced in the wild, the effect of water temperature on juvenile steelhead growth would likely be different. For example, the above Beakes et al. (2014) study found that treatments of high water temperature and low rations resulted in the lowest growth rate. Additionally, a field study conducted between 2006 and 2009 estimated that average summer and fall growth ofjuvenile steelhead in the American River ranged from 0.98 to 1.12 mm/day despite maximum summer temperatures regularly exceeding 68°F (Sogard et al. 2012). This rate of growth is unusually high for CV salmonids and exceeds growth rates obtained by fish rearing on managed floodplains in the CCV (e.g., Katz et al. 2017). Sogard et al. (2012) postulate that this rate of accelerated growth is likely the result of low steelhead density and high food availability, which further illustrates the interactive role of water temperature and food availability in modulating growth in salmonids (Manhard et al. 2018). Even with this tolerance for warmer water temperatures, steelhead in the lower American River exhibit symptoms of thermal stress. Elevated water temperatures can increase physiological stress and subsequently, decrease immune system function. For example, the occurrence of a bacterial-caused inflammation of the anal vent (commonly referred to as "rosy anus") of American River steelhead has been reported by CDFW (formerly CDFG) to be associated with warm water temperatures (Figure 2.5.4-7). Sampling in the summer of 2004 showed that this vent inflammation was prevalent in steelhead throughout the river and the frequency of its occurrence increased as the duration of exposure to water temperatures over 65°F increased. At one site, the frequency of occurrence of the anal vent inflammation increased from about 10 percent in August, to about 42 percent in September, and finally up to about 66 percent in October (Bratovich et al. 2005). Figure 2.5.4-7 Anal vent inflammation in a juvenile steelhead from the American River (Bratovich et al. 2005). 299 Biological Opinion for the Long-Term Operation of the CVP and SWP The juvenile steelhead immune system properly functions up to about 60°F, and then is dramatically compromised as water temperatures increase into the upper 60°Fs (Bratovich et al. 2005). CDFW reports that, in 2004, the anal vent inflammation occurred when juvenile steelhead were exposed to water temperatures above 65°F (Bratovich et al. 2005). From 1999 through 2018, daily mean water temperatures during the summer at Watt Avenue were most often above 65°F, and during 2001, 2002, 2004, 2007, 2008, 2013, 2014, 2015, and 2016 water temperatures were often over 68°F (Figure 2.5.4-8). CDFW has suggested that these observations are associated with the debilitation of the steelhead's immune system responses (Bratovich et al. 2005); they, therefore may be indicative of an increased susceptibility to and decreased ability to deal with disease, which would decrease fitness. a 78 - -... LL 0 76 74 Q) E "'... 8. E t!... s I 72 • ••• • •• • •• • • 70 ••• • ••• •• 68 c: "' Q) c"' 62 :r- 60 8/1 8/11 8/21 8/31 9/10 9/20 1999 • 2000 • 2001 2002 l' 2003 • 2004 + 2005 - 2006 • 2007 • 2008 • 2009 x 2010 2011 • 2012 2013 2014 • 2015 2016 • 2017 x 2018 9/30 Figure 2.5.4-8 Lower American River water temperature during August and September from 1999 through 2018 represented as the daily mean at the Watt Avenue gage. The 65°F line is indicated in red because visible symptoms of thermal stress in juvenile steelhead are associated with exposure to daily mean water temperatures above 65°F. Data were provided by Reclamation. Based on water temperature modeling results presented in the ROC on LTO BA, water temperatures associated with visible symptoms of thermal stress in juvenile steelhead (i.e., >65°F) are expected to occur from June through September under both the PA and COS. Exceedance plots of monthly water temperatures at Watt Avenue show that temperatures are expected to be at or above 65°F for about 58 percent of the cumulative distribution in June (Figure 2.5 .4-9), 100 percent in July (Figure 2.5.4-1 0), and about 95 percent of August (Figure 2.5.4-11) under both PA and COS. In September, model results show that 65°F will be exceeded 93 percent of the time under the COS and 96 percent of the time under the PA (Figure 2.5.4-12). Additionally, historic data between 1999 and 2018 show that on average only 43 percent of days from July through September are amenable to steelhead rearing using a temperature metric of 65°F; that number increases to 80 percent using a temperature metric of 68°F (Figure 2.5.4-13). 300 Biological Opinion for the Long-Term Operation of the CVP and SWP When reviewing historic data, NMFS assumes potential climate change scenarios ( + 1°F and +3°F applied to historical water temperatures), would further reduce the temperature suitability of the lower American River for Steelhead with less than 30 percent of days able to meet a 65°F temperature metric. In the exceedance plots of monthly water temperatures (Figure 2.5.4-9 through Figure 2.5.4-12), the PA shows some improvements over COS at high temperatures, but the modeling results do not reflect the yet to be determined planning minimum carryover storage target intended to improve water temperatures. While the modeling includes a "soft" goal to maintain a minimum end-ofSeptember storage of 275 thousand acre feet (TAF), this was partially intended to conceptually emulate the undefined end-of-December planning level minimum that (according to a meeting from Reclamation on May 31st) is expected to land between 200 TAF and 300 TAF. According to Reclamation in a meeting on May 31,2019, Reclamation explained that the current planning level minimum is 200 TAF and has been used historically for seasonal planning. Reclamation intends to share the final planning level minimum with NMFS along with the expected actions that the water users intend to take to improve storage conditions in years when the planning level minimum cannot be met solely by fl exibility in CVP operations. Based on Reclamation's understanding of the expected performance from the planning level minimum, the CalSim modeling is the best representation of the PA. While the planning level minimum is not explicitly modeled, the increase from the existing planning level minimum is expected to improve storage conditions in certain years and help to protect the storage gains from the decreases in the minimum required releases in the PA as compared to the COS. Despite best efforts, lower American River water temperatures have not improved over at least the last 20 years. Although the PA, when compared to the COS, shows reductions in the frequency of the highest temperatures, the resulting temperatures are not assumed to solve the thermal challenges in the lower American River as the BA does on pages 5-196 and 5-197 (Appendix Al): "The implementation ofthe proposed 2017 FMS measures under the proposed action would provide suitable habitat conditions in the lower American River for CV Steelhead, particularly during drought conditions and improve conditions for this life stage." The BA does not include information supporting the notion that the lower American River habitat will be thermally suitable during drought. 301 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - -Proposed Action 011519 Current OIP w 9. !!' 74 72 i'!!" 70 .,E 68 .... .2:- -6 !5 ::0 66 64 62 60 100% ' - - - - - - - - - - - - - - - - -..... - - - - - - - - - ""1- - - - - - - - - -.. - - - - - - - - - - ... - - - - -· - - - - . , . - - - - - - - - -.. ,.. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - . - 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Exceedance Probability •All scenarios are simulat ed at Ell (Early Long-Term) 05 with 2025 climate change and 15 em sea level rise. •These are draft results meant for qualitative analysis and are subject to revision. Figure 2.5.4-9 Exceedance plots of modeled water temperatures in the lower American River near Watt Avenue during June (HEC-SQ Temperature Model results, 2019). 302 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - -ProposedAdion01 1519 Current Operations 011319 82 -------- --r----------,----------;----------.,----------.,.----------..- ------------------------------------------ 80 --------- T - -- - - - - - - - - - - - - - - - - - o----------"--------------------------------"---------------------------- _J_I I 78 -------------------------------.----------1------------------------------------------------------------, -- 76 --------- T - ------------------- o----------'-------------------------------------------------------- - ------ 74 -------------------------------. ----------1------------------------------------------------I 72 " ------------ 70 68 _______________________________ .! ___________ - - - - - - - -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 66 64 100% 90% 80% TO% 60% 50% 40% 30% 20% 10% 0% Exceedance Probability • All scenarios are simulated at ELT (Early Long-Term) QS with 2025 climate change and 15 em sea level rise. "These are draft results meant for qualitative analysis and are subject to revision. Figure 2.5.4-10 Exceedance plots of modeled water temperatures in the lower American River near Watt Avenue during July (HEC-SQ Temperature Model results, 2019). 303 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - -Proposed Action 01 1519 Current Operations 01 1319 80 78 76 rL 0 w 74 e. 72 8. .,E 70 8 68 .. ::;: ' - ------............ ------------------- .................................................................................................................................. .. : 66 ' 64 62 100% :' ................,.. - - -........ - - -.................. ., ..........................................T .................... T .................. ""!" ..................... 90% 80% 70% 60% 50% 40% 30% .................. ""I"" ................ .. 20% 10% 0% Exceedance Probability • All scenarios are simulated at ELT (Early Long-Term) QS w ith 2025 climate change and 15 em sea level rise. • These are draft results meant for qualitative analysis and are subj ect to revision. Figure 2.5.4-11 Exceedance plots of modeled water temperatures in the lower American River near Watt Avenue during August (HEC-SQ Temperature Model results, 2019). 304 Biological Opinion for the Long-Term Operation of the CVP and SWP - - - -ProposedAdioo011519 Current Operations 011319 76 74 lL 72 <.!> w B !? ::> 70 8. E 68 --=-.:.-.,..._.----------------------------- -.L----------.1.----------J..----------1...---------...l---------- £ 8 :; 66 64 --r---------------------------...----------.. .----------""----------"'----------,.----------,..-------------------- 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Exceedance Probability 0 AII scenarios are simulated at ELT (Early Long-Term) Q5 with 2025 climate change and 15 em sea level rise. 'These are draft results meant fo r qualitative analysis and are subj ect to revisio n. Figure 2.5.4-12 Exceedance plots of modeled water temperatures in the lower American River near Watt Avenue during September (HEC-SQ Temperature Model results, 2019). 305 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.4-2 Percent of days with temperatures in the lower American River amenable to steelhead rearing under historic and potential climate change conditions (Data were obta ined from the CDEC webpage). Percent Days with Lower American River Temperature Amenable to Steelhead Rearing (65°F or 68°F) in Key July through Septerrber Period Urder Historic (+0°F) or Climate Change(+ 1•r I 3°F) Scenarios Year 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 Average +O•F 100"/o 100"/o 38% 93% 100"/o 50% 100"/o 100"/o 92% 18% 100"/o 100"/o 100"/o 100"/o 77% 33% 2o/o 88% 100"/o 100"/o 80% 68°F Melric +J•f 97% 91% 20% 71% 100"/o 30% 100"/o 100"/o 65% 5o/o 97% 100"/o 100"/o 100"/o 49% 5o/o Oo/o 62% 100"/o 99% 70% +3°F 59% 32% 8o/o 32% 43% 5o/o 100"/o 100"/o 22% Oo/o 39% 85% 100"/o 71% 16o/o 0"/o Oo/o 15% 100"/o 32% 43% 306 +O•F 59% 32% 8o/o 32% 43% 5% 100"/o 100"/o 22% Oo/o 39% 85% 100"/o 71% 16% 0"/o Oo/o 15% 100"/o 32% 43% 65°F Me llie +]•f +3°F 32% 9o/o 21o/o 2o/o 7o/o 5o/o 17% 7o/o 14% 0"/o 1o/o 1o/o 74% Oo/o 67% 9o/o 13% 0"/o 0"/o Oo/o 30% 13% 55% 13% 99% 61o/o 36% 9o/o 13% 0"/o 0"/o Oo/o Oo/o Oo/o 12% 7% 59% 5% 7% Oo/o 28% 7% Biological Opinion for the Long-Term Operation of the CVP and SWP Lower American River Temperature Suitability for Steelhead Rearing Decreases With Anticipated Climate Wanning Comparing Historic Daily Average Temperarures (Green) with Potential Climate Change Increases of+ I°F (Yellow) + 3°F (Red) overlaid with 65°F I 68°F temperamre ranges (Black Horizomal Dashes) from May IS - Oct 31 for Juvenile Steelbead Over-Summer Rearing at Wall Ave Bridge n 76 1S . 7< G:' 7l a .. I 71 i . t' 70 R69 !-" 67 .l 60 6S . T.'1 I I IH 6S° F Metric 6) l99P lOOO lOOl 2002 1001 2004 lOOS 2006 10Cl7 2001 2009 7010 lOll lOl l lOl l l014 lOIS 2016 2017 lOll Year • + 3°F + I°F · Historic Figure 2.5.4-13 Lower American River temperature suitability for steelhead rearing under historic an d potential climate change conditions (Data were obtained from tbe CDEC webpage). As described in Water Forum (2005), Folsom Reservoir is commonly operated to meet water quality objectives and demands in the Delta. These operations limit coldwater pool availability in Folsom Reservoir, thereby potentially resulting in elevated water temperatures in the lower American River, which likely results in increased predation rates on juvenile rearing steelhead. According to CDFW (2005 op. cit. Bratovich et al. 2005), water temperatures above 65°F are associated with a large (i.e., 30-40 species) complex warmwater fish community, including highly piscivorous fishes such as striped bass (Morone saxatilis), largemouth bass (Micropterus salmoides), and Sacramento pikeminnow. Juvenile rearing steelhead may be exposed to increased predation due to both increased predator abundance and increased digestion and consumption rates of these predators associated with higher water temperature (Vigg and Burley 1991, Vigg et al. 1991). Some striped bass reportedly reside in the lower American River year-round, although their abundance greatly increases in the spring and early summer as they migrate into the river at roughly the same time that steelhead are both emerging from spawning gravels as vulnerable fry and migrating out of the river as smolts (Surface Water Resources Inc. 2001 ). Striped bass are opportunistic feeders, and almost any fish or invertebrate occupying the same habitat eventually appears in their diet (Moyle 2002). Empirical data examining the effect of striped bass predation on steelhead in the lower American River have not been collected, altlhough one sucih study was conducted in the Delta (California Department of Water Resources 2008). Results of this study concluded that steelhead of smolt size had a mortality rate within Clifton Court Forebay that ranged from 78 ± 4 percent to 82 ± 3 percent over the various replicates of the study. The primary source of mortality to these steelhead is believed to be predation by striped bass. 307 Biological Opinion for the Long-Term Operation of the CVP and SWP Although Clifton Court Forebay and the lower American River are dramatically different systems, this study does demonstrate that striped bass are effective predators of steelhead. Considering that striped bass are abundant in the lower American River during the spring and early summer (Surface Water Resources Inc. 2001), when much of the steelhead initial rearing and smolt emigration life stages are occurring, striped bass predation on juvenile steelhead is considered to be an important stressor to this population. Although the predation stressor by striped bass is also considered in the baseline, the decrease in water temperatures and continued low flows that exist in both the COS and the P A are unlikely to reduce the magnitude of this stressor. As described in the Section 2.5.4.2.3 below, low releases from Nimbus Dam force juvenile steelhead into areas that provide less cover from predation. The P A shows less frequent low flows. The model results show that, under the PA, American River flow below Nimbus is less than 500 cfs once in July, twice in August, and twice in September in the whole 82 year (984 month) simulation period. Under the COS, however, this occurs more frequently: one occurrence in October, 3 occurrences in (each of the following months) January, February, April, May, June, August, and 4 occurrences in (each of the following months) March, July, and September. Overall, the PA includes some improvement (reduction) in water temperature but direct sublethal impacts and indirect lethal impacts (predation) for a high proportion of the American River steelhead population in nearly all years is still expected, supporting a high magnitude classification for this stressor. 2.5.4.1.2 Smolt Emigration To successfully complete the parr-smolt transformation, a physiological and morphological adaptation to life in saline water, smolting steelhead require cooler water temperatures than for the rearing life stage. Adams et al. (1975) reported that steelhead undergo the smolt transformation when reared in water temperatures below 52.3°F, but not at warmer water temperatures. In a report focusing on the thermal requirements of Central Valley salmonids, Myrick and Cech Jr (2001) came to a similar conclusion stating that steelhead successfully smolt at water temperatures in the 43.7°F to 52.3°F range. Others have suggested that water temperatures up to about 54°F will allow for successful steelhead smoltification (Zaugg et al. 1972, Wedemeyer et al. 1980, U.S. Environmental Protection Agency 2001). Steelhead smolt emigration in the lower American River occurs from January through June (Surface Water Resources Inc. 2001). Monitoring data from 1999 through 2018 showed that lower American River water temperatures frequently exceeded 52°F by March and exceeded 54°F in all but 5 years by April (Figure 2.5.4-2). Based on the thermal requirements for steelhead smolts described above, it could be hypothesized that smolt transformation is likely inhibited by exposure to lower American River water temperatures. However, recent research has shown that most steelhead in the lower American River express an anadromous life history (Satterthwaite et at. 20 I 0, Sogard et at. 20 12). Their results support the conclusion that the majority of juvenile steelhead undergo smolt transformation and emigrate as they reach age 1 (Satterthwaite et al. 2010, Sogard et al. 2012). However, Sogard et al. (2012) caution that this early emigration may be associated with high water temperatures in the lower American River and that "there may be negative aspects that were not addressed in [their] study, such as disease or reduced thermal tolerance of older juveniles." It remains uncertain how increased warming associated with climate change will impact successful transformation of parr to smolts in the lower American River. 308 Biological Opinion for the Long-Term Operation of the CVP and SWP Reclamation's modeled water temperatures demonstrate that the PAis expected to result in similar conditions to the COS that will inhibit the successful transformation from parr to smelts. For example, exceedance plots show that water temperatures at Watt Avenue will be warmer than 54°F for 83 percent of the years in April (Figure 2.5.4-5) under both the COS and the PA scenarios. In May water temperatures are expected to exceed 58°F in 85 percent of the years (Figure 2.5.4-6) and in June modeling results suggest that they will always be over 58°F under both the COS and the PA (Figure 2.5.4-9). These data suggest that smelts are expected to experience sublethal thermal impacts under both the COS and the PA for at least the small proportion of steelhead emigrating in April, May, and June. 2.5.4.1.3 Minimum Flow Schedule and Water Temperature Standards Reclamation proposes to adopt the minimum flow schedule and approach proposed by the Water Forum in 2017 12 and highlights a new planning minimum process. The ROC on LTO PA (Appendix Al) states that: "Reclamation proposes to work together with the American River water agencies to define an appropriate amount ofstorage in Folsom Reservoir that represents the lower boundfor typical forecasting processes at the end of calendar year (the "planning minimum "). The planning minimum brings Reclamation's forecasting process together with potential local actions that either increase Folsom storage or reduce demand out ofFolsom Reservoir. The implementation ofa planning minimum allows Reclamation to work with the American River Group to identify conditions when local water actions may be necessary to ensure storage is adequate for diversion from the municipal water intake at Folsom Dam and/or the extreme hydrology presents a risk that needs to be properly communicated to the public and surrounding communities. This planning minimum will be a single value (or potentially a series ofvalues for different hydrologic year types) to be used for each year's forecasting process into the future. The objective ofincorporating the planning minimum into the forecasting process is to provide releases ofsalmonid-suitable temperatures to the lower American River and reliable deliveries (using the existing water supply intakes and conveyance systems) to American River water agencies that are dependent on deliveries or releases from Folsom Reservoir. This planning minimum is expected to be initially defined in 2019; however, it will be continuously evaluated between Reclamation and the Water Forum throughout implementation." Based on the modelling information provided in the ROC on LTO BA, the temperature standard of 65°F described in the ROC on L TO PA cannot always be met. According to the PA, the temperature management planning process will aim to attain the best possible temperature schedule for the compliance point at Watt Avenue Bridge. In conditions when the target temperature can not be met, higher temperatures will be targeted to most efficiently use the available coldwater pool. Reclamation states that the draft temperature management plan will be shared with the American River Group before finalization, where NMFS assumes Reclamation will receive input on potential higher temperatures due to limited coldwater pool availability. The PA states the following: 12 The BA refers a 2017 proposal, however the subject document provided to NMFS by Reclamation is dated December 2018 and has the title of: Lower American River - Standards for Minimum Flows. 309 Biological Opinion for the Long-Term Operation of the CVP and SWP • "Reclamation proposes to manage the Folsom/Nimbus Dam complex and the water temperature control shutters at Folsom Dam to maintain a daily average water temperature of65°F (or other temperature as determined by the temperature modeling) or lower at Watt Avenue Bridge from May 15 through October 31, to provide suitable conditions for juvenile Steelhead rearing in the lower American River. " • "During the May 15 to October 31 period, if the Temperature Plan defined temperature requirement cannot be met because of limited cold water availability in Folsom Reservoir, then the target daily average water temperature at Watt Avenue may be increased incrementally (i.e., no more than JOF every 12 hours) to as high as 68°F. The priority for use of the lowest water temperature control shutters at Folsom Dam shall be to achieve the water temperature requirement for listed species (i.e., Steelhead), and thereafter may also be used to provide cold water for Fall-Run Chinook Salmon spawning. " Modeling ofboth the PA and the COS provided in the ROC on LTO PA indicate 65°F will be regularly exceeded. NMFS assumes that this exceedance will occur under the implementation of the PA due to similar constraints under the COS. These include: (I) operational (e.g., Folsom Reservoir operations to meet Delta water quality objectives and demands and deliveries to M&I users in Sacramento County) and structural (e.g., limited reservoir water storage and coldwater pool) factors limit the availability of coldwater for water temperature management; (2) despite careful planning and the annual development of a water temperature management plan, in most years since the late 1990s, Reclamation has not achieved the temperatures (NMFS 2009 Opinion and analysis of recent temperatures presented in this Opinion); (3) climate change impacts are expected to continue, which will likely further constrain lower American River water temperature management. A comparison of north-of-Delta deliveries to CVP M&I contractors, which are mostly in the American River Basin, using CalSim II modeling, shows that the COS and PA values are relatively similar in most year-types, with slightly higher deliveries being made in BN WYTs under the PA compared to the COS. This slight increase is supported by Table 5-3 in the ROC on LTO BA (Appendix D, Attachment 3-1), which shows decreases in Folsom Lake storage in BN WYTs under the PA compared to the COS. It is worth noting that the temperature standards do not include the steelhead embryo incubation or smolt emigration life stages, even though lower American River water temperatures during those life stages often reach and exceed levels that result in sublethal effects and increased mortality (see Sections 0 Embryo Incubation and 2.5.4.1.2 Smolt Emigration). 2.5.4.1.4 Conservation Measure- Water Temperature Management During Drought Reclamation proposes the following conservation measure in the ROC on LTO PA (Appendix AI) that involves temperature management in the American River: 310 Biological Opinion for the Long-Term Operation of the CVP and SWP "Drought Temperature Management: In severe or worse droughts, Reclamation proposes to evaluate and implement alternative shutter configurations at Folsom Dam to allow temperature flexibility." The level of detail provided in ROC on LTO PA on this: measure is not sufficient to determine the level of potential effect on CCV steelhead. Based on conversations with Reclamation in May 2019, NMFS understands that this action refers to a practice known as "deganging" the current temperature shutters to allow a more efficient use of the available coldwater pool. Deganging may be more efficient owing to the increased ability to fine tune release temperatures via the increased number of potential shutter configurations. The benefits of this action for future drought years has not been modeled but is expected to allow for longer use of the warmer water in the reservoir and reserve cooler water for later in the temperature management season. Historically, this operation has only occurred once, in 2015. We assume the conservation measure may continue to minimize temperature-related impacts to CCV steelhead in a more efficient matter than annual temperature shutter operations. 2.5.4.1.5 Magnitude of Water Temperature as a Stressor to American River Steelhead This effects analysis indicates that the thermal impacts on lower American River steelhead expected to occur with implementation of the PA will be similar to the impacts associated with the recent past operations of the American River Division ofthe CVP. Water temperature under the PA is considered a high to medium magnitude stressor based on the exposure of multiple steelhead life stages to lethal and sublethal conditions in all but the wettest and coldest years, and without structural modifications to Folsom Dam, this stressor would continue. 2.5.4.2 Lower American River Flow Management 2.5.4.2.1 Flood Control and Delta Water Quality (D-1641) Releases from Folsom Reservoir, are made, in part, for flood control and to meet Delta water quality objectives and demands. These operations can result in release events during the winter and spring that are clharacterized by rapid flow increases for a period of time followed by rapid flow decreases. Releases from Folsom Dam are re-regulated approximately 7 miles downstream by Nimbus Dam. A few examples of these types of flow fluctuations can be seen in the Nimbus Dam release pattern, which occurred in 2004 (Figure 2.5.4-14). Reclamation operates for flood control in accordance with the 2019 Water Control Manual. The PA does not propose changes to flood control operations from the current water control manual and therefore, these impacts from passing high flow events would be consistent between the COS and the PA. Reclamation and the U.S. Army Corps of Engineers constructed a new spillway (completed in 2017), known as the Joint Federal Project (JFP), which allows Reclamation to make releases for flood control at lower elevations than the original spillway, but at significantly higher elevations than the River Outlet Tubes. Use of the JFP allows for more stable high flows during storm events by allowing lower release volumes to occur sooner and have a longer duration but with lowered peak flow. Additionally, the use of the JFP should improve the cold water pool volume by avoiding releases thru the River Outlet Tubes which draw from a colder elevation. The Water Control Manual that accompanies this new facility has undergone separate ESA consultation with the Corps as the federal action agency (National Marine Fisheries Service 20 18e), and analyses and terms and conditions in that Opinion are in the baseline for this consultation. The 311 Biological Opinion for the Long-Term Operation of the CVP and SWP operation under the new Water Control Manual with the new spillway is expected to result in decreases of peak flows with potential longer durations of flood releases to evacuate the same volume when compared to historical operations. For this reason, using historical data for flood control is not appropriate. 2.5.4.2.2 Flow Fluctuations Flow fluctuations in the lower American River have been documented to result in steelhead redd dewatering and isolation (Hannon et al. 2003, Water Forum 2005, Hannon and Deason 2008). Redd dewatering can affect salmonid embryos and alevins by impairing development and causing direct mortality due to desiccation, insufficient oxygen levels, waste metabolite toxicity, and thermal stress (Becker et al. 1982, Reiser and White 1983). Isolation ofredds in side channels can result in direct mortalities due to these factors, as well as starvation and predation of emergent fry. Hannon et al. (2003) reported that five steelhead redds were dewatered and 10 steelhead redds were isolated in a backwater pool at the lower Sunrise side channel when Nimbus Dam releases were decreased on February 27, 2003. When releases were decreased on March 17, 2003, seven steelhead redds were dewatered and five additional redds were isolated from flowing water at the lower Sunrise side channel. In April 2004 at the lower Sunrise side channel, five steelhead redds were dewatered and "many" redds were isolated (Bratovich et al. 2005). Redd dewatering at Sailor Bar and Nimbus Basin occurred in 2006, with most of the redds being identified as Chinook salmon redds, at least one was positively identified as a steelhead redd, and several more redds were of unknown origin (Hannon and Deason 2008) (Figure 2.5.4-15). 312 Biological Opinion for the Long-Term Operation of the CVP and SWP 9,000 Spawning and Embryo Incubation Fry and Fingerling Rearing 8,000 7,000 6,000 - 5,000 4,000 3,000 2,000 1,000 0 1/1/04 2/1/04 3/1/04 4/1/04 5/1/04 6/1/04 7/1/04 Figure 2.5.4-14 Mean daily release rates from Nimbus Dam in January through July of 2004. The timing of the steel head life stages that are most vulnerable to flow fluctuations during these months are displayed. Although reports of steelhead redd dewatering and isolation in the lower American River are limited to 2003, 2004, and 2006, these effects have likely occurred in other years because: (1) the pattern of high releases followed by lower releases which occurred during the steelhead spawning period (i.e., primarily January through March) in 2003, 2004, and 2006, is similar to the pattern observed during the spawning period in many other years [CDEC data (http://cdec.water/caJgov/) from 1994 through 2019]; and (2) monitoring was not conducted during many release events and, consequently, impacts were not documented. Impacts associated with flow fluctuations are expected to continue to occur with implementation of the PA through 2030 because operations that would address this stressor (i.e., ramping rates) were not described in the PA. Juvenile steelhead isolation has also been reported to occur in the lower American River. For example, Bratovich et al. (2005) reported that juvenile steelhead became isolated from the river channel in both 2003 and 2004 following a flow increase and decrease event associated with meeting Delta water quality objectives and demands. Isolated fish are exposed to warm water temperatures and fish and avian predation within habitats that are disconnected from the river, likely increasing their mortality risk. If the isolated habitat is not reconnected to the river with a subsequent increase in river stage, all steelhead in that habitat are assumed to die. 313 Biological Opinion for the Long-Term Operation of the CVP and SWP Flow fluctuations in the American River under the PA are expected to impact a small proportion of steel head eggs and juveniles with a medium annual frequency, supporting a medium stressor magnitude classification for both life stages. Figure 2.5.4-15 Dewatered redds at Nimbus Basin and Sailor Bar, February 2006 (figure was modified from Hannon and Deason 2008). 2.5.4.2.3 Low Flows In addition to flow fluctuations, low flows also can negatively affect lower American River steelhead. Yearling steelhead are found in bar complex and side channel areas characterized by habitat complexity in the form of velocity shelters, hydraulic roughness elements, and other forms of cover (Surface Water Resources Inc. 2001). At low flow levels, the availability ofthese habitat types becomes limited, forcing juvenile steelhead densities to increase in areas that provide less cover from predation. With high densities in areas of relatively reduced habitat quality, juvenile steelhead become more susceptible to predation as well as disease. Low flows are included in both the PA and the COS; however, the PA shows less frequent low flows. The model results show that, under the PA, American River flow below Nimbus is less than 500 cfs once in July, twice in August, and twice in September in the whole 82 year (984 month) simulation period. Under the COS, however, this occurs more frequently: one occurrence in October, 3 occurrences in (each of the following months) January, February, April, May, June, August, and 4 occurrences in (each of the following months) March, July, and September. Periodic exposure of a small proportion of American River juvenile steelhead to these low flow 314 Biological Opinion for the Long-Term Operation of the CVP and SWP conditions is expected during implementation of the PA through 2030, although less frequently than under the COS. 2.5.4.2.4 2017 Flow Management Standard Releases and "Planning Minimum" See Section 2.5.4.1 .3 Minimum Flow Schedule and Water Temperature Standards 2.5.4.2.5 Spawning Habitat Availability Modeling results show that flows under the PA provide slightly lower steelhead spawning habitat for about 10 percent of years, relative to current operations, but otherwise the PA matches the COS (Figure 2.5.4-16). Steelhead Spawning, All Years Vl :!::::: c ::J ro Q) !..... <( Q) ...0 ro Vl ::J -o 400,000 350,000 300,000 250,000 200,000 .... 100,000 .Qj 50,000 Q) .!: tl.O s - 150,000 0 100% 90% 80% 70% 60% 50% 40% coss - 30% PA20 20% 10% 0% Probablility of Exceedance Figure 2.5.4-16 Steelhead Spawning Habitat Availability under the Proposed Action (PA20) and under Current Operations (COSS) over all Water Year Types. Results provided by Reclamation. 2.5.4.2.6 Magnitude of Flow Management as a Stressor to American River Steelhead This effects analysis indicates that the flow-related impacts on lower American River steelhead expected to occur with implementation of the PA will be similar to the impacts associated with the recent past operations of the American River Division of the CVP. Flow management under the PA is considered a medium magnitude stressor based on the expected periodic occurrence of lethal and sublethal impacts resulting from redd dewatering, fry stranding, and juvenile isolation. 2.5.4.3 Nimbus Fish Hatchery Steelhead Program The PA includes operation ofthe Nimbus Fish Hatchery Steelhead Program. The ROC on LTO BA states, "Reclamation has ongoing activities that would continue, including fish hatchery programs at Coleman and Nimbus, because these faci lities were intended as mitigation for the construction ofCVP dams." However, the ROC on LTO BA provides no information regarding how the Nimbus Hatchery Steelhead Program will be operated. 315 Biological Opinion for the Long-Term Operation of the CVP and SWP Generally speaking, effects range from beneficial to negative for programs that use local fish for hatchery broodstock and from negligible to negative when a program does not use local fish for broodstock. Hatchery programs can benefit population viability but only if they use genetic resources that represent the ecological and genetic diversity of the target or affected natural population(s). When hatchery programs use genetic resources that do not represent the ecological and genetic diversity of the target or affected natural population(s), NMFS is particularly interested in how effective the program will be at isolating hatchery fish and avoiding cooccurrence and effects that potentially disadvantage fish from natural populations. Nimbus Fish Hatchery on the American River has been a substantial producer of stedhead in the Central Valley since 1955 (Leitritz 1970) and, during the first several decades of operation, broodstock was imported periodically from coastal steelhead populations, including the Eel, Mad and Russian rivers (Lee and Chilton 2007). The effects of this out-of-basin stocking are apparent in both individual and population analyses, in which the Nimbus Fish Hatchery and American River populations are intermediate between the coastal steelhead populations and all other Central Valley populations (Pearse and Garza 2015). Notably, the closest relationship ofthe American River populations outside of the Central Valley is to fish from Northern California, in the group that includes the Eel and Mad rivers, rather than to more geographically proximate populations in San Francisco Bay. For this reason, the Nimbus Fish Hatchery stock is not currently part of the CCV steelhead DPS, and its impacts to the natural American River population include both genetic and behavioral effects (Myers et al. 2004). As des·cribed in Pearsons et al. (2007), the selective pressures in hatcheries are dramatically different than in the natural environment, which can result in genetic differences between hatchery and wild fish (Weber and Fausch 2003) and subsequently differences in behavior (Metcalfe et al. 2003). The continued use of out-of-basin (Eel River/Mad River) broodstock is concerning, particularly for Central Valley populations that not geographically proximate to the American River. According to Pearse and Garza (20 15), "The clustering of other Central Valley below-barrier populations with Nimbus and American River samples, particularly those from the Calaveras and Tuolumne Rivers, indicates that introgression of natural populations by fish with coastal steelhead ancestry has occurred through straying/migration ofNimbus Hatchery steelhead." This issue has been perpetuated by the long-time practice of releasing hatchery steelhead production far downstream from the hatchery (e.g., at Discovery Park which is adjacent to the confluence mile 0), which contributes to adult returns straying to nonwith the Sacramento River; natal rivers and creeks thereby spreading out-of-basin genetics throughout the Central Valley. The California Hatchery Scientific Review Group made the following comments about these practices (California Hatchery Scientific Review Group 2012): "There is evidence that Nimbus Hatchery steelhead may stray throughout the Central Valley and spawn naturally in other streams where hatcheries are not present. Both juvenile releases and hatchery strays from Nimbus have the potential to affect naturally spawning steelhead in other watersheds." 316 Biological Opinion for the Long-Term Operation of the CVP and SWP "Although this is intended to be a segregated program, genetic evidence confirms that Eel River genes are throughout the Sacramento System. " "The current broodstockfor this program should be replaced with an alternative broodstock that is appropriate for the American River. " "Investigate straying rates for Jibboom release site (Discovery Park). We do not consider a release site 21 miles downstream ofthe hatchery to be an on-station release. Transporting and releasing juveniles to areas outside ofthe American River or to the lower American River should be discontinued. Juvenile fish should be released at the hatchery, or if not possible, as far upstream in the American River from the confluence of the Sacramento River as possible to reduce adult straying and increase the number of adults returning to the hatchery. Consider necessary facility modifications or equipment purchases that will facilitate on-site releases. Release locations for steelhead may take into consideration ecological and predation effects on other fish populations but should not compromise homing ofadults to the hatchery. " The Nimbus Fish Hatchery Steelhead Program has been working to address these concerns. Regarding the release site concern, in recent years, juvenile CCV steelhead from Nimbus Fish Hatchery have been released at locations further upstream than Discovery Park. In March 2019, all of the steelhead production from Nimbus Fish Hatchery was released at the Sunrise location ( 20). This location is just a few miles downstream from the hatchery and is expected to minimize straying, relative to the Discovery Park location. Assuming 100 percent of the steelhead production continues to be released at the Sunrise location, the Nimbus Fish Hatchery Steelhead Program is considered a stressor of medium magnitude. However, if the release location shifts back to Discovery Park or further downstream (Bay-Delta), then the program would be considered a high magnitude stressor, given the known genetic impacts to steelhead throughout the Sacramento River basin associated with the use of Eel River origin broodstock at Nimbus Fish Hatchery. 2.5.4.4 Conservation Measures 2.5.4.4.1 Spawning and Rearing Habitat Restoration In ROC on LTO BA, Reclamation states "conservation measures include non-flow actions that benefit listed species without impacting water supply or other beneficial uses." "Spawning and Rearing Habitat Named Projects: Pursuant to CVPIA 3406(b)(l 3), Reclamation proposes to implement the Cordova Creek Phase II and Carmichael Creek Restoration projects, and increase woody material in the American River. Reclamation also proposes to conduct gravel augmentation and floodplain work at: Paradise Beach, Howe Ave, Howe Avenue to Watt Avenue, William Pond Outlet, Upper River Bend, Ancil Hoffman, Sacramento Bar- North, El Manto, Sacramento Bar- South, Lower Sunrise, 317 Biological Opinion for the Long-Term Operation of the CVP and SWP Sunrise, Upper Sunrise, Lower Sailor Bar, Nimbus main channel and side channel, Discovery Park, and Sunrise Stranding Reduction. " "Reclamation proposes to continue maintenance activities at Nimbus Basin, Upper Sailor Bar, and River Bend restoration sites. " The effects of these conservation actions are part of the environmental baseline because they previously have undergone ESA section 7 consultation either through individual or programmatic actions. Similarly, any past restoration activities that were completed under the NMFS 2009 Opinion are also considered part of the environmental baseline. The above restoration actions have been consulted on previously such that their past and future beneficial effects to increased spawning and rearing habitat for listed salmonids are factored into the environmental baseline. Reclamation proposes to continue supporting this program into the future. As a result, at the framework-level, we expect continued benefits to CCV steelhead, including increased production and growth and survival. 2.5.4.4.2 Nimbus Fish Hatchery Hatchery Genetics Management Plan The April30, 2019, track changes version ofthe ROC on LTO PA (Appendix A2) states that "Reclamation will complete a Hatchery Genetic Management Plan (HGMP) for steelhead and a Hatchery Management Plan for Fall-run Chinook Salmon as part of Nimbus Fish Hatchery management. Reclamation will work with CDFW and NMFS to establish clear goals, appropriate time horizons, and reasonable cost estimates for this effort." In order to provide enough certainty regarding how and when the PA component would be implemented, and to assess its effects, the HGMP will need to be developed further. Generally, an HGMP would be expected to have beneficial effects by improving the genetic management of steelhead within the Nimbus Fish Hatchery and decreasing the potential negative effects of environmental conditions and water operations. These general beneficial effects are included in this analysis of effects in this Opinion at the framework level. 2.5.4.5 American River Division Effects Analysis Summary The effects analysis results suggest that water temperature will be a high magnitude stressor on American River steelhead, flow management will be a medium stressor on American River steelhead, and operation of the Nimbus Fish Hatchery Steelhead Program will be a medium or high magnitude stressor on the population (and DPS), depending on the hatchery production release location. Based on the responses of steelhead exposed to the PA described above and summarized in Table 2.5.4-3, fitness consequences to individuals include reduced survival during embryo incubation, reduced survival and growth during juvenile rearing, reduced survival during smolt emigration, and reduced genetic integrity. 318 Biological Opinion for the Long-Term Operation of the CVP and SWP Late-Dec- May Late-Dec. - early Apr. Late-Dec. - early Apr Life Stage Timing Folsom/Nimbus releases- flow fluctuations Water temperatures warmer than life stage requirements, particularly occurring upstream of Watt Ave. in April and May Nimbus Hatchery - hatchery 0. mykiss spawning with naturalorigin steelhead Folsom/Nimbus releases - flow fluctuations Stressor Redd dewatering and isolation pwhibiting successful completion of spawning Response Reduced reproductive success Probable Fitness Reduction Reduced survival Reduced survival Reduced genetic integrity Late-Dec.- May Table 2.5.4-3 Exposure and summary of responses of American River steelhead to the proposed action. Life Stage/ Location Spawning Primarily upstream ofWattAve. area Spawning Primarily upstream of Watt Ave. area Embryo incubation Primarily upstream of Watt Ave. area Embryo incubation Primarily upstream of Watt Ave. area Reduced genetic integrity. Garza et at. (2008) showed that genetic samples from the population spawning in the river and the hatchery population were "extremely similar" and both exhibiting Eel River steelhead genetic. Sublethal effects - reduced early life stage viability; direct mortality; restriction of life history diversity (i.e., directional selection against eggs deposited in Mar., Apr., and May) Redd dewatering and isolation. Hannon et at. (2003) reported that 5 steelhead roods were dewatered and 10 steel head redds were isolated at the lower Sunrise side channel when Nimbus Dam releases were decreased on February 27, 2003. When releases were decreased on March 17,2003, seven steelhead redds were dewatered and five additional redds were isolated from flowing water at the lower Sunrise side channel. In April 2004 at the lower Sunrise side channel, five steel bead redds were dewatered and "many" redds were isolated (Bratovich et al. 2005). Redd dewatering at Sailor Bar and Nimbus 319 Life Stage/ Location Year-round Life Stage Timing Stressor Response Basin occurred in 2006 (Hannon and Deason 200!D. Fry stranding and juvenile isolation; low flows limiting the availability of quality rearing habitat including predator refuge habitat Physiological effects - increased susceptibility to disease (e.g., anal vent inflammation) and predation. Visible symptoms of thermal stress in juvenile steelhead are associated with exposure to daily mean water temperatures above 65°F (Bratovich eta!. 2005). From 1999 through 2018, daily mean water temperatures during the summer at Watt Avenue were most often above 65°F, and during 2001, 2002, 2004, 2007, 2008, 2013,2014,2015, and 2016 water te mperatures were often over 68°F (Figure 2.5.4-8). Modeled long-term average water temperatures at Watt Avenue from June through September under the proposed Project (including 2025 climate change simulation) range from approximately 66°F to 70°F (ROC on LTOBA). Physiological effects - reduced ability to successfully complete the smoltification process, increased susceptibility to predation Biological Opinion for the Long-Term Operation of the CVP and SWP Juvenile rearing Year-round Folsom/Nimbus releases - flow fluctuations; low flows, particularly during late summer and early fall Water temperatures warmer than life stage requirements, particularly occurring upstream of Watt Ave. during June through September Jan.- Jun. Water temperatures warmer than life stage requirements, particularly occurring downstream of Watt Ave. during March through June Primarily upstream of Watt Ave. area Juvenile rearing Primarily upstream of Watt Ave. area Smolt emigration Throughout entire river 320 Probable Fitness Reduction Reduced survival Reduced growth; Reduced survival Reduced growth; Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5 Bay-Delta Division During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, BA. Unless otherwise noted, Sections 2.5.5.1-2.5.2.1 0 of the effects description below are based on the modeling associated with the February 5, 2019 PA (Appendix A1 , the original PA) and associated modehng that NMFS requested. Section 2.5.5.11 provides a supplemental effects analysis to assess the effects ofthe June 14,2019 PA revisions reflected in the final PA (Appendix A3), including a discussion of whether and how the PA revisions modify the effects analyzed in Sections 2.5.5.12.5.5.10. Numerous stressors continue to affect the viability of salmonid populations. Table 2.5.5-1 provides a summary of which stressors from the "Recovery Plan for the Evolutionarjly Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley SpringRun Chinook Salmon and the Distinct Population Segment of California Central Valley Steelhead" (National Marine Fisheries Service 2014b) will be analyzed under each PA component within this effects analysis for the Bay-Delta Division. Table 2.5.5-1. Summary of primary stressors influenced by each Proposed Action component for the Bay/ Delta Division. Primary stressors are from the NMFS 2014 Recovery Plan for Central Valley Salmon ids, and NMFS 2018 Recovery Plan for sDPS of Green Sturgeon. An "X" indicates the stressor will be a nalyzed for at least one life-stage a nd species and a "-" indicates that t he stressor is not applicable for a particula r Proposed Act10n component. Project Component 2.5.6.3 Delta Cross Channel X X X X X X X X X X X X X X X X X 2.5.6.4 North Bay Aqueduct 2.5.6.5 Contra Costa Water D istrict Rock Slough Diversion 2.5.6.6 X Water Transfers 2.5.6.7 Suisun Marsh X X 2.5.6.8 South Delta Export Operations X 321 Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component 2.5.6.8.3.1 South Delta Salvage and Entrainment 2.5.6.8.4.1. 1 Integrated Early Water Pulse Protection Turbidity Event 2.5.6.8.4 .1.2 Salmonid Onset Trigger 2.5.6.8.4 .2 EndofOMR Management 2.5.6.8.4.3 Additional RealtimeOMR Management 2.5.6.8.4.4 Storm Related OMR Flexibility 2.5.6.8.5.1 Minimum Export Rate 2.5.6.8.5.2.1 Predator Removal (C02 Injection) 2.5.6.8.5.2.2 Tracy Fish Collection Facility Release Sites Improvements 2.5.6.8.5.3.1 Predator Removal from Clifton Court Forebay - PRES 2.5.6.8.5.3.2 Predator Removal from Clifton Court Forebay - PFRS 2.5.6.g.5.3.3 X X X X X X X X X X X X X X X X X X X X X X X X X X 322 X Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component Aquatic Weed Control for Predator Habitat 2.5.6.8.5.3.4 Operational Changes when Listed Fish are Present 2.5.6.8.5.3.5 Clifton Court Forebay Aquatic Weed and Algal Bloom Control 2.5.6.9 South Delta Agricultural B arriers 2.5.6.1 0 .1.1.1.1 Fall Delta Smelt Habitat 2.5.6.10.. 1.1.2 San Joaquin Basin Steel head Telemetry Study 2 .5.6.10.1.1.3 Sacramento Deep Water Sihip Channel Food Study 2.5.6.1 0 .1.1.4 North delta Food Subsidies/ Colusa B asin Drain and Suisun Marsh R oaring River Distribution System Food Subsidy Studies X X X X X X X X X X X X X 2.5.6.1 0.. 1.3.2 X X X X X X X X X X X X X 2.5.6.1 0.. 1.2.1 Tidal Habitat R estoration of 8,000 acres 2.5.6.1 0 .. 1.2.2 P redator H ot Spots X X X X X X X 323 X Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component Delta Fish Species Conservation Hatchery 2.5.5.1 Delta Conceptual Model and Recent Delta Science There are a variety of stressors affecting juvenile salmonids outmigrating through the Delta, many of which likely interact with project operations (Figure 2.5.5-1). The many interacting factors make it hard to isolate or quantify the effect of any one stressor, especially on "largescale" effects metrics such as through-Delta survival. The correlations among environmental variables add to the challenge. NMFS considers several types of water project-related effects on salmonids in the south Delta as captured in the focal framework of the 2017 Salmonid Scoping Team (SST) report which links hydrodynamics to migration behavior and finally to survival Figure 2.5.5-2). The SST report (Salmonid Scoping Team 2017a) summarizes recent science relevant to key, but not all, project-related effects (Table 2.5.5-3, Table 2.5.5-4, Table 2.5.5-4). Some key elements ofNMFS 's conceptual model of salmonid survival in the Delta, in the context of water operations, include: • • • Effects of exports outside the facilities likely diminish with distance (Cavallo et al. 2015). Near-field effects on fish at the export facilities are just one element of project-related mortality in the Delta; more negative OMR flows are a proxy measure for changed hydrodynamics within the Delta. Those hydrodynamic effects are likely to increase residence time in the Delta, even for fish not entrained into the fish salvage facilities, increasing their exposure to predation and other stressors within the central and south Delta. Near-field effects of the CVP and SWP export facilities such as entrainment and loss, and far-field effects, such as potential migratory disruptions at junctions or in channels, may be linked to salmonid survival via different mechanisms- so studies at one location may not be applicable Delta-wide. For example, a study that does not show an effect ofOMR on salmonid routing at Turner Cut should not be cited as support for no OMR effects on through-Delta migration. In the analysis of PA effects, NMFS considers whether and how different P A components may affect the following elements of through-Delta migration and survival, which all have different mechanistic links to flows and exports. These three elements are discussed at a conceptual model 324 Biological Opinion for the Long-Term Operation of the CVP and SWP level in the sections immediately below, and discussed, when relevant, in the analysis for each PA component: • • • Routing at junctions on the mainstem Sacramento River and San Joaquin River (e.g., Delta Cross Channel and Head of Old River); Movement rates and survival in channel reaches of the mainstem San Joaquin River and the interior channels of the south Delta; and Entrainment into the SWP and CVP fish salvage facilities and loss at those facilities. For an overview of recent science relevant to Delta management, NMFS incorporates by reference the comprehensive January 2017 report, "Effects of Water Project Operations on Juvenile Salmonid Migration and Survival in the South Delta" (Salmonid Scoping Team 2017a). Written by the SST convened by the Collaborative Adaptive Management Team (which included technical staff from multiple agencies and stakeholder groups), the report provides an overview of the findings and uncertainties related to salmonids and water opera1tions in the South Delta. Additional highlights from selected reports and articles are summarized in Appendix I. 2.5.5.1.1 Routing at junctions on the mainstem Sacramento River and San Joaquin River Because the routing "decision" occurs at the time the fish reaches the junction, local flow conditions at the time of arrival (including tidal effects), rather than daily or longer-term average flows, affect the outcome. However, proportional routing offish can be estimated based on longer-term hydrodynamic measures assuming a uniform arrival of fish at the junction throughout the averaging period. NMFS is aware that routing at a junction depends on instantaneous flow fields and velocities at the junction in three dimensional space, the spatial distribution of fish as they enter the region of the junction space, and the individual behavior of the fish to the environmental variables it encounters in this space. However, in the vast majority of instances, there is little or no data that can be provided with the available tools at hand in a way that we can evaluate and quantify the specific hydrodynamics at a given junction. In light of the absence of this information, we use the next best approach, which may be more simplistic, but provides a platform for analysis. On the mainstem San Joaquin River, especiaiiy in the tidal reaches downstream ofthe Head of Old River, flow changes due to the tides are greater than flow changes due to export rates. One way which high San Joaquin Rlver inflow may improve through-Delta survival is that it moves the region of tidal influence farther downstream and may lead to flow conditions at junctions that reduce routing into the interior Delta. Our conceptual model assumes that individual fish will enter the junction space over a discrete period of time (daily) and that daily net flows (tidally averaged in tidal regions) will influence the pattern of flow dispersal at the junction over the diurnal tidal cycle in which the fish is present in the junction space. Stronger downstream flows (more positive daily net flows) will move the tidally influenced zone farther downstream, and the junction will have less water flowing into it, either by magnitude or duration. The extensive work by Perry et al. (20 18) parallels this concept, although in much greater detail for the Sacramento River adjacent to the DCC gates. Higher flows in the Sacramento River mute the tidal effect and less flow and fish go into the DCC route when the gates are open. Hydrodynamic conditions downstream of the junction have more pronounced riverine characteristics when flows are high, and there is less tidal influence in the area of the junction. A more detailed discussion of routing is provided in later sections of the 325 Biological Opinion for the Long-Term Operation of the CVP and SWP opinion (specific to the DCC or Head of Old River junction) and in Appendix B ofVolume 1 of the 2017 SST report (Salmonid Scoping Team 2017a). 2.5.5.1.2 Movement rates and survival in channel reaches of the mainstem San Joaquin River and the interior channels of the south Delta Much work in both the north and south Delta focuses on routing at junctions and reach-specific travel-time or survival for release groups offish that may transit the Delta in a several-week period. However, few studies for example, (Vogel2002) have addressed in-channel movements of individuals at finer temporal and spatial scales that may be most appropriate to link to mechanistic models ofbehavior. Since fish likely spend a majority of their time in channels, not at junctions, behaviors in response to flows in Delta channels are also important for understanding migratory behavior.. Concern about fish behavior and survival in channels is one important element underlying concerns about minimizing disruptions to South Delta hydrodynamics, which can be influenced by many factors, but primarily tides, CVP and SWP exports, and inflow from the San Joaquin River to the Delta (usually referred to as "Vernalis inflow"). Of those three factors, exports and Vernalis inflow are the two project-related components. Examples of how exports and inflow affect South Delta hydrodynamics are shown in Figure 2.5.5-3 in Section 2.5.5.]2 below. Net daily flows are a proxy measure for velocity distributions (more negative net daily flow is associated with a velocity distribution that includes more frequent and/or more extreme negative velocities compared to the velocity distribution associated with a less negative net daily flow) that is a more practicable management knob than instantaneous flows or velocity distributions. The specifics of how net daily flow relates to the underlying velocity distribution depends on location in the Delta, local channel geometry, and the associated stage discharge relationship. For example, the same increase in net flow will be associated with a smaller change in the underlying velocity distribution on the larger-channel mainstem San Joaquin River compared to the smaller-channel Old River. In another example, a location in the western Delta (with high tidal influence) and a location farther upstream (with less tidal influence) could have the same net flow but very different magnitudes of positive and negative velocities. At a given location (for example, at the Old River and Middle River gage locations used to measure OMR), NMFS considers a change in net daily flow a useful proxy meastl!re for qualitative, directional changes in the underlying velocity distribution. The ROC on LTO BA provides data on both net flows (Old and Middle River flow, OMR) and velocity distributions under the COS (current modeling representation of project operations at the time of consultation) and PA. Throughout this effects section, when NMFS refers to effects of net OMR flow, NMFS is using it as a proxy for the underlying hydrodynamic conditions that mechanistically link to salmonid behavior and survival, both in terms of vulnerability to nearfield project-related effects (entrainment to the export facilities) and far-field project-related effects (such as potential migratory disruptions at junctions or in channels). OMR flow is a net daily flow that is a composite measure from two gages in Old River and Middle River downstream of the export facilities near Bacon Island. As noted previously, effects of exports outside the facilities likely diminis.h with distance, so net daily flows in the south Delta are expected to be more negative (or less positive) between the export facilities and the OMR gage locations, and less negative (or more positive) downstream of the OMR gage locations. A change in OMR flow is expected to be associated with changes (in the same direction, but not necessarily magnitude) in net flows and underlying velocity distributions across this "export effect gradient." Because exports can affect the flow split at the Head of Old River at a given 326 Biological Opinion for the Long-Term Operation of the CVP and SWP Vernalis flow, export rates (particularly at low Vernalis flows) can affect flows in the mainstem San Joaquin River immediately downstream of the Head of Old River junction. For this reason, OMR changes due to export changes (especially at low, steady, Vernalis flows) can also be used as an indirect proxy for potential changes to mainstem San Joaquin River flows - not because of the observed flows in Old River and Middle River, but because the OMR metric is a proxy for export change if Vernalis flows are relatively steady. Similarly, if exports are steady, the OMR metric is a proxy for Vernalis flow change and associated changes in flow on the mainstem San Joaquin River. Based on the level of exports reported in the COS and PA scenarios in the BA, South Delta hydrodynamics will generally look like scenarios in the top row under the COS, and like scenarios in the middle row under the PA. Since the BA modeling reports monthly export levels, daily export levels under either regime would be expected to have a greater range. This is an area that needs further study. The 2017 SST Report identifies a gap in linking hydrodynamics to in-channel fish behavior-- smaller scale, mechanism-oriented, studies may be necessary (as a complement to measures of through-Delta survival) to better understand how fish react to local conditions. Appendix H "Bay-Delta Aquatics Effects Figures" of the ROC on LTO BA provides several types of results related to hydrodynamic conditions in the Delta. The "proportion overlap" figures shown for the North Delta and South Delta for 3-month periods summarize the overlap of velocity distributions under two paired scenarios. NMFS focused on comparisons between the PA and COS, especially for the period including April and May, when the PAis most different from the COS in the Delta (Figure 2.5.5-4). Because overlaps of more than approximately 50 percent show as green, the distinctions between PA and COS are a bit difficult to discern but one can see that, as expected, the hydrodynamic changes from the increased exports in the MarchMay period (due primarily to changes in April and May in the PA) are greatest in the southernmost Delta near the export facilities and in the Old and Middle River corridor. The change in velocity distributions is more clearly captured in the location specific velocity overlap plots (Figure 2.5.5-5), which show that (again for the March-May period) that the magnitude and frequency of positive, downstream flows, are decreased in the PA relative to the COS. 2.5.5.1.3 Entrainment into the SWP and CVP facilities and loss at those facilities Once a fish is entrained into the CVP or SWP export facility, higher export rates may improve salvage efficiency. However, the bigger picture is that higher exports likely also increase overall entrainment, and modifies hydrodynamic conditions outside of the fish salvage facilities, as discussed above. The SWP has very poor salvage rates compared to the CVP. 2.5.5.1.4 Delta Survival Several studies conducted on salmonid migration through the Sacramento-San Joaquin Delta provide an understanding of how Delta inflow affects juvenile salmonid survival (Newman 2003, Perry et al. 2010, Perry et al. 20 13). These studies help to define the relationship of Sacramento River flow (at Freeport) and survival of juvenile salmon through the Delta, as well as the importance that fish migration routing has on migratory success. The acoustic tag studies (Perry et al. 2010, Perry et al. 2015, Perry et al. 20 18) indicate that survival probability increases with increasing flows, and changes in survival are steepest when flows are below 30,000 cfs at Freeport. The flow-survival relationship is strongest at lower flows, and in the reaches that 327 Biological Opinion for the Long-Term Operation of the CVP and SWP transition from riverine to strong tidal influence. The relationship between flow and survival is in agreement with the assumptions and results of the velocity and entrainment analyses that indicated low, slack, and reverse velocities increase entrainment risk and increase travel time, which reduce survival probabilities. For example, entrainment into the interior Delta via Georgiana Slough or Delta Cross Channel (DCC) is increased when flows in the mainstem Sacramento River are low, reversing, or stagnant, and the proportion of fish remaining in the Sacramento River or entering Sutter or Steamboat slough increase under high inflows (Perry et al. 20 18). While the mechanisms causing reduced survival probabilities are likely combinations of reduced velocities, route selection, and increased entrainment into the interior Delta, the flowsurvival relationship can be used to collectively evaluate effects of flow changes on throughDelta survival. NMFS uses three models that predict survival probabilities for smolts that enter the Delta through the Sacramento River Basin: DPM, WRLCM using Newman (2003), and Perry et al. (2019). NMFS also incorporated into the Opinion the Salvage Density model. These models analyze how entrainment loss in the south Delta fish salvage facilities changes under the scenarios, and we also use those analyses to help assess effects on overall south Delta effects. Perry et al. (20 19) and DPM are based on telemetry data which allowed for collection of environmental and hydrological data synchronous with the fate of individual fish as they migrate through the north and central Delta. The equation from Newman (2003) relating exports to survival used in the WRLCM is based on coded-wire tag studies over multiple years and relies heavily on statistical correlation between fish recapture and more broad or generalized environmental/hydrological data. Delta Passage Model The DPM integrates operational effects of the COS and PA that could influence survival of migrating juvenile Chinook salmon through the Delta. This includes differences in channel flows (flow-survival relationships), differences in routing based on flow proportions (e.g., entry into the interior Delta, where survival is lower), and differences in south Delta exports (exportsurvival relationships). The DPM provides estimates of through-Delta survival for both scenarios over the five water year types, as well as overall survival covering the full 81 years ( 1923 2003) of simulation through DSM2 and CaiSimJI. The DPM estimated through Delta survival for winter-run, CV spring-run, fall-run and late fall-run Chinook salmon. The DPM used 75 iterations of the model for each scenario and reported the mean survival value as well as the 25th and 75th percentile values for each year within the 81 years used in the CalSimll and DSM2 modeling. The DPM output conveyed survival as a decimal fraction of survival (i.e., 1.00 is 100 percent survival, and 0.500 is 50 percent survival). For the purposes of this assessment, only the reported mean survival value was used for the comparisons between the PA and the COS scenarios. NMFS compared the two scenarios by talGng the difference between reported mean survival values between the PA and COS scenarios for each year within the 81 year period used for the CaiSimJI and DSM2 modeling; that is, PA -COS= difference in mean survival for each year. The results were summarized for all water years combined for the 81 year period from 1923- 2003, and by individual water year type, i.e., Wet, Above Normal, Below Normal, Dry, and Critical). The difference reported in the modeling was in absolute decimal fractions (that is 0.50 survival is equivalent to 50 percent survival). Summary statistics were run for each group of results (i.e., all years, and by water year types) and the median value reported 328 Biological Opinion for the Long-Term Operation of the CVP and SWP for the difference between the P A and COS scenarios. These median values were then reported here as percentages (i.e., a difference of0.001 decimal fraction in survival is 0.1 percent difference in survival). Finally, relative changes between the COS and the PA were determined by calculating the differences between the median values of the PA and COS scenarios and presenting that value as a percentage of the COS value (i.e., (PA-COS/COS) *100; the percentage difference in relative terms to the COS value). Winter-run Chinook Salmon Overall, winter-run Chinook salmon had the best estimated through-Delta survival of the four different Chinook salmon runs modeled using the DPM. The median through Delta survival, as modeled by the DPM, was approximately 34 percent for all years simulated for both the COS and PA operations, with only slight differences between the two scenarios. The absolute throughDelta survival was highest in below normal water year types for both scenarios (-45 percent through Delta survival). Based on the differences in through-Delta survival between the two scenarios, the PA had slightly better through-Delta survival estimates for Wet, Above Normal, and Below Normal water year types, but was slightly lower than the COS during Dry and Critical water year types. Over all the years in the modeling simulation, the PA was slightly lower in overall median through-Delta survival by 0.070 percent. The absolute differences in modeled median through-Delta survival ranged from approximately +0.009 to -0.24 percent between the PA and COS for each water year type are as follows: • • • • • Wet Above Normal Below Normal Dry Critical <0.010 percent (PA greater survival rate) <0.01 percent (PA greater survival rate) -0.02 percent (PA lower survival rate -0.24 percent (PA lower survival rate) -0.21 percent (PA lower survival rate) Overall, both the absolute and relative differences in through-Delta survival are slight between the PA and COS. The relative difference in survival is less than 1 percent across all years in the simulation. This is to be expected as the most substantial changes in export levels in the south Delta occur in months when the majority of winter-run Chinook salmon have already migrated through the Delta. Increases in exports during April and May would only affect a small proportion of the emigrating population that is still within the Delta, as most winter-run Chinook salmon have exited the Delta by the end of March, and therefore would not be exposed to the increased export conditions. CV Spring-run Chinook Salmon As modeled by the DPM, CV spring-run Chinook salmon had a median through-Delta survival rate of approximately 30 percent over the 81 years modeled from the DSM2 and CalSimll simulations, ranging: from approximately 20 percent to 52 percent for both scenarios. The median through-Delta survival rate was highest in Wet water year types (-43 percent) for both the COS and PA scenarios. Across all years. and water year types, the PA had lower median through-Delta survival rates. Across all years in the 81-year simulation period, the median difference between the PA and COS through-Delta survival rate is -0.5 1 percent. The largest difference between the P A and COS occurred in above normal and below normal water year types. The absolute differences in modeled median through-Delta survival ranged from approximately -0.14 to -0.98 percent between the P A and COS for each water year type are as follows: 329 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • • Wet Above Normal Below Normal Dry Critical -0.98 percent (PA lower survival rate) -0.78 percent (PA lower survival rate) -0.66 percent (PA lower survival rate) -0.11 percent (PA lower survival rate) -0.14 percent (PA lower survival rate) The overall changes in through-Delta survival for CV spring-run Chinook salmon is also slight. However, the median P A through-Delta survival rate is lower than the COS in all but Critical water year types, and has a greater absolute and relative percentage change than was observed for winter-run Chinook salmon in the DPM modeling. The relative changes in median survival was 1.4 percent lower for the P A compared to the COS. The overlap ofthe CV spring-run emigration period with the increased exports in April and May are the likely cause for the reduced through-Delta survival rates modeled by the DPM. CV Fall-run Chinook Salmon The results of the DPM for CV fall-run Chinook salmon estimate that the median through-Delta survival is approximately 24 to 25 percent for both the P A and the COS, with the P A being slightly lower. The PA median through-Delta survival for all 81 years ofDSM2 CalSimii simulations included in the DPM was 0.32 percent lower than the COS for the same period. The largest differences between the PA and COS through-Delta survival rates occurred in Wet water year types (1.1 percent lower under the PA). The absolute differences in modeled median through-Delta survival ranged from +0.76 to -1.1 percent between the PA and COS for each water year type are as follows: • • • • • Wet Above Normal Below Normal Dry Critical -1.14 percent (P A greater survival rate) -0.95 percent (PA lower survival rate) -0.09 percent (PA lower survival rate) 0.76 percent (PA lower survival rate) 0.30 percent (PA lower survival rate) The overall changes in absolute through Delta survival for CV fall-run Chinook salmon are also slight. The PA has better through-Delta survival in Dry and Critical water year types, but then has lower survival in all of the remaining water year types. The overaU through-Delta survival rate over the 81-year DSM2 and CalSim II simulation period included in the DPM is also less for the PA compared to the COS, and is similar to the rate for winter-run Chinook salmon and CV spring-run Chinook salmon (-0.3 percent lower). Fall-run Chinook salmon emigrate at similar times as YOY CV spring-run Chinook salmon, and the effects of increased exports during the April and May period would negatively affect both runs. CV Late Fall-run Chinook Salmon The DPM results for late fall-run Chinook salmon estimate that the median through-Delta survival is approximately 21 to 25 percent for both the COS and P A, with the PA consistently lower across all years and by water year type. Over the 82-year DSM2 and CalSimii simulation period included in the DPM, the P A had a median through-Delta survival rate that was 0.23 percent lower than the COS. The largest differences between the PA and COS occurred in Wet water year types. The absolute differences in through-Delta survival ranged from -2.02 to -0.08 percent between the PA and the COS for each water year type are as follows: 330 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • • Wet Above Normal Below Normal Dry Critical -2.02 percent (PA lower survival rate) -0.08 percent (PA lower survival rate) -0.15 percent (PA lower survival rate) -1.14 percent (P A lower survival rate) -0.19 percent (PA lower survival rate) The overall changes in through-Delta survival are slight. In all water year types and over the 81year DSM2 and CalSimii simulation period included in the DPM, the PA has a lower throughDelta survival rate, particularly in Wet water year types where the difference is over 1 percent absolute (7.0 percent relative change). The lower overall survival is likely due to the earlier emigration period for late-fall run Chinook salmon, which spans a broader spectrum of flows in the Sacramento River and export actions in the South Delta during the fall and early winter. CCV Steelhead The DPM does not model CCV steelhead survival as it is based on the data derived from acoustic tag studies using Chinook salmon. Since the DPM is based on Chinook salmon, only a generalized association can be made with CCV steelhead smolts, which are typically larger and have somewhat different behaviors associated with their downstream migration as smolts (Chapman et al. 2013). Given that the majority of results for Chinook salmon through-Delta survival have slhown that survival under the PA conditions are less than under the COS conditions, it would be reasonable to conclude that CCV steelhead smolts emigrating through the Delta at the same time and under the same conditions assumed for the PA would also have reduced survival under the PA conditions compared to the COS, although the magnitude of the difference is uncertain due to differences between Chinook salmon and CCV steelhead. sDPS Green Sturgeon The DPM modeling does not apply to green sturgeon and is not used to assess impacts to survival under the PA for any life stage of sDPS green sturgeon. Winter-run Chinook Salmon Life Cycle Model (WRLCM) The WRLCM can estimate survival of emigrating winter-run Chinook salmon smolts to Chipps Island that have rear,e d in different habitats within the Sacramento River system, including those that have reared in the Delta. Although not a strict one-to-one comparison, the results of the WRLCM that estimates the survival of smolts rearing in the Delta to Chipps Island under the PA and COS conditions can be compared to the through-Delta survival estimates of the DPM in a parallel fashion. Factors which reduce survival (flows, exports, routing into the interior Delta, etc.) are components of both models. The WRLCM estimates that winter-run Chinook salmon smolts that emigrate in January of Wet water year types will have slightly better median survival (3 .2 percent) under the PA than the COS. Survival estimates remain higher for the PA compared to the COS in February and March, but are slightly less than January during the Wet water year types. By April and May, the survival under the PAis estimated to be less than the COS, up to 7 percent (absolute) in April, and 3 percent in May. The reductions in survival under the PA are likely due to the increases in south Delta exports during these months compared to the COS conditions, which ar,e modeled using the equations from Newman (2003) relating exports to survival. This reduction in survival during the month of April for winter-run Chinook salmon 331 Biological Opinion for the Long-Term Operation of the CVP and SWP smolts originating in the Delta holds true for all water year types for the months of April and May, though most winter-run Chinook salmon juveniles have exited the Delta by mid-April. The estimates of survival to Chipps Island for Delta origin winter-run Chinook salmon smolts is consistently higher for the COS conditions compared to the PA conditions for the remaining water year types. April consistently has the greatest difference in survival between the PA and COS conditions, with up to 9.4 percent difference in bdow normal years. Overall the PA has lower survival rates for winter-run Chinook salmon smolts emigrating to Chipps Island for fish originating in the Delta, except for the period of January through March in Wet water year types. This parallels the general findings of the DPM for winter-run Chinook salmon migrating through the Delta, which found reduced survival for the PA for Below Normal, Dry, and Critical water year types, and only slightly higher survival for Wet and Above Normal water year types. Perry Survival Model The Perry Survival Model (STARs model) combines equations from statistical models that estimate the relationship of Sacramento River inflows (measured at Freeport) on reach-specific travel time, survival, and routing of acoustic-tagged juvenile late-fall Chinook salmon. Given these equations, daily cohorts of juvenile Chinook salmon migrating through the Delta under the CalSim simulations of the PA and the COS were simulated. Daily Delta Cross Channel gate operations from the DSM2 simulations of the PA and COS were also included. Statistical analysis of travel time and survival in eight discrete reaches of the Delta was used for assessing travel time and survival under the PA and COS scenarios. This analysis was based on acoustic telemetry data from several published studies where details of each study can be found (Perry et al. 2010, Perry et al. 2013, Michel et al. 2015). The data for the analysis consisted of2,170 acoustic tagged late fall-run Chinook salmon released during a 5-year period (2007-2011) over a wide range of Sacramento River inflows (6,816 -76,986 ft3/s at Freeport). There is the potential that flows outside of this range may not be adequately represented in the model. The model does not use any export-survival relationships, and thus reflects only the influence of Delta inflow, routing, DCC gate operations, and travel time on through Delta survival. The simulation output for each day was summarized graphically to provide a number of useful statistics for each daily cohort: • • • • • The proportion of fish using each unique migration route. The median daily travel time through the Delta. The median daily through-Delta survival. The probability of entering the interior Delta. Daily difference in survival, routing into the Delta interior, and median travel time between the PA and COS. The difference in daily through-Delta survival between the PA and COS was summarized with graphics that display the distribution of survival differences among the 82 years of the simulation for a given date from October through July. This analysis is unique in that it summarizes daily through-Delta survival of the paired scenarios so it is more realistic of differences in survival that fish would experience under the scenarios on any given day (though it still captures limited variability in flow due to the underlying monthly CaiSimii modeling). This is a more realistic representation of effects experienced by outmigrating smolts than the summary statistics used in some of the other methods used in this opinion. Results of the DPM and Winter-run Life Cycle 332 Biological Opinion for the Long-Term Operation of the CVP and SWP Model, for example, provide data summarized over the entire year for each of the 82 years and then summarize those differences collectively and by water year type. This grouping of results can dampen the level of effect that an individual fish may experience at a smaller time scale which may underestimate the actual impact to survival. To understand how survival differences arise, it is useful to examine how the individual components of migration routing, survival, and travel time contribute to overall survival in a particular year. Figure 2.5.5-6, Figure 2.5.5-7, and Figure 2.5.5-8 illustrate detailed model output for 1979, a below normal year water year that exhibited flows ranging from 10,000 cfs to 30,000 cfs in the Sacramento River at Freeport. Delta inflow, specifically Freeport flow, is ll.lSed as a predictor of survival, travel time, and route entrainment into the interior Delta. When Freeport flows are higher, through-Delta survival increases, and travel time decreases through the Delta. In addition, the probability of entering the Delta interior increases when the DCC gates are open, but also decreases when Freeport flows are higher. In Figure 2.5.5-6, there are differences in the flows at Freeport early in the water year (October through January) with modeled flows in the PA higher in October, but lower from November through December compared to the COS. The modeling of the operations of the DCC gates results in differences between the two scenarios and reflect differences in upstream operations between the two scenarios. Because the model cannot capture Knights Landing Catch Index (KLCI) or the Sacramento Catch Index (SCI), it uses a flow-based relationship to estimate the number of days when fish are likely to be present. Specifically, the CalSimll model estimates the number of days that the flow at Wilkins Slough would be greater than 7,500 cfs using a relationship derived from historical monthly flows and closes DCC for that many days in a month within the Oct 1-Dec 14 period. While the model code is exactly the same for the COS and the PA, higher flows at Wilkins Slough result in a greater number of days of closure. Because the COS scenario includes the 2008 USFWS Opinion Fall X2 component in wet and above normal years, flows at Wilkins Slough are higher for the COS than for the P A in those year types, and there are more frequent exceedances of the 7,500 cfs threshold and associated modeled closures ofthe DCC gates. The modeled flows in October and November of wet and above normal years are generally lower under the PA and therefore do not trigger closure of the DCC as often (Sumer 2019). In real-time operations, gate closure would be governed by the KLCI and the SCI and thus may provide equal or better protection than exhibited in the modeling. This difference in DCC gate operations between the COS and PA is particularly apparent in October and November where through-Delta survival is approximately 45 percent in November for the COS, compared to approximately 30 percent for the PA (middle panel), with a difference in through-Delta survival of about 12-15 percent (bottom panel). In spring (May through June) the modeled flows at Freeport are slightly higher for the PA than for the COS, which translate into slightly higher through-Delta survival (middle panel), and a slightly positive difference in through-Delta survival of about 1-2 percent (bottom panel; PA is greater than COS). The responses for routing into the interior Delta and travel time through the delta reflect the expected responses to changes in Delta inflow and DCC gate position. With the DCC gates open for the PA and closed for the COS, and lower Freeport flows for the PA compared to the COS, there is a higher probability of entering the Delta interior under the PA (Figure 2.5.5-7; middle and bottom panels). Conversely, in spring, the DCC gates are closed for both scenarios, but Freeport flow is higher for the PA, and thus there is a lower probability of entering the interior Delta for the PA compared to the COS. In Figure 2.5.5-8, higher Freeport flows for the COS coupled with a 333 Biological Opinion for the Long-Term Operation of the CVP and SWP closed DCC gate reduces the median travel time through the Delta compared to the PA by almost 2 days in the fall. Conversely in spring, when the PA has slightly higher Freeport flows and the DCC gates are closed for both the PA and COS conditions, the PA has slightly faster median travel times through the Delta of approximately 1 day. These general relationships between Delta inflow at Freeport, and the position of the DCC gates are observed throughout the modeled 82 years. In Figure 2.5.5-9, the boxplots show the distribution ofthe probability that through-Delta survival for the PA scenario is less than survival for COS over the 82-year period of the modeling for each individual day between October and July. The box plots for each day summarize the data for the 82 years of simulation, with the median depicted as a point in each box, and the box hinges representing the 25th and 75th percentiles. The whisker bars represent the minimum and maximum values over the 82-year period. In fall (October through November), the median point of each boxplot shows that in 50 percent of the years, the probability that the difference between the PA and COS is less than zero is between 60 percent and - 100 percent. By late November- early December, the median probability (50 percent of years) that the difference between the PA and COS is less than zero has fallen to approximately 20 percent. From late December through mid-January, the median probability increases so that in 50 percent of the years, the probability that the through-Delta survival for the PAis less than the COS has risen to nearly70 percent. For the period between February and late March, the median probability (i.e., in 50 percent of years) that the PA through-Delta survival is less than the COS is approximately 20 percent. An additional increase in the probability that the PA has a lower through-Delta survival occurs during the first half of April. From late April through June, the probability that in 50 percent of the years that the PA has a lower through-Delta survival than the COS is essenbally zero. In summary, the COS condition has a high potential to have greater throughDelta survival during three periods of the year: fall (October and November), from midDecember through mid-January, and again in early April. The probability that the difference in median travel times through the Delta between the PA and COS conditions is greater than zero is depicted in Figure 2.5.5-1 0. This means that travel time is longer for the P A compared to the COS. The box plots for each day summarize the data for the 82 years of simulation as described in the previous paragraph. Similar to the previous figure, the probability that the median travel time is greater for the PA compared to the COS is high for several periods during the year. From October through November, the probability that the difference in median travel times through the Delta between the PA and COS being greater than zero is greater than 60 percent for 50 percent of years modeled. There are two additional large peaks in the probability that the PA has longer median travel times during the year, one occurring in January, and the second occurring in April. In contrast, there is little or no probability that the differences between median travel tiimes through the Delta between the PA and COS scenarios are greater than zero from February to April and from late April to mid-June. Figure 2.5.5-11 depicts the distribution in the probability that the PA will have a greater potential to have fish routed into the Delta interior compared to the COS over the 82-year period of the modeling for each individual day between October and July. The box plots are constructed as previously described. There is a higher probability that from October through November, the PA will have a greater potential to route fish into the Delta interior, with 50 percent of the years having up to an 80 percent probability that the difference between the PA and COS will be greater than zero. From December through late May, there is low probability that the PA will 334 Biological Opinion for the Long-Term Operation of the CVP and SWP have a greater potential to route fish into the Delta interior compared to the COS. This is to be expected as the DCC gates are typically closed during this time for both scenarios. The DCC gates typically open up for the summer starting in June, and the increase in the difference between the PA and COS conditions may reflect operational differences upstream of the Delta under the PA rather than DCC gate conditions, as under both scenarios the gates are open. Figure 2.5.5-12 depicts the daily median differences in through-Delta survival between the PA and COS. During the fall period (October through December), through-Delta survival is better under the COS compared to the P A. Differences in survival can range up to 15 percent better under the COS (whisker bars) but can be approximately 10 percent better in up to 25 percent of the years modeled (25 percent interquartile hinge point). The median difference is slightly less than zero in absolute terms for most of this period, and the 75th percentile is essentially zero from October through November. In December, there is a slight reversal in survival differences (75th percentile quartile is slightly positive, approximately 1 percent) but the daily median difference of through-Delta survival shows little difference between the PA and COS, essentially tracking the zero line. From mid-April through June there is a slight increase in the difference between the PA and COS, with the PA having slightly better (I-2 percent better 751h percentile interquartile) through-Delta survival. Figure 2.5.5-13 and F igure 2.5.5-14 depict the daily differences in median travel time through the Delta and the percentage of fish routed into the Delta interior between the PA and COS conditions for each individual day based on the 82 years in the modeling. The figures show the effect of the changes in Delta inflow and operations of the DCC gate during the fall period (October through November). In response to lower flows in the PA and a greater potential for periods of open DCC gates, there is an increase in the median travel time through the Delta for the PA and a greater percentage of routing into the Delta interior. This shows up as a positive difference between the PA and COS. The median difference in travel time through the Delta is approximately O.I days, but the 75th percentile value can reach up to a difference of I day in November. In contrast, the PA has faster travel times in the spring (mid-April through June) and the differences are negative (shorter travel time for the PA compared to the COS). The median difference can be as much as half a day faster travel time through the Delta, with the lower 25th percentile values being nearly I day in late May and early June. It is not unexpected that the travel time through the Delta is longer in the fall under the PA, as the potential to be routed into the Delta interior is also increased during this period. This is a reflection of lower Delta inflows in November under the PA and a higher likelihood that the DCC gates will be open compared to the COS. The box plots in Figure 2.5.5-15 depict the differences in through-Delta survival between the PA and COS by water year type. In each of the water year types, the PA has a greater potential to have lower through-Delta survival in the fall. The median values of the differences are little different than zero, however the 25th percentile values indicate that differences in survival may range up to 10 percent less for the PA than the COS. There is less difference in critical years compared to the other four water year types. For the remainder of the year (December through June) there is little difference in the through-Delta survival between the PA and the COS. In wet years there is a small increase (- 1 percent) in survival under the PA scenario compared to the COS in December. There are also similar increases in below normal and dry water year types during this December period, but the magnitude is much smaller. As seen previously, there is 335 Biological Opinion for the Long-Term Operation of the CVP and SWP also a small increase in through-Delta survival under the PA conditions in the spring, centered on May and June, but it is very small in magnitude (< 1 percent). The box plots in Figure 2.5.5-16 depict the differences in median travel time between the PA and COS conditions by water year type. In all water year types, there is an increase in the median travel time difference between the PA and COS in the fall period (October through November) indicating that the travel time in the PA is longer than the COS. The peak difference between the PA and COS during the fall occurs in early November. The 75th percentile values for the wet, above normal, below normal, and dry water year types are approximately 1 day longer for the PA than the COS during this period. The difference in critical water years is slightly less. In wet water years, the PA has slightly shorter travel times than the COS in December, which is also reflected by the increased through-Delta survival for the PA during this period. During the remainder of the year, but particularly in the spring period, there are periods in which the PA has reduced travel times compared to the COS. From December through May, these reductions in through-Delta travel times are typically slight. Larger reductions in the through-Delta travel times for the PA compared to the COS are seen in May and June. The box plots in Figure 2. 5.5-17 depict the daily median differences in the interior routing between the PA and COS conditions by water year type. In each water year type, there is a higher likelihood that a greater percentage of fish will be routed into the Delta interior during October through November under the PA scenario than under the COS. While the median value of the differences between the PA and COS is typically little different than zero, the 75th percentile of the box plot indicates that the PA can be 5 to I 0 percent higher in routing fish into the Delta interior during this period. This is expected given the lower Delta inflows for the PA during this period and the greater likelihood that the DCC gates are open. The difference between the PA and COS routing is less in critical water year types compared to the other water year types. As expected, during the spring, when the PA tends to have slightly better inflows to the Delta, the percent of fish routed into the Delta interior is slightly lower for the PA compared to the COS. Winter-run Chinook Salmon Exposure and Risk The Perry Survival Model comprehensively looks at factors that affect survival, such as travel time, routing into the Delta interior, and operations of the DCC gates, to evaluate how changes in Delta inflow will affect smolt migratory success between the PA and COS scenarios. Since daily results are segregated by month and then further by water year type, we can thoroughly examine the exposure and risk associated with these changes for winter-run Chinook salmon smolts. The main migratory period for winter-run Chinook salmon juveniles is October through April. Based on the modeling outputs, juvenile winter-run entering the Delta from the Sacramento River in October or November will have a greater risk of being routed into the Delta interior through open DCC gates associated with lower Delta inflows under the PA compared to the COS (Figure 2.5.5-14 and Figure 2.5.5-17). These routes have the potential to have longer travel times through the Delta for the PA compared to the COS (Figure 2.5.5-13 and Figure 2.5.5-16), which in tum is expected to create conditions that have lower through-Delta survival for migrating winter-run Chinook salmon (Figure 2.5.5-12 and Figure 2.5.5-15). Based on the modeling, survival could be reduced up to approximately 10 percent (lower 25th percentile) during the October through November period in wet, above normal, below normal, and dry years. In critical years, the reduction js less. This would affect approximately 5 percent of the brood year 336 Biological Opinion for the Long-Term Operation of the CVP and SWP population based on historical fish monitoring. In wet years, higher Delta inflows in December under the PA, coupled with closed DCC gates would provide a small improvement in throughDelta survival for winter-run emigrants entering the Delta. Increased flows reduce travel times and the potential for routing into the Delta interior at other junctions (i.e., Georgiana Slough). This would benefit approximately 10 to 25 percent ofthe winter-run brood year population which enter the Delta during December. For the rest of the juvenile winter-run Chinook salmon migration period (January through April) the modeling shows little difference in through-Delta survival and routing into the Delta interior, and very minor improvements in through-Delta travel times. Overall, the PA is expected to negatively affect approximately 5 percent of the annual brood year population that may potentially emigrate into the Delta in October or November. Positive survival effects are likely to occur only in wet years during December, to approximately 10 to 25 percent of the annual brood year population emigrating into the Delta. CV spring-run Chinook salmon Exposure and Risk The main migratory period for CV spring-run Chinook salmon juveniles is December through May. Older yearling CV spring-run Chinook salmon are expected to start emigrating into the Delta starting in October and continuing through January and into February. Like juvenile winter-run Chinook salmon, yearling CV spring-run Chinook salmon w ill be exposed to the higher risks of being routed into the Delta interior through open DCC gates. The open gates are associated with lower Delta inflows under the PA as compared to the COS. Fish following these routes will potentially have longer travel times through the Delta under the P A compared to the COS. Longer routes are associated with conditions that may lead to a reduction in through-Delta survival under the PA. This is expected to occur in all water year types (Figure 2.5.5-15), however the reduction will be a lower in critical water year types. Like juvenile winter-run Chinook salmon, yearling CV spring-run Chinook salmon that emigrate into the Delta in December of wet water year types will likely see better conditions and have higher through-Delta survival. This is in part due to the higher forecasted Delta inflows in December of wet years, coupled with closed DCC gates reducing routing into the Delta interior. Increased flows reduce travel times and the potential for routing into the Delta interior at other junctions (i.e., Georgiana Slough). Very few juvenile CV spring run Chinook salmon would be present emigrating to the Delta prior to January. From January through the beginning of April there is very little difference between the through-Delta survival rate for the PA and COS. Improvements in the PA through-Delta survival rate begin to occur in mid-April when the difference between the PA and COS becomes positive. This indicates that the P A has better survival than the COS, although the magnitude of improvement is fairly small (approximately 1-2 percent at the 75th percentile level). Part ofthis improvement is due to higher levels of Delta inflow proposed for the P A. Based on historical monitoring, the last 50 percent of the annual brood year of CV spring-run Chinook salmon would be moving into the Delta during April and May. These fish would be exposed to the better through-Delta survival rates found in the mid-April through June period under the PA and would be expected to benefit from the improved conditions. CCV Steelhead Exposure and Risk The Perry Survival Model does not model CCV steelhead survival and movements as it is based on data derived from studies using acoustic tagged Chinook salmon in the Delta. Given that 337 Biological Opinion for the Long-Term Operation of the CVP and SWP steelhead and Chinook salmon have generally similar, but not identical migratory behaviors, only a generalized association can be made. CCV steelhead smolts are present within the Delta in most months of the year but the main migratory season for smolts to move through the Delta is from November through June. It is reasonable to assume that CCV steelhead smolts emigrating through the Delta at the same time and under the same conditions assumed for the Perry Survival Model for Chinook salmon would experience the same Delta inflows, DCC gate operations, and hydraulic conditions at river junctions. The magnitude of response by CCV steelhead smolts may be different, but the general trends should be similar. For CCV steelhead smolts emigrating in the fall period during October and November, there is an increased likelihood that more fish will be entrained into the Delta interior through open DCC gates under the PA as compared to the COS. Fish that do so will have longer travel times through the Delta interior and more than likely have reduced through-Delta survival. Only a small proportion of the emigrating population of CCV steelhead smolts is expected to be present in the Delta during October and November. From December through April, there would be little difference between the PA and COS regarding routing and travel times, and therefore through-Delta survival should not vary much between the two scenarios. This is the period in which most CCV steelhead from the Sacramento River Basin emigrate through the Delta. From mid-April through June, the slight increase in flows coming into the Delta under the PA scenario should help reduce both travel time through the Delta and routing into the Delta interior at river junctions compared to the COS. These changes should increase through-Delta survival, although the fraction of the CCV steelhead affected during tlhis period would be quite low as most steelhead from the Sacramento Basin have already emigrated. sDPS of North American Green Sturgeon The Perry Survival Model does not apply to sDPS green sturgeon and is not used to assess impacts to survival under the PA for any life stages of sDPS green sturgeon. Summary Based on the results of the Perry Survival Model, winter-run Chinook salmon juveniles and yearling spring-run Chinook salmon are the two groups of salmonids that will be affected most by the PA. Those fish that migrate through the Delta during October and November will see the largest differences in through-Delta survival, routing into the Delta interior, and travel times. Based on the results of the modeling for the October and November period, the PA will decrease through-Delta survival compared to the COS, increase the number of fish routed into the Delta interior compared to the COS, and increase the through Delta travel time of fish compared to the COS. It should be noted that these differences are driven in part by the operations of the DCC gates, which respond to the differences in river flow between the two scenarios as described above. Operations of the gates in real time, based on observations of fish in monitoring programs, may differ from the operations of the gates in the modeling, and thus provide equal or better protection than exhibited in the modeling. Finally, since the Perry Survival Model does not use any specific relationships between exports and survival, the model is relatively insensitive to the effects of changing exports. Likewise, the Perry Survival Model does not specifically use any data from studies conducted in the San Joaquin River side of the Delta, and therefore should not be used to interpret survival, routing, or travel times for salmonids entering the Delta from the San Joaquin River side of the Delta. 338 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.2 Presence of the Species within the Bay-Delta Division The approach used for this analysis was to identify which ESA-listed species would likely to be present in the Bay-Delta region during the PA and exposed to the PA-related stressors. NMFS conducted a review of nearby CDFW and USFWS monitoring locations, run timing, and fish salvage data to determine the likelihood ofESA-listed fish presence (Table 2.5.5-5, Table 2.5.5-6, Table 2.5.5-7 and, Table 2.5.5-8. Adult salmonids typically migrate through the Delta within a few days. Juvenile Chinook salmon spend from 3 days to 3 months rearing and migrating through the Delta to the mouth of San Francisco Bay (Brandes and McLain 2001, MacFarlane and Norton 2002). Steelhead smolts have varied behaviors in their use of the Delta. Juvenile hatchery steelhead used in studies in the San Joaquin and southern Delta had longer transit times to Chipps Island than juvenile Chinook salmon released in the same location on the lower San Joaquin River. In contrast, Chapman et al. (2015), found that steelhead smolts rapidly moved through the San Francisco estuary system and entered the Pacific Ocean at the Golden Gate within days of entering the upper estuary (Suisun Bay). Some individual sOPS green sturgeon may move through the Delta region quickly from either upstream locations or from the estuary during their migratory behaviors, while others may spend a protracted amount of time within the Delta ranging from days to years while holding or rearing. The Bay-Delta waterways function primarily as migratory corridors for winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon, but they also provide some use as holding and rearing habitat for each of these species as well. Juvenile salmonids may use the area for rearing for several months during the winter and spring before migrating to the marine environment. Green sturgeon use the area for rearing and migration yearround. Generally, as flows increase in the fall and through the winter, adult salmon, CCV steelhead, and sDPS green sturgeon migrate upstream through the Sacramento and San Joaquin rivers and juveniles migrate downstream in the winter and spring. Adult winter-run Chinook salmon typically migrate through the estuary/Delta from November to June with the peak occurring in March (Table 2.5.5-5). Adult CV spring-run Chinook salmon migrate through the Delta from January to June (Table 2.5.5-6). Adult CCV steelhead migration into the Sacramento River watershed typically begins in August, with a peak in September and October, and extends through the winter to as late as May (Table 2.5.5-7). Adult sDPS green sturgeon start to migrate upstream to spawning reaches in February and their migrations can extend into July (Table 2.5.5-8), but may also be found holding in waters of the Sacramento River basin and Delta yearround. 2.5.5.2.1 Sacramento River Winter-run Chinook Salmon Adult winter-run Chinook salmon are expected to be in the Bay-Delta region from November through June with a peak presence from February to April (Table 2.5.5-5) as they migrate upstream to spawn in the upper Sacramento River. Since the Delta is a transition zone between tidal and riverine sections of the Sacramento River, adult salmon sometimes wander through the Delta searching for specific olfactory cues that lead them to their natal spawning area. Winterrun Chinook salmon adults have been known to stray into the Sacramento Ship Channel (SSC) and around the Delta islands and sloughs as they make their way through the maze of channels leading to the main stem Sacramento River upstream ofthe Delta, including the Yolo Bypass when inundated. 339 Biological Opinion for the Long-Term Operation of the CVP and SWP For juvenile winter-run Chinook salmon, a review offish monitoring data from 2000-2016 from the Chipps Island trawl and the Sacramento River trawl (Sherwood Harbor) showed very low numbers present from July through October (Speegle et al. 2013, Barnard et al. 2015, Miller et al. 2017, University of Washington Columbia Basin Research 20 19) [USFWS DFJMP data 2000-2016 (U.S. Fish and Wildlife Service 2019)] (Figure 2.5.5-18 and Figure 2.5.5-19). Juvenile winter-run Chinook salmon occur in the Delta primarily from November through early May with a peak occurrence in March, using length-at-date criteria from trawl data in the Sacramento River near Sherwood Harbor (Speegle et al. 2013, Barnard et al. 2015, Miller et al. 2017) (Table 2.5.5-5). There are no reported populations of winter-run Chinook salmon that spawn in the San Joaquin River basin. Presence of adults is unlikely in the channels of the Delta south of the main stem of the San Joaquin River. Adults may be stray into the channels of the Central Delta north of the main stem San Joaquin River as they try to regain access to the main stem Sacramento River through one of the major distributaries (i.e., Georgiana Slough and portions of the lower Mokelumne River system). Based on acoustic telemetry studies using late fall-run hatchery Chinook salmon (Perry et al. 2010, Perry et al. 20 12, Perry et al. 2013, Romine et al. 20 13), substantial fractions of the emigrating juvenile winter-run Chinook salmon population are expected to take alternate routes through the Delta, in addition to the mainstem Sacramento River route. In the north Delta, emigrating salmon are expected to utilize Sutter and Steamboat sloughs as well as the mainstem Sacramento River to reach the western Delta. In addition, alternate routes through the Delta interior are possible through Georgiana Slough and, when the radial gates are open, the Mokelumne River system via the DCC. These interior Delta waterways will route fish to the San Joaquin River mainstem via the terminus of the Mokelumne River. During the period that juvenile winter-run Chinook salmon are moving through alternate routes, they may utilize the Delta for rearing. A study by del Rosario et al. (2013) found that winter-run Chinook salmon are present in the Delta for an extended period oftime, with an apparent residence time ranging from 41 to 117 days, with longer apparent residence times for juveniles arriving earlier at Knights Landing. Individual fish present in the mainstem San Joaquin River are subject to tidal forcing and may move into the channels of Old and Middle rivers, as well as other channel junctions in this reach, rather than moving towards the western Delta. Juvenile winter-run Chinook salmon from the Sacramento River basin have been observed in salvage at the Tracy Fish Collection Facility (TFCF) and Skinner Delta Fish Protection Facility (SDFPF) in the south Delta, indicating that juvenile winter-run Chinook salmon have the potential to be present in the waterways leading to these facilities. Due to extensive tidal movement and the creation of reverse flows in the two main channels (Old and Middle rivers) leading to the export faci lities due to the diversion of water at these facilities, juvenile winter-run may disperse into many of the waterways adjacent to the export facilities, including those waterways that contain the three south Delta agricultural barriers. There are no spawning areas in the Bay-Delta region that could be used by adult winter-run Chinook salmon, therefore the potential that eggs would be present in the Bay-Delta region is nonexistent. Likewise, the potential for alevins/yolk sac fry to be present in the Bay-Delta region is also unlikely due to the distance of the spawning reaches in the upper Sacramento River locations from the Delta. Although it is improbable, heavy precipitation events in the upper river watersheds adjacent to the spawning reaches of the Sacramento River could create high river 340 Biological Opinion for the Long-Term Operation of the CVP and SWP flow conditions that stimulate fry and parr to migrate downstream to the Delta after emergence in the late summer and early fall, although precipitation events of this magnitude are more likely to occur later in the rainy season. Studies by Miller et al. (20 10) and Sturrock et al. (20 15) have shown that for Central Valley fall-run Chinook salmon, sizeable fractions of the adult escapement is made up of fish that left freshwater and entered the marine environment as fry or parr life stages, along with the typical smolt life stage that is expected. Miller et al. (2010) found that among the parr and fry life stages leaving the freshwater environment, a large fraction (25 percent of parr and 55 percent offry migrants) spent time rearing in the brackish waters ofthe Bay-Delta region. A similar diversity of life history strategies may exist for winter-run Chinook salmon. 2.5.5.2.2 CV Spring-run Chinook Salmon Adult CV spring-run Chinook salmon are expected to migrate upstream through the Bay-Delta region from January to June with a peak presence from February to April (Table 2.5.5-6). Like adult winter-run Chinook salmon, adult CV spring-run Chinook salmon could stray into the SSC or the network of sloughs and waterways surrounding the northern and central Delta islands during their upstream migration. Juvenile CV spring-run (young of the year [YOY]) are present in the Bay-Delta region as they migrate to the ocean in the spring. Yearling spring-run Chinook salmon are expected to enter the Delta in late fall and early winter (late October through January). Juvenile spring-run Chinook salmon are expected to be present in the northern Delta region from December through May with a peak presence in March and April (Speegle et al. 2013, Barnard et al. 2015, Miller et al. 2017, University of Washington Columbia Basin Research 2019) [USFWS DFJMP data 2000-2016 (U.S. Fish and Wildlife Service 2019)] (Table 2.5.5-6, Figure 2.5.5-20, and Figure 2 .5.5-21 ). Currently there are no documented non-experimental populations of CV spring-run Chinook salmon in the San Joaquin River basin that would likely occur in the Bay-Delta region. However, there is anecdotal evidence of Chinook salmon occurring in the Stanislaus and Tuolumne rivers that may represent residual populations of spring-run Chinook salmon or individuals that have strayed from other river basins and use the Stanislaus and Tuolumne rivers for spawning based on their run timing and the presence of fry and juveniles that show traits characteristic of springrun populations such as hatching dates and seasonal sizes (Franks 2013, National Marine Fisheries Service 20 16a). Furthermore, the San Joaquin River Restoration Program (SJRRP) goal of re-establishing an experimental population of CV spring-run Chinook salmon in the San Joaquin River basin will create the potential that CV spring-run Chinook salmon will be present in the southern Delta and San Joaquin River regions ofthe Bay-Delta area over the lifetime of the P A. Note that in the CV spring-run Chinook Integration and Synthesis Section (Section 2.8.3), NMFS discusses the San Joaquin experimental population and associated 4(d) rule with respect to fmdings under this Biological Opinion. There are no spawning areas in the Bay-Delta region that could be used by adult spring-run Chinook salmon, therefore the potential that eggs would be present in this area is nonexistent. Likewise, the potential for alevins and yolk-sac fry to be present in the Bay-Delta region is also unlikely, since only extreme precipitation events in the fall and early winter resulting in high river flows in the Sacramento or San Joaquin river basins could flush alevins out of their natal tributaries into the Delta. Fry and parr are more likely to be present in the Delta region in response to high river flows due to the timing of winter storms and the progressive maturation of 341 Biological Opinion for the Long-Term Operation of the CVP and SWP the fish. This period would be from approximately November through March. By April, juvenile spring-run Chinook salmon are reaching the size that smoltification occurs, and the majority of smelts would be moving downriver to enter the Delta on their emigration to the ocean. Springrun Chinook salmon smelt outmigration is essentially over by mid-May with only a few late fish emigrating in early June. There is the potential that some juvenile CV spring-run Chinook salmon will remain in the tributaries through the summer and outrnigrate the following fall and winter as yearlings (Table 2.5.5-6). Adult CV spring-run Chinook salmon are expected to be migrating upstream through the Bay-Delta from January to June with a peak presence from February to April (Table 2.5.5-6). In the San Joaquin River basin, adult migration is also likely to be strongly influenced by the flow levels in the San Joaquin River basin that provides access to the upstream holding and spawning areas. The broodstock for the spring-run Chinook salmon experimental population came from the Sacramento River basin (Feather River Fish Hatchery spring-run Chinook salmon) and are expected to exhibit similar migration timing behavior for both adult and juvenile life stages in the San Joaquin River basin. 2.5.5.2.3 CCV Steelhead The majority of CCV steelhead originate in the Sacramento River basin and its multiple tributaries and are comprised of the Northern Sierra Nevada, Northwestern California, and Basalt and Porous Lava diversity groups. However, small, but persistent populations of CCV steelhead are present in the Calaveras River and San Joaquin River basin and are part of the Southern Sierra Nevada Diversity Group. Both adults and smolts are detected by monitoring efforts in these basins, indicating spawning is occurring in the basins' tributaries. Natural CCV steelheadjuveniles (smelts) can start to appear in the northern Bay-Delta region as early as October, based on the data from the Sacramento River and Chipps Island trawls (Speegle et al. 2013, Barnard et at. 2015, Miller et at. 2017, University of Washington Columbia Basin Research 2019); Figure 2.5.5-22 and Figure 2.5.5-23) and CVP/SWP fish salvage facilities (California Department ofFish and Wildlife 2018a). In the Sacramento River, juvenile CCV steelhead generally migrate to the ocean from early winter to early summer at 1 to 3 years of age and 100 to 250 mm FL, with peak migration through the Delta occurring in March and April (Reynolds et al. 1993). In the San Joaquin River basin, CCV steelhead smelts are expected to appear in the southern Bay-Delta regional waterways as early as January, based on observations in tributary monitoring studies on the Stanislaus River, but in very low numbers. The peak emigration in the lower San Joaquin River, as determined by the Mossdale trawls near the Head of Old River, occurs from April to May, but with presence of fish typically extending from late February to late June. Juvenile CCV steelhead presence in CVP/SWP fish salvage facilities increases from November through January (12.4 percent of average annual salvage) and peaks in February (40.4 percent) and March (26.9 percent) before rapidly declining in April (13.3 percent) and May (4.4 percent) (National Marine Fisheries Service 2016b). By June, emigration essentially ends (Table 2.5.5-7), with only a small number of fish being salvaged through the summer at the CVP/SWP fish salvage facilities. Juvenile steelhead detected at the salvage facilities may arise from either the Sacramento River watershed or from the San Joaquin River watershed. Based on the timing of steelhead juveniles and smelts obs,erved in monitoring programs, Sacramento River basin fish tend to enter the Delta earlier in the winter and spring than their counterparts in the San Joaquin River basin. 342 Biological Opinion for the Long-Term Operation of the CVP and SWP Adult steelhead begin to migrate through the northern portion of the Bay-Delta region (lower Sacramento River) starting in July and continue through late fall, with a secondary peak occurring in late spring (presumably adults returning downstream as post spawn fish, or "kelts"). The majority of adult steelhead migrate into the Sacramento River basin in late summer and fall on their upstream spawning run. The percentile of adult migration passage during this period is 2 percent for July, 12 percent for August, 44.5 percent for September, and 25 percent for October (Hallock et al. 1957, Hallock et al. 1961). Adult steelhead in the San Joaquin River basin are expected to start moving upstream through the southern portion of the Bay-Delta region into the lower San Joaquin River as early as September, with the peak migration period occurring later in the fall during the November through January period, based on Stanislaus River fish weir counts. Adult CCV steelhead will continue to migrate upriver through March, with kelts moving downstream potentially through the spring and early summer, although most are expected to move back downstream earlier than later (Table 2.5.5-7). 2.5.5.2.4 Southern DPS of North American Green Sturgeon Adult green sturgeon begin to enter the Bay-Delta in late February and early March during the initiation of their upstream spawning run (Moyle et al. 1995, Heublein et al. 2009). The peak of adult entrance into the Delta appears to occur in late February through early April, with fish arriving upstream of the Glen-Colusa Irrigation District's water diversion on the upper Sacramento River in April and May to access known spawning areas (Moyle 2002). Adults continue to enter the Delta until early summer (June-July) as they move upriver to spawn in the upper Sacramento River basin. It is also possible that some adult green sturgeon will be moving back downstream as early as April and May through the Bay-Delta region, either as early postspawners or as unsuccessful spawners. The majority of post-spawn adult green sturgeon will move down river to the Delta either in the summer or during the fall. Fish that over-summer in the upper Sacramento River will move downstream when the river water cools and rain events increase the river's flow and either hold in the Delta or migrate directly to the ocean. Data on green sturgeon distribution are extremely limited and out-migration appears to be variable occurring at different times of year. Eleven years of recreational fishing catch data for adult green sturgeon (California Department ofFish and Game 2008,2009, 2010a, 2011,2012, California Department ofFish and Wildlife 2013a, 2014a, 2015a, 2016a, 2017a, DuBois and Danos 2018) show that they are pr·esent in the Delta during all months of the year (Figure 2.5.5-24). Although the majority of green sturgeon are expected to be found along the Sacramento River corridor and within the western Delta, observations of green sturgeon occur in the San Joaquin River and upstream of the southern Delta region based on the information provided in the CDFW sturgeon fishing report cards. Presence of fish occurs during all seasons of the year, but primarily from fall through spring. Few fish are caught during the summer period. Juvenile green sturgeon migrate to the sea when they are 1 to 4 years old (Moyle et al. 1995). According to Radtke ( 1966), juveniles were collected year round in the Delta during a 1-year study in 1963-1964. The DJFMP rarely collected juvenile green sturgeon at the seine and trawl monitoring sites. From 1981 to 2012, 7,200 juvenile green sturgeon were reported at the CVP/SWP fish salvage facilities (Figure 2.5.5-25), which indicates a higher presence of juvenile 343 Biological Opinion for the Long-Term Operation of the CVP and SWP green sturgeon during the spring and summer months in the south Delta where the export facilities are located. Based on the above information, adult and juvenile sDPS green sturgeon were determined to be present in the Delta year-round (Table 2.5.5-8). 2.5.5.3 Delta Cross Channel Operations 2.5.5.3.1 Physical Description of the Delta Cross Channel Gate Infrastructure The Delta Cross Channel (DCC) gates are located in Walnut Grove, California and are a part of Reclamation's Central Valley Project, Delta Division. The DCC is operated by the San Luis and Delta Mendota Water Authority. The DCC is a controlled diversion channel on the left (eastern) bank of the Sacramento River approximately 30 miles dlownstream of the city of Sacramento. The DCC was constructed by Reclamation in 1951 to redirect high quality Sacramento River water southwards through Snodgrass Slough into the channels of the Mokelumne River system for a distance of 15 miles until it meets the San Joaquin River, and then another 35 miles through Old and Middle rivers to the CVP and SWP export facilities near Tracy. The manmade channel of the DCC is 6,000 feet long and has a bottom width of approximately 210 feet, with side slopes of 3: 1 giving a total width of the 350 feet. The water depth of the channel is 26 feet deep with a nominal capacity of 3,500 cfs under normal conditions, but can divert up to 6,000 cfs if needed (Low and White 2004, 2006). Flow into the channel is controlled by two radial gates, each 60 feet wide by 30 feet tall, weighing a total of 243 tons. The gates extend 245 feet across the channel, creating a slight constriction of the channel. The two gates are normally operated together. During high flows on the Sacramento River (greater than 20,000 to 25,000 cfs), the DCC gates are closed to prevent downstream flooding in the Snodgrass Slough and Mokelumne River systems. In addition, flows of this magnitude create scouring conditions at the DCC gate location and downstream of the facility, creating the potential for undercutting of the gate structure. 2.5.5.3.2 Deconstruct the Action - Proposed Operations of DCC Gates Currently, Reclamation operates the DCC in the open position to (1) improve the transfer of water from the Sacramento River to the export facilities at the Banks and Jones Pumping Plants, (2) improve water quality in the southern Delta, and (3) reduce saltwater intrusion rates in the lower San Joaquin River in the western Delta. During the late fall, winter, and spring, the gates are often periodically closed to protect out-migrating salmonids from entering the interior Delta per the criteria in D-1641 and the NMFS 2009 BiOp (National Marine Fisheries Service 2009b) and to facilitate meeting the D-1641 Rio Vista flow objectives for fish passage. The conditions for closing the DCC gates to protect fishery resources were first instituted in the State Water Resource Control Board's (SWRCB) D-1485 decision in 1978. In 1995, the Water Quality Control Plan (WQCP) for the Bay Delta (95-1) instituted additional operations of the DCC for fisheries protection (State Water Resources Control Board 1995). These criteria were reaffirmed in the SWRCB's D-1641 (State Water Resources Control Board 1999). Under the D1641 criteria, the DCC gates may be closed for up to 45 days between November 1 and January 31 for fishery protection purposes. From February 1 through May 20, the gates are to remain closed for the protection of migrating fish in the Sacramento River. From May 21 through June 344 Biological Opinion for the Long-Term Operation of the CVP and SWP 15, the gates may be closed for up to 14 days for fishery protection purposes. Reclamation determines the timing and duration of the closures after discussion with USFWS, CDFW, and NMFS. These discussions occurred through the water operations management team (WOMT) as part of the weekly review of CVP/SWP operations. WOMT used input from the Salmon Decision Process to make its gate closure recommendations to Reclamation. Reclamation's current proposal (as discussed in the consultation meeting on May 21 , 20 19) under the PA is to operate the DCC gates to reduce juvenile salmonid entrainment risk beyond actions described in D-1641, consistent with Delta water quality requirements in D-1641 (U.S. Bureau of Reclamation 2019). From October 1 to November 30, if the KLCI or SCI are greater than three fish per day, Reclamation proposes to operate in accordance with Table 2. 5.5-9 and Table 2.5.5-10 to determine whether to close the DCC gates and for how long. The KLCI and the SCI are computed from the daily catch per unit information from the Knights Landing rotary screw trap (RST) monitoring program, the Sacramento regional beach seines, and the Sacramento River trawl monitoring efforts and adjusted for a standardized 24 hours of effort (one day of monitoring effort). From December 1 to January 31, the DCC gates will be closed. If drought conditions are observed (i.e. fall inflow conditions are less than 90 percent of historic flows) Reclamation and DWR will consider opening the DCC gates for up to 5 days for up to two events within this period to avoid D-1641 water quality exceedances. Reclamation and DWR will coordinate with USFWS, NMFS and the SWRCB on how to balance D-1641 water quality and ESA-listed fish requirements. Reclamation and DWR will conduct a risk assessment that will consider the Knights Landing RST, Delta juvenile fish monitoring program (Sacramento trawl, beach seines), Rio Vista flow standards, acoustic telemetered fish monitoring information as well as DSM2 modeling informed with recent hydrology, salinity, and tidal data. Reclamation will evaluate this information to determine if fish responses may be altered by DCC operations. If the risk assessment determines that survival, route entrainment, or behavior change to create a new adverse effect not considered under this proposed action, Reclamation will not open the DCC. During a DCC gates opening between December 1 and January 31, the CVP and SWP will divert at Health and Safety pumping levels. The primary avenues for juvenile salmonids emigrating downstream in the Sacramento River to enter the interior Deha, and hence becoming vulnerable to entrainment by the export facilities, is by diversion into the DCC and Georgiana Slough. Therefore, the operation of the DCC gates may significantly affect the survival of juvenile salmoniids emigrating from the Sacramento River basin towards the ocean. Survival in the Delta interior is substantially lower than the mainstem Sacramento River (Perry et al. 2010, Perry et al. 2012, Romine et al. 2013) (Need to add citation when in library). NMFS made the following assumptions regarding the proposed operations for the analysis of effects, informed by the conversations during the consultation meeting on May 21, 2019, and analyzed effects accordingly: • • Frequency of DCC gate operations (opening gates) for water quality concerns during the fall and early winter remain similar to past water years; The Fish Monitoring Working Group, which is a new creation ofthe PA, will function in a similar manner to the currently existing DOSS working group and will meet at least once a week to provide near real-time analysis of fish monitoring data from the Central Valley to Reclamation; however, it is unclear what role the new group will have in 345 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • providing recommendations for gate operations to Reclamation or to NMFS as has been done by the DOSS working group since 2010; Monitoring of older juvenile Chinook salmon (by length-at-date) catch will be the basis of the KLCI and SCI threshold triggers for closing the DCC gates; The DCC gates may be opened for up to 5 days for up to two water quality concern events from December 1 to January 31 when drought conditions are observed and gate opening will help to address water quality concerns; this operation is assumed to occur in less than 1 in 10 years. The proposed DCC gate operations follow the criteria for gate operations set forth in D1641, and do not have more frequent gate openings than allowed during the February 1 through May 20 period. 2.5.5.3.3 Assess Species Exposure to Proposed DCC Operations For the purposes of this analysis, "exposure" is defined as the temporal and spatial co-occurrence of the life stages of listed species (winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon) and the stressors associated with the PA. A few steps are involved in assessing listed species exposure. First, the life stages and associated timings of listed species are identified. The second step is to identify the spatial distribution of each life stage. The last step is to overlay the temporal and spatial distributions ofPA-related stressors on top of the temporal and spatial distributions of the listed species with the location of the DCC gates and the effects ofthe stressors associated with its operations. A summary of the effects of the proposed DCC operations is provided in Table 2.5.5-61 in Section 2.5.5.13 Summary Tables of Stressors for each Project Component. NMFS does discuss, for comparative purposes, how DCC operations under the PA might differ from operations in the COS scenario. There are four general periods for operations of the DCC gates under Reclamation's proposed procedures which differ slightly from those contained in the D-1641 operational criteria. From October 1 through November 30, the gates are operated per the actions described in Table 2.5.5-9. This period is different than the operations described in the D-1641 criteria. In general, Reclamation proposes for the DCC gates to remain open unless a trigger threshold is met by the observed catch indices at the Knights Landing RST monitoring location or from either of the monitoring efforts that comprise the SCI (Sacramento regional beach seines or the Sacramento trawl located near Sherwood Harbor on the Sacramento River). From December 1 through January 31, the DCC gates are proposed to be closed, unless drought conditions are observed and Reclamation determines that it can avoid D-1641 water quality exceedances by opening the DCC gates for up to 5 days for up to two events within this period. As noted earlier, this operation is assumed to occur in less than 1 in 10 years. Under the COS, which includes actions required by the NMFS 2009 BiOp, the DCC gates are to be closed from December 1 through December 14 if the water quality criteria identified in D1641 are met, with an exception for NMFS-approved experiments. If the water quality criteria identified in D-1641 were not met, and the Knights Landing Catch Index (KLCI) or Sacramento Catch Index (SCI) are less than three fish per day, the gates could be opened until the water quality criteria are met, then closed within 24 hours of compliance. If the KLCI or SCI were greater than 3 fish per day, then the Delta Operations for Salmonids and Sturgeon (DOSS) working group would review the monitoring data and make recommendations to NMFS and 346 Biological Opinion for the Long-Term Operation of the CVP and SWP WOMT for gate operations. From December 15 through January 31, the gates are closed except for permitted experiments (maximum of 5 days of gates in the open position) with NMFS approval for ESA compliance. COS procedures also permitted a one-time gate opening between December 15 and January 5 for up to 3 days, upon NMFS concurrence, when necessary to maintain Delta water quality in response to the astronomical high tide, coupled with low inflow conditions. The DCC gates were to be operated such that the gates were opened one hour after sunrise to one hour prior to sunset, then return to full closure. During this period of gate openings, Reclamation and DWR were required to reduce exports down to the minimum health and safety level (1,500 cfs combined exports). Under the proposed operations scenario, the DCC gates may potentially be opened more frequently (twice) after December 15 and for a longer period of time (up to 5 days each) than allowed under COS ,conditions. In addition, the opening of the gates may be determined by reaching a water quality "concern level" based on modeling outputs, rather than an actual exceedance of the water quality criteria required in D-1641. However, DCC opening will only occur when drought conditions are observed (defined during the May 21, 2019 consultation meeting as "fall inflow conditions are less than 90 percent of historic flows" and clarified in the June 14, 2019 PA; Appendix A3) and modeling shows that DCC opening will avoid exceedance of a water quality concern level. This joint condition is expected to occur in less than 1 in 10 years, and Reclamation and DWR will coordinate with USFWS, NMFS and the SWRCB on how to balance D-1641 water quality and ESA-Iisted fish requirements. From February 1 through May 20, the gates are proposed to remain closed to protect listed fish. This action parallels the actions required by D-1641. From May 21 to June 15, the gates will be closed for 14 days to provide protection for listed fish consistent with D-1641 criteria. From June 16 through September 30, the gates are proposed to remain open, unless water quality criteria for Delta outflows or electrical conductivity exceedances in the lower Sacramento River require the gates to close to alleviate these water quality concerns. 2.5.5.3.3.1 Sacramento River winter-run Chinook salmon The timing of observations of natural (i.e., non-clipped fish) juvenile winter-run Chinook salmon captured in the Sacramento trawl (Sherwood Harbor) will serve as a proxy for their presence in the vicinity ofthe DCC gates (Table 2.5.5-11). For the period of October 1 to November 30, few natural juvenile winter-run Chinook salmon are observed in the catch ofthe Sacramento Trawl. On average, the date of the first observation of natural juvenile winter-run Chinook salmon for the period covering brood years 1994 to 2017 is December 5, the median date of the first observation of natural winter-run Chinook salmon in the trawl for this period oftime is November 25. The earliest date of the first appearance of natural winter-run Chinook salmon in the Sacramento trawl is September 10 (1998 - a wet year) and the latest date for the first appearance of a natural juvenile winter-run Chinook salmon is March 3 (20 16 -a drought year). From December 1 through January 31 , approximately 50 percent ofthe natural juvenile winterrun Chinook salmon population has moved past the Sherwood Harbor location into the vicinity of the DCC gates. The average date for 50 percent passage is February 1, with the median date of February 13, for the period of 1994 to 2017. During the period of February 1 to May 20, when the gates are closed, the remainder of the natural juvenile winter-run Chinook salmon cohort has passed through the Sherwood Harbor location. The average last date of the observation of natural juvenile winter-run Chinook salmon in the trawl is March 3 I , with the median date of the last 347 Biological Opinion for the Long-Term Operation of the CVP and SWP observation being slightly later on April 9. Typically, no observation of natural juvenile winterrun Chinook salmon occurs from May 21 to September 30. Approximately 30 percent to 40 percent of these emigrating juveniles are expected to enter Sutter and Steamboat sloughs (Perry et al. 2010) and will avoid the location of the DCC gates. The majority of downstream emigrating fish (60-70 percent) are expected to stay in the main stem of the Sacramento River, and encounter the location of the DCC gates during their downstream migration. Hatchery produced winter-run Chinook salmon from the Livingston Stone National Fish Hatclhery are typically released into the upper Sacramento River in early to mid-February and would arrive in the Delta after the DCC gates are closed for the period from February 1 through May 20. Adult winter-run Chinook salmon are expected to start moving into the vicinity of the DCC gates starting in November and continue migrating past the DCC gate location through June with a peak presence from February to April. A flow of 400 cubic meters per second (14,126 cfs) or more on the Sacramento River is associated with a spike in catch of winter-run Chinook salmon at the Knights Landing rotary screw trap monitoring location (del Rosario et al. 2013), Figure 2.5.5-26). Most adult winter-run Chinook salmon are expected to remain in the main channel of the Sacramento River during their upstream migration. However, some fish may use alternate routes to move upstream. These include the channels of Sutter and Steamboat sloughs to the north of the main stem Sacramento River channel, which would avoid the location of the DCC gates, as well as channels from the south, such as Georgiana Slough, which reconnects with the main stem Sacramento River downstream of the DCC gate location. During the period from November through January, when adult winter-run Chinook salmon are expected to be migrating upriver, the gates may be either open or closed, depending on water quality conditions and the presence ofjuvenile listed fish (winter-run and yearling spring-run Chinook salmon). When the DCC gates are closed, any false attraction flows through the DCC into the Mokelumne River system will likely be minimized. Conversely, when the gates are open during this period oftime, false attraction flows from the main stem Sacramento River will flow into the Mokelumne River system and potentially attract adult winter-run Chinook salmon into the system from the San Joaquin River main stem. From February 1 through May 20, the DCC gates are closed and there should be no false attraction flows to encourage straying into the Mokelumne River system. From May 21 through the end of the adult winter-run Chinook salmon migration (June), the gates may be either closed or open. This may encourage straying in any late migrating adult winter-run Chinook salmon encountering the open gate condition. 2.5.5.3.3.2 CV spring-run Chinook salmon The timing of observations of natural juvenile young-of-the-year (YOY) CV spring-run Chinook salmon captured in the Sacramento trawl (Sherwood Harbor) will serve as a proxy for their presence in the vicinity of the DCC gates (Table 2.5.5-12). For the period of October 1 to November 30, very few natural YOY CV spring-run Chinook salmon juveniles are observed in the catch of the Sacramento TrawL On average, the date ofthe first observation ofthreatened natural YOY juvenile spring-run Chinook salmon for the period covering brood years 1994 to 2017 is December 29, the median date ofthe first observation ofCV spring-run Chinook salmon in the trawl for this period of time is December 13. The earliest date of the first appearance of a natural YOY CV spring-run Chinook salmon in the Sacramento trawl is November 23 (2016- a below normal year) and the latest date for the first appearance of a natural YOY CV spring-run 348 Biological Opinion for the Long-Term Operation of the CVP and SWP Chinook salmon juvenile is February 16 (2000- an above normal year). From December 1 through January 31, less than 5 percent ofthe natural YOY juvenile CV spring-run Chinook salmon population has moved past the Sherwood Harbor location into the vicinity of the DCC gates. The average and median date for 50 percent passage is April I 1, for the period of 1994 to 2017. During the period of February 1 to May 20, when the gates are closed, nearly all of the remaining YOY juvenile CV spring-run Chinook salmon population has passed through the Sherwood Harbor location, with very few individuals observed after May 20. On average, by April27, 95 percent of the juvenile CV spring-run Chinook salmon population has moved past the Sherwood Harbor trawl location. The average date of the last observation of natural YOY juvenile CV spring-run Chinook salmon in the trawl is May 15, with the median date of the last observation being slightly earlier on May 11. Historically, very few natural YOY juvenile spring-run Chinook salmon are observed in the trawl dU!ring the period of May 21 to June 15, and essentially none from June 16 to September 30. Hatchery-produced spring-run Chinook salmon from the Feather River Fish Hatchery are typically released in the spring in March and April, and normally would encounter the DCC gates when they are closed. There is the potential that if fish where slow in migrating downstream from their upstream releases, they may encounter the gates when they are opened periodically between May 21 and June 15. An alternate life history strategy for CV spring-run Chinook salmon is to emigrate as yearlings during the fall and early winter after over summering in rivers and stream upstream of the Delta where conditions are suitable for their survival (i.e., Mill Creek, Deer Creek, and other Sacramento River tributaries supporting spring-run spawning). Typically, these fish emigrate as much larger fish than juvenile YOY spring-run Chinook salmon, and are thus less likely to be observed in the trawls and other monitoring actions due to their ability to avoid them. Yearling spring-run Chinook salmon are expected to enter the Delta after precipitation events in the upper Sacramento River basin increase flows in the tributaries and the mainstem Sacramento River and stimul ate the yearling spring-run to start emigrating downstream. This may occur as early as October and extends through January and February. These fish would likely encounter the open DCC gates prior to December 1, and anytime the gates are opened from December 1 through January 31 for water quality issues. Ofthe fish moving downstream in the mainstem Sacramento River, approximately 30 percent to 40 percent of these emigrating juveniles are expected to enter Sutter and Steamboat Sloughs (Perry et al. 2010) and will avoid the location of the DCC gates. The majority of downstream emigrating fish (60-70 percent) are expected to stay in the main stem of the Sacramento River, and encounter the location of the DCC gates during their downstream migration. Adult CV spring-run Chinook salmon in the Sacramento River are expected to start moving into the vicinity of the DCC gates starting in January and continue migrating past the DCC gate location through June with a peak presence from February to April. Adult CV spring-run Chinook salmon are expected to encounter the DCC gates in a similar fashion and timing to that already described for adult winter-run Chinook salmon. 2.5.5.3.3.3 CCV Steelhead The timing of observations of natural juvenile CCV steelhead captured in the Sacramento trawl (Sherwood Harbor) will serve as a proxy for their presence in the vicinity of the DCC gates 349 Biological Opinion for the Long-Term Operation of the CVP and SWP (Table 2.5.5-13). For the period of October 1 to November 30, very few juvenile CCV steelhead have been observed in the catch of the Sacramento Trawl. On average, the date of the first observation ofjuvenile CCV steelhead for the period covering brood years 1998 to 2017 is January 16, the median date of the first observation of CCV steelhead in the trawl for this period of time is January 15. The earliest date of the first appearance of CCV steelhead in the Sacramento trawl is January 2 (2003 - an above normal year) and the latest date for the first appearance of a steelhead juvenile is January 31 (2013 - a dry year). From December 1 through January 31, less than 10 percent ofthe natural juvenile CCV steelhead population has moved past the Sherwood Harbor location into the vicinity of the DCC gates. The average date for 50 percent passage is February 18, for the period of 1998 to 2017. The median date for 50 percent passage is February 16. During the period of February 1 to May 20, when the gates are closed, nearly all of the juvenile CCV steelhead population has passed through the Sherwood Harbor location. On average, by April 18, 95 percent of the juvenile CCV steelhead population has moved past the Sherwood Harbor trawl location. The average date of the last observation of juvenile CCV steelhead in the trawl is July 1, with the median date of the last observation a month earlier on June 2. Historically, very few juvenile CCV steelhead are observed in the trawl during the period of May 21 to June 15, and essentially none from June 16 to September 30. Hatchery-produced steelhead are typically released in January and February, but may be released as early as mid-December and as late as April and May. Therefore, hatchery steelhead may encounter the DCC gates if they are opened in December or January for water quality issues. Using the assumption that juvenile CCV steelhead will distribute into different river channels in a similar proportion as do juvenile Chinook salmon, approximately 30 to 40 percent of these emigrating juvenile CCV steelhead are expected to enter Sutter and Steamboat Sloughs (Perry et al. 20 I 0) and will avoid the location of the DCC gates. The majority of downstream emigrating fish (60-70 percent) are expected to stay in the main stem ofthe Sacramento River, and encounter the location ofthe DCC gates during their downstream migration. Adult CCV steelhead begin to migrate through the lower Sacramento River starting in July and continue through late fall, with a secondary peak occurring in late spring (presumably adults returning downstream as kelts). For most of the upstream migratory period, 90 percent of the adult CCV steelhead will encounter the DCC gates when they are open (July through November). From December through January, an additional 5.5 percent of migrating adults will encounter the gates in a primarily closed position, but may also encounter them in an open position if water quality is a concern. Less than 5 percent of the population will migrate during the February 1 through May 20 period when the gates are closed and the May 21 through June 15 periods when the gates are typically closed half of the time. 2.5.5.3.3.4 sDPS of North American Green Sturgeon Both adult and juvenile sDPS green sturgeon are expected to be within the waters ofthe Delta year-round. Individual sOPS green sturgeon may encounter the DCC gates in multiple configurations as fish may hold and rear in the vicinity of the gates or encounter it as they move upstream and downstream during their behavioral movements. Adult sDPS green sturgeon are likely to encounter closed DCC gates during their upstream spawning migration in w inter and early spring, but encounter open gates during their downstream migration in summer and fall following spawning. Juvenile sDPS green sturgeon rearing in the Delta may encounter the gates 350 Biological Opinion for the Long-Term Operation of the CVP and SWP year round in an open position (typically mid-June through September), intermittently closed (October and November), or in a closed position (December through mid-May). 2.5.5.3.4 Assess Response of Species to the Proposed DCC Gate Operations The DCC can divert a significant proportion of the Sacramento River's water into the interior of the Delta. The DCC is a controlled diversion channel with two operable radial gates. When the gates are fully open, up to 6,000 cfs of water to pass down the DCC into the North and South Forks of the Mokelumne River in the central Delta (Low and White 2006). During the periods of winter-run Chinook salmon emigration when the DCC gates are proposed to be operational (i.e., October to January) through the lower Sacramento River, approximately 40 percent of the Sacramento River flow (as measured at Freeport) can be diverted into the interior ofthe Delta through the DCC and Georgiana Slough when both gates are open. When the gates are closed, approximately 15 to 20 percent (as measured at Freeport) ofthe Sacramento River flow is diverted down the Georgiana Slough channel 13 . The operations of the gates affect the flow conditions surrounding the junction of the DCC with the main stem Sacramento River and create complex hydrodynamic interactions as a result. Operations of the DCC gates create the following stressors related to changes in flow conditions, exposure to predation, and increased risk of straying or delayed migration: • • • • • fish routing into various migratory pathways, alterations to transit times related to routing and alterations in flow(Hom and Blake 2004), increased risk to predation due to routing and increased transit times, increased risk to entrainment at the CVP and SWP export facilities, and creation of false attractant flows through the open DCC gates. 2.5.5.3.4.1 Routing As acoustic-tagged Chinook salmon migrate downriver in the mainstem Sacramento River, fish have t!he opportunity to be diverted into alternative migratory routes. At the junctions of Sutter and Steamboat sloughs, approximately 30-40 percent of the migrating fish in the mainstem Sacramento River were detected moving into these routes, leaving approximately 60-70 percent of the migrating fish to move downstream towards the location ofthe DCC gates. When the DCC gates are open, juvenile fish moving within the main stem ofthe Sacramento River adjacent to the DCC junction may be entrained into the open channel and pass downstream into the Mokelumne River system and subsequently into the waterways of the interior Delta. Numerous acoustic tagging studies have confirmed that when the gates are open, a substantial proportion of juvenile fish are routed into the DCC channel (Newman and Brandes 2010, Perry et al. 2010, 2012, Romine et al. 20 13). The proportion of acoustically-tagged Chinook salmon entrained into the Delta interior varied over the years. Perry et al. (20 10) found that for studies in 2006 and 2007, when the DCC gates were open, 38.7 percent of the fish present in the main stem Sacramento River at the DCC junction (the 60 to 70 percent that were left in the mainstem Sacramento River downstream of Sutter and Steamboat slough junctions) were entrained into the DCC and 16.1 percent were entrained into Georgiana Slough. When tlhe DCC gates were closed, 13 Instantaneous percentages can be much higher depending on the interaction of river flow and tidal flow as describe in Hom and Blake (2004). 351 Biological Opinion for the Long-Term Operation of the CVP and SWP 15 to 20 percent of the fish in the Sacramento River present at the Georgiana Slough junction were entrained into the Georgiana Slough route. Of the fish that were not entrained into the interior Delta, 45.2 percent remained in the Sacramento River when the DCC gates were open, and nearly twice that percentage (80.0 to 85.0 percent) remained in the main stem of the Sacramento River when the DCC gates were closed. For studies conducted in 2008-2009, Romine et al. (2013) reported that the percentage of fish entering the DCC junction from the Sacramento River when the gates were open ranged between 13.6 and 66.7 percent with an overall average of 47 percent. For studies conducted in 2009-2010, Perry et al. (2012) reported that of fish present in the Sacramento River/ DCC junction when the gates were open, 20 percent of those fish entered the DCC, consistent with previous studies in 2007-2008. When the DCC gates are closed, more fish are entrained into the Georgiana Slough route because more fish remain in the Sacramento River main stem past the DCC junction. However, the proportion of fish that remain in the Sacramento River below both junctions (DCC and Georgiana Slough) into the interior Delta typically increases when the DCC gates are closed. 2.5.5.3.4.2 Transit times Fish that enter the interior Delta through the open DCC gates or Georgiana Slough will have a longer migratory route than fish that emigrate through either the main stem Sacramento River or Sutter and Steamboat sloughs. Longer migratory routes would be expected to have lower survival rates in part due to longer transit times to the western Delta (Chipps Island), exposure to the effects of the export facilities in the southern Delta, and a prolonged exposure period to predators along these migratory routes (Perry et al. 2012). Perry et al. (2012) examined survival rates for unit distance travelled in the Delta and indicated that mortality rate per kilometer travelled actually increased as fish travelled from the upper Delta to the lower Delta, becoming the greatest in the tidal zone. The greatest decline in survival was observed for fish entering the interior Delta and travelling through the main stem San Joaquin River from the mouth of the Georgiana Slough/ Mokelumne River complex to Chipps Island, a region of increased tidal influence. NMFS expects that environmental conditions that would require the opening of the DCC gates during the November through January period of juvenile Chinook salmon and steelhead emigration would be associated with lower river inflows from the Sacramento River and San Joaquin rivers, leading to the reduced water quality conditions that would necessitate the gate openings. Low flow conditions in the main stem Sacramento River would increase transit times within the region's channels leading to the DCC junction. Opening the gates would allow fish to enter the Delta interior under low flow conditions, leading to a longer migratory route with increased transit times and lower survival. It would also exacerbate the transit times for fish remaining in the main stem Sacramento River due to a smaller volume of water remaining in that channel after passing the DCC junction with the open gates. The reduction in flow in the main stem Sacramento River coupled with the open DCC gates would alter the local hydrodynamics surroll!nding the junctions of the DCC and Georgiana Slough, potentially leading to higher cumulative levels of entrainment into the Delta interior with the associated lower levels of survival for salmonids (Perry et al. 2015, Plumb et al. 2016). These changes in local hydrodynamics are discussed below. 352 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.3.4.3 Influence of local hydrodynamics related to flow Perry et al. (2015) and Plumb et al. (2016) found that there is a tidal-flow threshold for entrainment into the interior Delta. When flows in the Sacramento River upstream of the DCC junction were less than approximately 12,000 cfs, flood tides caused the lower portions of the Sacramento River to reverse direction during flood tides, but not at flows above this threshold. Reverse flows during flood tides increased the amount of flow entering the DCC and the probability offish being entrained into the Delta interior via that route. Fish that arrived at the DCC junction during ebb tides had a lower entrainment probability into the DCC route. In contrast, fish that arrived during flood tides with flow reversal had a high probability of entrainment into the delta interior via the open DCC gates. Perry et at. (2018) modelled the interacting influences of river flows and tides on travel time, routing, and survival ofjuvenile late-fall Chinook salmon migrating through the Delta. Their modelling found that travel time was inversely related to river inflows in all river reaches examined. Survival was positively related to river inflow only in the reaches that transitioned from bi-directional (tidal) to unidirectional (riverine) with increasing river inflows. The researchers also found that the probability of entering alternative routes to the interior delta declined with increasing river inflows. Thus, by keeping river flows elevated in the main stem of the Sacramento River, such as by keeping the DCC gates closed, tidal fluctuations downstream of the junction are dampened in all but the most tidal reaches. Perry et at. (20 18) found evidence that operating the DCC gates, which removes water from the Sacramento River channel, was associated with lower survival in the reaches of the Sacramento River downstream of the DCC junction. In addition, the modelling showed that as flow in the main stem Sacramento River increases, the probability of entering Georgiana Slough, when the DCC gates are closed, decreased by 16 percent. Likewise, an open DCC gate reduces the percentage offish entering Georgiana Slough, but this is in part due to less fish being present at the Georgiana Slough junction to be entrained, since there is an increased percentage of fish that went into the DCC route through the open gates and into the interior Delta. The cumulative percentage of fish that are entrained into the Delta interior (DCC plus Georgiana Slough) was 15 percent higher than the probability of entering Georgiana Slough alone when the gates are closed. 2.5.5.3.4.4 Survival related to transit routes and predator exposure Perry et al. (2010), Perry et al. (20 12), Perry et al. (2013), and Romine et al. (2013) have stated that survival is lowest for Chinook salmon entrained into the Delta interior. The interior Delta routes are longer than the routes using the Sacramento River or Sutter/ Steamboat sloughs and, therefore, would expose migrating Chinook salmon to more predation risk than shorter routes (Perry et at. 201 2). Cumulative survival over a given route is a product of migration distance or migration rate and mortality per unit distance, and interacts to affect total survival for each route. The acoustic tag studies by Perry et al. (20 12), Perry et al. (20 18) found that not only were the interior Delta routes longer, but they had higher mortality rate per unit distance travelled than other routes through the Delta. Thils fmding indicates that even if the migration routes through the Delta interior were the same distance as other routes, overall survival would still be less due to the higher mortality rate per unit distance. Higher mortality rates per unit distance combined with longer migration distance provides one mechanism for explaining the consistently lower survival for fish entering the interior Delta relative to the Sacramento River. In a tidal environment, where prey migration speeds are likely slower relative to predator swimming 353 Biological Opinion for the Long-Term Operation of the CVP and SWP speeds, such that multiple encounters with predators are possible, the probability of survival is dependent on travel time through the reach and not necessarily the distance travelled. In the tidal reaches of the Delta, salmon movement patterns shift from downstream-only directed movements to both upstream and downstream movements. Thus, in the lower reaches of the Delta a fish may pass through a given reach more than once as they move upstream w ith the flood tide and then back downstream on the ebb tide, increasing not only the time it takes to move through this reach, but also increasing the absolute distance travelled. This could increase the number of predator encounters relative to the length of the reach, therefore increasing mortality rates per a unit distance travelled. In addition, as fish are moved back and forth in a given tidally-influenced river channel reach, they may be exposed multiple times to any waterway junctions present within a given reach. With each passage past the junction, the probability of routing into the alternate route increases. If that route leads into habitat that has less sUIVival potential, such as the interior Delta via Georgiana Slough, the overall survival probability for that individual fish is reduced, and hence the overall survival fraction of the population may be reduced with each additional individual that is routed into the less favorable migratory route. There have been recent efforts to test alternative technologies to create non-physical and physical barriers at such junctions that dissuade movement into those junctions (California Department of Water Resources 2012, 2015, 20 16) as a requirement of the NMFS 2009 Opinion, RP A Action IV.1.3 (National Marine Fisheries Service 2009b). DWR has tested a bioacoustics barrier and a floating fish guidance structure in the Georgiana Slough junction with the mainstem Sacramento River under various flow conditions. Results indicated that at certain flow ranges the barriers could be effective at keeping emigrating salmonids in the mainstem of the Sacramento River and reducing the fraction that could enter the Georgiana Slough route. 2.5.5.3.4.5 Increased risk of entrainment at the CVP and SWP fish salvage facilities Salmonids that are entrained through the open DCC gates and into the Delta interior also have a greater probability of eventually being entrained at the SWP and CVP fish salvage facilities (Low and White 2006, Newman and Brandes 2010) than fish that remain in the Sacramento River migratory route. Fish that exit from the downstream end of the DCC routes through the Delta interior enter the tidally-influenced lower San Joaquin River main stem. Tidal forcing can redirect fish into the channels of Old and Middle rivers, where the influence of the exports is manifested as net reverse flows towards the export facilities. 2.5.5.3.4.6 Increased risks of straying or delayed migration due to DCC gate operations In situations where the DCC gates are open, additional flows from the Sacramento River enter the Delta interior via the Mokelumne River system. Flows from the Sacramento River into this waterway system may provide false olfactory cues for adult Chinook salmon, steelhead, and green sturgeon. Acoustic tracking studies by CDFG (CalFed 2001) indicated that adult fall-run Chinook salmon may make extensive circuitous migrations through the Delta before finally ascending either the Sacramento or San Joaquin rivers to spawn. These movements included "false" runs up the main stems with subsequent returns downstream into the Delta before their final upriver ascent. Tagged fish moved up to the location of the DCC gates and either passed through the open gates or were blocked by closed gates, forcing them to return downstream and fmd another route to the main stem Sacramento River to continue their upstream migration. 354 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.3.5 Risk to Sacramento River winter-run Chinook salmon Juvenile winter-run Chinook salmon in the Sacramento River can start migrating into the v icinity of the DCC gates starting as early as September or October based on the earliest dates for recorded captures in the Sacramento trawl, but more typically are not observed until November. As indicated in Tabl,e 2.5.5-11, the average first date of observation in the Sacramento trawl is in late November or early December. During the October 1 to November 30 period, the DCC gates may be closed to protect pulses of early emigrating juvenile winter-run Chinook salmon if the KLCI or SCI triggers are exceeded. This typically occurs when the first major precipitation event occurs in the fall or early winter period and Sacramento River flow exceeds about 14,000 cfs at Wilkins Slough (del Rosario et al. 2013). This initial migration event has been shown to include over 50 percent of the annual winter-run Chinook salmon population sampled at Knights Landing (del Rosario et al. 20 13). If flows exceed approximately 20,000 to 25,000 cfs at Freeport, then the DCC gates are closed for flood protection in downstream river reaches. This would also be protective of winter-run Chinook salmon or other listed salmonids moving downstream under the elevated flows. From December 1 through January 31, the DCC gates are normally closed, but may be opened for water quality concerns. By the end of January, typically 50 percent of the juvenile winter-run Chinook salmon for that year has entered the Delta and is in the vicinity of the DCC gates. Closure of the gates during this period will protect a substantial proportion of the cohort. If gates are opened (up to two times for 5 days each) for water quality concerns, then a substantial proportion of the juvenile winter-run Chinook salmon cohort may be at risk of entrainment into the DCC waterway for the less than 1 in 10 years the gates are expected to be open between December 1 and January 31. As described above, these fish would enter the migratory routes through the Delta interior and be subject to a much lower rate of survival due to multiple factors previously explained. In addition, reduced flows downstream of the open DCC in the main stem Sacramento River would be expected to reduce survival due to increased transit times and the potential to be entrained into Georgiana Slough. Water quality concerns typically arise during dry years, when salinity criteria are in danger of being exceeded at key locations in the Delta (Table 2.5.5-1 0). During dry years, juvenile winterrun Chinook salmon downstream migration is usually delayed until January or February, when winter storms first arrive. The delay in juvenile winter-run Chinook salmon entering the Delta region adjacent to the location of the DCC gates may ameliorate the increased potential risk due to the need to open the gates for water quality concerns during the December through January period when drought conditions ar,e observed. After February 1, the gates are closed until May, when all of the juvenile winter-run Chinook salmon have characteristically exited the Delta. Closure ofthe DCC gates from February 1 to May 20 protects the last 50 percent of the population that is entering the Delta from entrainment into the interior Delta via the DCC route. Adult winter-run Chinook salmon start entering the Delta in November and continue through June with a peak presence from February to April. Based on the proposed gate operations for the DCC, adult fish will typically encounter open gates in November when the first fish start to arrive. Upstream passage into the main stem Sacramento River should not be impeded, even though fish have strayed into the Mokelumne River system. After December and through the end of January, the DCC gates will typically be closed, and adult winter-run Chinook salmon are unlikely to be attracted into the Mokelumne River system due to the false attraction of Sacramento River water coming through the system in substantial amounts. This will change, however, if the gates need to be opened for water quality purposes. Under this scenario, when the 355 Biological Opinion for the Long-Term Operation of the CVP and SWP gates are open, there is a risk of adult winter-run Chinook salmon being attracted into the Mokelumne River system by the additional flow of Sacramento River water through the gates, though this effect is expected in less than 1 in 10 years. When the gates are closed after 5 days, these fish then run the risk of being caught behind the closed gates and their upstream migration delayed until they drop back downstream and find an alternative route into the Sacramento River watershed. Since adult Chinook salmon have been observed to make several movements upstream and downstream in the Delta waterways before finally moving upstream towards their spawning grounds, the temporary delay should not cause any permanent physiological impairment. 2.5.5.3.6 Risk to CV spring-run Chinook salmon Natural yearling CV spring-run Chinook salmon are expected to enter the Delta in late fall and early winter (late October through January). Natural juvenile CV spring-run Chinook salmon are expected to be present in the northern Delta region from December through May with a peak presence in April. By the end of January, about 5 percent of a given juvenile CV spring-run Chinook salmon cohort has entered the Delta region near the DCC gates (Table 2.5.5-12), with the first demonstrable arrival of juveniles occurring in mid- to late-December. Based on the proposed operations of the DCC gates, up to 5 percent of the juvenile cohort will be exposed to the potential opening of the gates (December through January) in less than 1 in 10 years, which in those years will create an elevat,e d risk of entraining fish into the Delta interior, where survival is reduced compared to remaining in the Sacramento River migratory route. After February 1, when il:he gates are closed through May 20, approximately 95 percent of the juvenile CV springrun Chinook salmon cohort will enter the Delta and move through the Sacramento River adjacent to the DCC gates. The effects of operations of the DCC gates for water quality concerns should be similar to that already described for juvenile winter-run Chinook salmon and occur only in drier conditions when exceedances of salinity thresholds at key Delta locations are forecasted to occur. Thus, the overall risk of entraining juvenile CV spring-run Chinook salmon into the percent of the cohort). interior Delta through the DCC gates is low Adult CV spring-run Chinook salmon enter the Delta starting in starting in January and continue migrating past the DCC gate location through June with a peak presence from February to April. Therefore almost all of the adult migratory period will occur when the gates are closed. There is a small probability that some adults will enter the Delta when the gates are open for water quality purposes in January, and be attracted to migrate up through the Mokelumne River system to the open DCC gates, but these impacts are expected in less than 1 in 10 years. This should not impede migration. As previously explained for adult winter-run Chinook salmon, any adults in the DCC when the gates close following a water quality operation are expected to drop back downstream and re-enter the Sacramento River through a different route. There is no expectation that this minor delay will cause any adverse physiological impacts to adult CV spring-run Chinook salmon. 2.5.5.3.7 Risk to CCV Steelhead Wild juvenile CCV steelhead are expected to be present in the Sacramento River near the DCC gates year-round, as observations of fish captured in the Sacramento River trawl have occurred in most months. However, few fish are actually observed from May through the following fall. Starting in mid-January, observations of juvenile CCV steelhead begin to increase in the 356 Biological Opinion for the Long-Term Operation of the CVP and SWP Sacramento River trawl at Sherwood Harbor. By the end of January and into early February, approximately 25 percent of the current year's juvenile CCV steelhead passage through this region has occurred. Therefore, this fraction of the annual juvenile CCV steelhead population is at risk for being entrained into the interior Delta through open DCC gates following any water quality associated actions (expected to occur in less than 1 in 10 years), although the actual fraction present at the time the gates are physically open is expected to be quite less. Exposure of the juvenile CCV steelhead is expected to result in entrainment into the Delta interior through the open gates, and reductions in survival similar to that already described for Chinook salmon is anticipated. Adult CCV steelhead migrating into the Sacramento River basin will be present in the Sacramento River adjacent to the DCC gate location during their upstream spawning migration primarily from July through November, peaking in September and October. There is a much smaller peak in February, potentially consisting ofkelts returning downstream after spawning from the Sacramento River basin. Therefore, most of the adult CCV steelhead population migrating upstream will encounter the DCC gates in an open position from July through November. Adult CCV steelhead from the Sacramento River basin populations will be able to pass upstream either from the main stem Sacramento River migratory route, or from the Mokelumne River system through the open DCC gates ifthey had strayed into the San Joaquin River system. Kelts returning downstream in late winter/early spring will pass by the DCC gates while they are closed and remain in the main stem of the Sacramento River. Remaining in the main stem channel will allow fish to have shorter transit times to the lower tidal Delta and follow a more direct route to the estuary. 2.5.5.3.8 Risk to sDPS Green Sturgeon Little information exists regarding the behavior of juvenile sDPS green sturgeon and their risk of entrainment through the DCC gates when open. Acoustically tagged juvenile sDPS green sturgeon have been detected entering the DCC when the gates are open during their downstream movements. Furthermore, the changes in survival for juvenile sDPS green sturgeon using different routes through the Delta is unknown. The fact that juvenile sDPS green sturgeon may spend an extended period oftime rearing in the waterways of the Delta (months to 2-3 years) complicates assigning a survival rate to any given potential migratory route. Adult sDPS green sturgeon may be impacted by the potential for delay behind the closed gates during their upstream migration. Acoustic tagging efforts to date indicate that tagged fish typically move upriver through the main stem of the Sacramento River in the Delta and not within the interior delta waters adjacent to the downstream channel of the DCC. However, observations of adult sDPS green sturgeon in areas such as theYolo Bypass following inundation indicate that adults may follow alternate routes if flows and olfactory cues from the upper Sacramento River are present. If the DCC gates are open, some adult migrants may inadvertently enter the downstream sections of the Mokelumne River system and continue upstream in this system to the location ofthe DCC gates, following the scent of the Sacramento River inflow. If the gates are then subsequently closed before they reach the location of the DCC gates, they would be subject to migrational delays during their spawning runs below the closed DCC gates. In this situation, adult sDPS green sturgeon could drop back downstream and find an alternative route back to the mainstem of the Sacramento River to continue their spawning migration upriver. 357 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.3.9 Delta Cross-Channel Gate Improvements The DCC radial gates are older structures which require operators to be physically onsite to manually operate the gates in order to open or close them. Increased use could result in the radial gates breaking in either the open or closed positions. Improvements to the DCC would allow greater operational flexibility, faster, automated operations, and increased gate reliability. Without these improvements, the risk of gate failure increases which could lead to higher rates of entrainment of winter-run Chinook salmon, CV spring-run Chinook salmon, or CCV steelhead should the gate fail in an open or partially open position. Further, improved DCC operational flexibility along with improved biological and physical monitoring would likely minimize salmonid routing into the interior Delta with its associated greater level of mortality. Reclamation proposes to make renovations to the DCC gate structure and operating mechanisms during the summer seasonal work window when few winter-run Chinook salmon, CV spring-run Chinook salmon, or CCV steelhead are expected to be exposed to construction improvements. Future operations of the gates may include diurnal openings with nocturnal closures to take advantage of salmonid migratory behavior. However not enough information has be,en presented in the PA (February 5, 2019; Appendix A 1) description to conduct an effects analysis for this form of future operations ofthe DCC gates. This PA component will be considered as a programmatic consultation. 2.5.5.4 North Bay Aqueduct Operations 2.5.5.4.1 Physical Description of the Barker Slough North Bay Aqueduct Infrastructure The North Bay Aqueduct (NBA) is part of the SWP. The Barker Slough Pumping Plant (BSPP) diverts water from Barker Slough into the NBA for delivery to the Solano County Water Agency (SCWA) and the Napa County Flood Control and Water Conservation District (Napa County FC&WCD) (NBA entitlement holders). The NBA is an underground pipeline that runs from Barker Slough in the northern Delta to Cordelia Forebay, just outside of Vallejo. From Cordelia Forebay, water is pumped to Napa County, Vallejo, and Benicia. The NBA also serves Travis Air Force Base. The size of the pipeline varies from a diameter of72 inches at Barker Slough, to 54 inches at Cordelia Forebay. Maximum pumping design capacity is 175 cubic feet per second (cfs) (pipeline capacity). During the past few years, daily pumping rates have ranged between 0 and 140 cfs. The current maximum pumping rate, as determined through testing of the existing pumps, is 142 cfs. Tlhe difference between the design maximum and the tested maximum is due to the physical limitations of the existing pumps. Growth ofbiofilm in a portion of the pipeline also limits the NBA ability to reach its full pumping capacity. The NBA intake is located approximately 10 miles from the main stem Sacramento River at the end of Barker Slough. Each of the 10 NBA pump bays is individually screened with a positive barrier fish screen consisting of a series of flat, stainless steel, wedge-wire panels with a slot width of 3/32 inch that meets CDFW and NMFS fish screening criteria. This configuration is designed to exclude fish approximately 1 inch or larger from being entrained. The inlet bays tied to the two smaller pumping units have an approach velocity of about 0.2 feet per second (ft/s). The larger units were designed for a 0.5 ft/s approach velocity, but actual approach velocity is about 0.44 ft/s. The screens are routinely cleaned to prevent excessive head loss, thereby minimizing increased localized approach velocities ("hotspots" on the screen). 358 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.4.2 Deconstruct the Action Water Diversion - DWR proposes to operate the NBA intake in the North Delta through the operation of the BSPP to deliver water to the NBA entitlement holders as has been previously done. Current pumping capacity is limited to 140 cfs due to the functional capacity ofthe existing pipeline at the facility and the capacity of the existing pumps. The proposed operations of the BSPP also includes a maximum 7-day average diversion rate that would not exceed 50 cfs from January 15 through March 31 of dry and critically dry years (per the current forecast based on D-1641) if larval Delta Smelt are detected at Station 716 during the annual Smelt Larval Survey. Pumping is typically lower in the winter and early spring (December through April) than in the summer and fall (May through November) (Table 2.5.5-14 and Table 2.5.5-15) and DWR believes there will be no change in the pattern of pumping from what has occurred in the past. An additional pump is required to reach the pipeline design capacity of 175 cfs. The BSPP facility is equipped with a positive barrier fish screen designed and constructed to meet CDFW and NMFS fish screening criteria and DWR intends to maintain its function and compliance with the CDFW and NMFS fish screen criteria under the PA component. The BSPP facility entrains water from Barker Slough and surrounding waterbodies, including Campbell Lake, Calhoun Cut, and Lindsey Slough. It is approximately 10 miles upstream of the confluence of Lindsey Slough with Cache Slough. Due to the entrainment of water from the surrounding sloughs, the intake has the potential to entrain migrating salmonids and sDPS green sturgeon that may be present in the Cache Slough complex of channels, which includes waters discharging from the Yolo Bypass and Miners Slough. NMFS makes the following assumptions regarding the operations of tlhe BSPP and NBA under the PA (February 5, 2019; Appendix Al) component: • • • Proposed operations will not change appreciably from historical operations at the facilities; Future export flows and volumes will remain consistent with historical operations; and Seasonal patterns of exports will remain consistent with historical patterns. Sediment removal - Sediment accumulates in the concrete apron sediment trap in front of the BSPP fish screens and within the pump wells behind the fish screens. DWR proposes to continue sediment removal from the sediment trap and the pump wells as needed. Aquatic weed removal - DWR proposes to remove aquatic weeds, as needed, from in front of the fish screens at BSPP. Aquatic weeds accumulate on the fish screens, blocking water flow, and causing water levels to drop behind the screens in the pump wells. The low water level inside of the pump wells causes the pumps to automatically shut off to protect the pumps from cavitation. Aquatk weed removal system consists of grappling hooks attached by chains to an aluminum frame. A boom truck, staged on the platform in front of the BSPP pumps, will lower the grappling system into the water to retrieve the accumulated aquatic vegetation. The removed aquatic weeds will be transported to two aggregate base spoil sites located near the pumping plant. 359 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.4.3 Assess Species Exposure to Proposed Barker Slough Pumping Plant/ North Bay Aqueduct Operations Listed salmonids may be present in the waterways adjacent to the BSPP, however several years of monitoring have not consistently captured any salmonids during the winter Delta smelt surveys (1996 to 2004) in Lindsey Slough or Barker Slough. Captures of juvenile Chinook salmon have occurred in the months ofFebruary and March and typically are only a single fish per net haul (CDFG Catch summary: http://www.dfg.ca.gov/delta/datalnba/catchsummary.asp?type=species). Most juvenile Chinook salmon captured have come from Miners Slough, which is a direct distributary from the Sacramento River via Steamboat and Sutter sloughs. However, one fish was captured at site 721 in Barker Slough near the location of the BSPP (Figure 2.5.5-27 and Table 2.5.5-16). No steelhead or green sturgeon have been captured in the monitoring surveys from 1996 to 2004, the range of dates available on the CDFW website. Green sturgeon are assumed to occur in the waters of Cache Slough and the Sacramento ship channel as green sturgeon have been caught in these waters by sport fisherman. Adult salmonids are assumed to be at low risk of impingement on the fish screens, and due to the lack of inflow to the channel are unlikely to be attracted! upstream to the vicinity of the BSPP location during their spawning migrations. Adult green sturgeon may use the waters of the Cache Slough complex opportunistically while holding in the Delta, but like adult salmonids, are unlikely to be affected by the screens. A summary of the effects of the proposed North Bay Aqueduct Operations is provided in Table 2.5.5-62 in Section 2.5.5.13 Summary Tables of Stressors for each Project Component. 2.5.5.4.4 Assess Response of Species to the Proposed NBA Operations During the winter period, exports from the BSPP are expected to remain low, ranging from a monthly average of 10.9 cfs in March to 29.5 cfs in January based on historical patterns for the past 10 years (2008 to 2018). From May to November, the average diversion flow ranges from a monthly average of 66.4 cfs in November to 91.4 cfs in August for the same 10-year period (Table 2.5.5-15). Monitoring by CDFW for the NBA larval fish survey indicates that some Chinook salmon have been observed at the most western monitoring location (site 721) in Barker Slough, but in general, observations of Chinook salmon are rare, and occur farther to the east near the confluence of Miners Slough with the Cache S]ough complex. The low diversion rate during the period from December to April is unlikely to entrain fish from the lower reaches of the Cache Slough complex to locations adjacent to the BSPP Barker Slough. Even in May, the 71 cfs, with a range of 33 to 108 cfs. Even at the current average monthly diversion rate is maximum diversion rate of 140 cfs, the size of the channels in the Cache Slough complex would mute any flow towards the BSPP from the lower reaches of the Cache Slough complex. The fish screens, which were designed to protect juvenile Delta smelt and meet the NMFS criteria for salmonids, should prevent entrainment and greatly minimize any impingement of fish against the screen itself. Furthermore, the location of the pumping plant on Barker Slough is substantially removed from the expected migrational corridors utilized by emigrating Chinook salmon and steelhead juveniles in the North Delta system. Green sturgeon may be present in the waters of Lindsey and Barker sloughs since they are present in Cache Slough and the 360 Biological Opinion for the Long-Term Operation of the CVP and SWP Sacramento Deepwater Ship Channel. Green sturgeon are expected to be fully screened by the positive barrier fish screen in place at the pumping facility. Cleaning of the sediment that has accumulated in front of the fish screens may increase the risk of fish entrainment, depending on the method used. DWR did not describe the methodology to be used, but NMFS can make reasonable assumptions regarding this procedure. Using water jets to resuspend the sediments in front of the fish screens and then drawing this water through the screens will avoid any adverse impacts related to entrainment. In contrast, if a suction vacuum or hydraulic dredge is used to remove the sediment in front of the screens, then fish may be entrained into the suction hose or dredge head and deposited along with the sediment in the dredge spoils waste area. Removal of sediment behind the fish screens will not impact fish as the water is already screened and no listed fish should be present within the pump wells. If cleaning takes place at a time when listed salmonids or green sturgeon are unlikely to be pres,ent (i.e., summer with high ambient water temperatures), then the risk of exposure is greatly reduced or nonexistent. Cleaning of the fish screen by removal of aquatic weeds and vegetation may harm fish if the grappling hooks or frame directly strike the fish, or if fish become entangled in the vegetation as it is being removed and is subsequently deposited in the waste pits to die. As previol!.lsly stated, if vegetation removal occurs at times when listed salmonids or sDPS green sturgeon are unlikely to be present, then the risk of negative effects is greatly reduced due to avoiding any temporal overlap between the listed species and the weed removal action. This is the likely scenario, since aquatic weeds grow fastest during the warmer seasons, and elevated exports at the BSPP would draw the weeds into the fish screens during the summer and fall seasons when water diversions are greatest. At this time of year, it is unlikely that listed salmonids or green sturgeon would be present in these shallow waterways. 2.5.5.4.5 Risk to Listed Salmonids The presence of listed salmonids (winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead) in the waters of Barker Slough appears unlikely based on the monitoring data available. If the fish are unlikely to be present in the vicinity of the NBA export pumps based on the one observation at site 721, then there is minimal likelihood of an increase in the encounter rates with the screens due to the diversion of water. Therefore, a minimal adverse effect from the NBA intake on juv,enile winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead from the Sacramento River basin is expected. Furthermore, the fish screens are designed to avoid any entrainment or impingement of salmonids. Therefore, it is unlikely that any fish will be negatively impacted by being present near the screens during water diversions. In regards to sediment removal and aquatic weed removal, the likelihood of listed salmonids being present near the BSPP fish screens when these actions are being carried out is very low, particularly if these actions occur during the summer season when water temperatures are elevated. It is not expected that the PA components by DWR to operate the NBA will alter the current risks to listed salmonids. 2.5.5.4.6 Risk to Listed sDPS Green Sturgeon For the same reasons described for listed salmonids, the risk of negative effects to sDPS green sturgeon is very remote. The fish screen is designed to protect Delta Smelt and salmonids and 361 Biological Opinion for the Long-Term Operation of the CVP and SWP will provide the same protection to juvenile sDPS green sturgeon. sDPS green sturgeon are unlikely to be affected by the cleaning of sediment or aquatic weeds. It is unlikely that they will be present at the fish screen location at any time and particularly during the summer when water temperatures are elevated, and therefore they are unlikely to be present when these cleaning operations are being implemented. 2.5.5.5 Contra Costa Water District- Rock Slough Operations 2.5.5.5.1 Description of the Contra Costa Water District/ Rock Slough Intake Infrastructure and Operations The Contra Costa Water District (CCWD) diverts water from the Delta for irrigation and municipal and industrial (M&I) us,es under its CVP contract, under its own water right permits and license issued by the SWRCB, and under CCWD's pre-1914 water right. The CCWD water system includes the Mallard Slough, Rock Slough, Old River, and Middle River (on Victoria Canal) intakes; the Rock Slough Fish Screen [constructed in 2011 under the authority of CVPIA 3406(b)(5)]; the Contra Costa Canal and shortcut pipeline; and the Los Vaqueros Reservoir. The Rock Slough Intake, Contra Costa Canal, and shortcut pipeline are owned by Reclamation, and operated and maintained by CCWD under contract with Reclamation. Mallard Slough Intake, Old River Intake, Middle River Intake, and Los Vaqueros Reservoir are owned and operated by CCWD. The Rock Slough Intake is located about four miles southeast of Oakley. Water is pumped west from Rock Slough through a positive barrier fish screen into the Contra Costa Canal using Pumping Plants #1 through #4. The fish screen at this intake was designed in accordance with the CVPIA and the 1993 USFWS Opinion for the Los Vaqueros Project to reduce take offish through entrainment at the Rock Slough Intake and became operational in 2012. The 1.75-mmopening, 0.2 ft/s-approach-velocity fish screen installed at the Rock Slough intake is intended to prevent entrainment of listed fish, including juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead, into the Contra Costa Canal. The Contra Costa Canal is 48 miles long. CCWD's Contra Costa Canal Replacement Project replaces the 4-mile long, earthlined portion of the Contra Costa Canal between the Rock Slough Fish Screen and Pumping Plant # 1 with a buried 10' -diameter concrete pipe. The remaining 44 miles of the Contra Costa Canal after Pumping Plant #1 are concrete-lined. The earth-lined portion of the Contra Costa Canal is subject to water quality degradation due to seepage into the canal from saline groundwater in the area, as well as seepage losses where the groundwater table is lower than canal water levels. Replacing the open channel with a buried pipe also eliminates evaporative losses. Removal ofthe open water facility also improves public safety, system security, and flood control, which are needed in light of the developing and planned urbanization in the vicinity. As of late 201 8, approximately 3 miles of the earth-lined portion of the Canal has been replaced (from Pumping Plant # 1 to the east) and the flood isolation structure near the fish screen has also been completed. Pumping Plant #1 has a permitted capacity to pump up to 350 cfs into the Canal. Diversions at Rock Slough Intake are typically taken under CVP contract or under CCWD's pre-1914 water right. CCWD diverts approximately 30 percent to 50 percent of its total annual supply through the Rock Slough Intake, depending upon water quality in a given year. 362 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.5.2 Deconstruct the Action Reclamation is consulting on the ongoing operations of the Rock Sloll!gh Intake that diverts water from Rock Slough, through the Contra Costa Canal to the pumping plants near Oakley. CCWD diverts approximately 127 T AF per year in total through Rock Slough (30-50 percent of its total annual supply). Approximately 110 T AF is CVP contract supply. In winter and spring months when the Delta is relatively fresh (generally January through July), deliveries to the CCWD service area are made by direct diversion from the Delta. Reclamation is not consulting on the biological opinions that govern CCWD's intakes and Los Vaqueros Reservoir, nor will this consultation amend or supersede those separate biological opinions. For the PA (February 5, 2019; Appendix AI) component in this consultation, CCWD's operations are consistent with the current implementation of the operational criteria specified in those separate biological opinions. Reclamation is requesting incidental take coverage for all water diverted at the Rock Slough Intake up to the maximum capacity ofthe intake (350 cfs) for the maximum annual diversion of 195 TAF. Diversions from 2008-2018 have been less than this (Figure 2.5.5-28). 2.5.5.5.3 Assess Species Exposure to Proposed CCWD Rock Slough Operations Juvenile winter-run Chinook salmon are present from approximately December through June based on salvage records from the CVP/SWP fish salvage facilities (Table 2.5.5-17). The peak occurrence ofjuvenile winter-run Chinook salmon in the south Delta is from January through March. Juvenile CV spring-run Chinook salmon are present in the South Delta in the vicinity of the CCWD diversions from January through June with peak occurrence from March through May (Table 2.5.5-18). CCV steelhead may also be present in the waters of the South Delta from October through July, but have peak occurrence from late February through early April (Table 2.5.5-19). Juvenile and adult sDPS green sturgeon are assumed to be present year-round in the Delta. A summary of the effects of the proposed CCWD Rock Slough operations is provided in Table 2.5.5-63 in Section 2.5.5.13 Summary Tables ofStressors for each Project Component. 2.5.5.5.4 Assess Response of Species to the Proposed CCWD/ Rock Slough Operations The positive barrier fish screen was completed and became operational in 2011. The screen is designed to meet both the NMFS and CDFW criteria for preventing salmonids from entrainment and impingement. The operation and maintenance of the fish screen is the subject of its own biological opinion with NMFS and has its own incidental take (National Marine Fisheries Service 2017e). The screen is located approximately 3.6 miles west of the junction of Old River with Rock Slough, and approximately 2.8 miles from the junction of Werner Cut with Rock Slough. Listed salmonids can access the fish screen at the terminal portion of the Rock Slough channel from either the route leading from the junction with Old River, which is the most direct route, or by the more circuitous route through Werner Cut which connects with Indian Slough to the south (4.4 miles) and then eastwards to Old River just north of the Highway 4 Bridge (2.4 miles; total 363 Biological Opinion for the Long-Term Operation of the CVP and SWP distance 6.8 miles). Listed salmonids are known to occur in the Old River channel, and may come from both the northern direction (lower main stem San Joaquin lliver) or from the south via Middle and Old rivers. Fish that come from the north may originate in the Sacramento lliver basin, the Mokelumne River basin, the Cosumnes River basin or the San Joaquin River basin, based on observations of listed fish at the CVP/SWP fish salvage facilities. Fish that come from the south would generally originate from the San Joaquin River basin via the Head of Old River, but would have to escape entrainment at the CVP Tracy Fish Collection Facility or SWP's Clifton Court Forebay (CCF) to travel northwards towards Rock Slough. Fish migrating within the Old River channel would experience tidal forcing into and out of these channels twice daily. Once fish are pushed into the Rock Slough channel, and have moved past the junction between Rock Slough and Werner Cut, they would begin to experience the effects of water diversion by CCWD through their Rock Slough facilities. The Rock Slough channel is approximately 600 feet wide at its junction w ith Old River, then becomes narrower as it approaches the location of the fish screen. The final channel width is approximately 230 feet for the final approach to the fish screen, with a depth of about 10 feet, and is a dead end channel, terminating at the screen. CCWD diverts water throughout the year, but not at consistent rates. Export rates are frequently much less than the permitted maximum (Figure 2.5.5-16). lfthe CCWD exports at its maximum permitted rate (350 cfs), the estimated average flow velocity in the terminal portion of the Rock Slough channel would be 0.15 feet per second (fps), based on a cross section of2,300 square feet (230-foot width x 10-foot depth) and the equation Q (flow volume) = Area (channel cross sectional area) x velocity (average flow velocity). The magnitude of tidal flow would be likely be much greater in this channel compared to the velocity generated at the maximum export rate. The sustained swimming: speed of a juvenile salmonid should be more than adequate to escape the 0.2 fps approach velocity of the screen and the ambient velocity in the channel created by the water diversion. While listed fish are most likely able to volitionally escape the effects ofthe fish screen and avoid impingement, the diversion of water and the small increase in net velocity towards the intake canal may delay or inhibit their normal movements and migratory behavior. This would increase their transit time through this region of the south Delta. As previously described in the section regarding the effects of the DCC, and increases in transit times during migration, any increase in transit time has the potential to increase the risk of mortality. This increase is most 1ikely related to an increase in the duration of exposure or the number of predators encountered by a migrating fish. For fish that increase their time remaining within the Rock Slough channel, the risk of exposure to predator increases. Rock Slough has habitat that is favorable to non-native predators such as striped bass in the open channel waters, and black bass along the channel shoreHnes. NMFS anticipates that any listed salmonids present in the Rock Slough channel would be more vulnerable to predation the longer it remained in those waters. 2.5.5.5.5 Risk to Listed Salmonids The CCWD has conducted fish monitoring in the Rock Slough channel headworks and within the Contra Costa Canal at Pumping Plant # 1 for several decades. Prior to the installation of the positive barrier fish screen (operational in 2011 ), monitoring efforts collected low numbers of Chinook salmon and steelhead at both the headworks location (adjacent to current fish screen location) and at Pumping Plant #1 downstream in the Contra Costa Canal (Table 2.5.5-20). Since the installation of the positive barrier fish screen in 201 1, no salmonids have been 364 Biological Opinion for the Long-Term Operation of the CVP and SWP observed in fish monitoring behind the screens for the period of2011 to 2018. The monitoring data from before the installation of the fish screen (1999- 201 1) would indicate that it is possible for salmonids to be present at the location of the fish screen on Rock Slough, but that they would present in low numbers. The potential for salmonids to occur in front of the fish screens during water diversions is anticipated to remain the same under current conditions. The more recent data for sampling behind the fish screen (2011-2018) indicate that the screens are functioning as designed, and listed! salmonids are unlikely to pass through the screens during water diversions. This indicates that there is a negligible risk to listed salmonids of entrainment through the fish screens during water diversions. It is possible that some impingement may occur due to localized "hot spots" on the screen face developing when aquatic weeds clog the screen face, creating localized high approach velocity regions. The cleaning operations for the fish screen are designed to reduce or eliminate the potential for the creation of"hot spots' along the face of the fish screen. For any listed salmonid present within the vicinity of the fish screens or within the Rock Slough channel leading up to the fish screens, the risk of predation is elevated the longer they remain in this location. 2.5.5.5.6 Risk to Listed sDPS Green Sturgeon The fish monitoring data for both the prescreen period ( 1999-2011) and post screen installation period (2011-2018) report that no sDPS green sturgeon have ever been observed in sampling. This would indicate the risk for exposure and potential for entrainment and impingement to the water diversion operations is negligible. It is unlikely that juvenile sDPS green sturgeon would have tlhe same predation risk as listed salmonids, and would see negligible increases in the rate of mortality due to remaining in this waterway for extended periods oftime. 2.5.5.6 Water Transfers 2.5.5.6.1 Deconstruct the Action Reclamation and DWR propose to transfer project and non-project water supplies through CVP and SWP south Delta export facilities. The effects of developing supplies for water transfers in any individual year or a multi-year transfer is evaluated outside of this proposed action. Water transfers would occur from July through November in volumes up to those described in Table 412 ofthe ROC on LTO BA [page 4-48; U.S. Bureau ofReclamation (2019)]. These volumes are the same as those proposed in 2008 by Reclamation for the NMFS 2009 BiOp consultation. The current transfer window extends from July 1 to September 30 of each year. Reclamation and DWR believe that extending the length of the transfer window will enhance the reliability of the water supply by providing greater flexibility to move water through the system when capacity is available at the export facilities. This may provide additional benefits in upstream actions such as improving Sacramento River temperature operations or providing for pulse flows in river reaches below dams when they would be beneficial to tailwater river reaches. Impacts from the proposed changes to the water transfer window include additional flows in Central Valley waterways and increased export levels over current operating conditions in October and November due to diverting transfer water when no additional pumping would have occurred without such transfers being made (i.e., the available capacity). Real-time operations may restrict transfers within the transfer window so that Reclamation and DWR can meet other authorized project purposes, e.g., 365 Biological Opinion for the Long-Term Operation of the CVP and SWP when pumping capacity is needed for CVP or SWP water. The proposed transfers require that NMFS make the following assumptions: • • • • Development of the water supplies for water transfers will be conducted in a manner that includes the necessary consultation process with NMFS for impacts to listed species as applicable; Any upstream impacts to listed species associated with operation ofnon-CVP/SWP facilities for transfer through the south Delta export facilities will be the subject of their own consultation process; This consultation covers the additional duration of the transfer window and the Shasta operations associated with transfers during dry conditions that are intended to support or improve Shasta temperatur·e management. Effects were analyzed assuming a quantity and timing similar to the transfer implemented in 2014. This consultation also covers north-to-north transfers along the Sacramento River. Effects were analyzed assuming a quantity and timing of Keswick releases as would occur absent the transfer. 2.5.5.6.1.1 Sacramento River winter-run Chinook salmon Neither adult nor juvenile winter-run Chinook salmon are likely to be present in the waters of the Delta during the majority of the proposed water transfer window (July 1 through November 30). There is a low potential for juvenile winter-run Chinook salmon to be present in the Delta during November if early season storms create flow conditions in the Sacramento River basin to stimulate downstream movements. Likewise, there is a low potential for adult winter-run Chinook salmon to be present in the Delta either at the very beginning of their upstream migration (November) or at the very tail end (late June) of their migration season. If transfer water originates at upstream locations such as Shasta Reservoir, then all life stages may be exposed to the release of waters from the reservoir for transfer through the river to the south Delta export facilities. This upstream exposure would be the subject of a separate consultation process (see assumptions). In the upper Sacramento River reaches below Keswick Dam, adult winter-run Chinook salmon, incubating eggs, alevins, and emergent fry are likely to be present during the transfer window July 1 through November 30. Adult winter-run Chinook salmon spawn from late-April through mid-August with peak spawning in May and June. Fry emergence occurs from mid-June through mid-October. Once fry emerge, juveniles move to slow moving, channel margin habitats to rear. From July I through September 30, only spawning adults, incubating eggs and alevins in the gravel are present in the upper Sacramento River below Keswick Dam. During the period of the water transfer extension (October 1 through November 30), some incubating winter-run Chinook salmon eggs are still in the gravel from late spawning adults, and may remain in the gravel until November until they hatch. The majority of eggs should have hatched by the beginning to middle of October and alevins are either still in the gravel or have emerged as fry to rear in the nearshore areas of the Sacramento River. During October and November, older fry are moving downstream and are observed at the Red Bluff Diversion Dam (RBDD) rotary screw traps (RSTs). 366 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.6.1.2 CV Spring-Run Chinook Salmon There is a slightly higher potential for CV spring-run Chinook salmon to be present in the Delta during the proposed water transfer window. Yearling CV spring-run Chinook salmon may be present in the Delta in October and November if upstream precipitation events in tributary watersheds stimulate downstream migration. Adult CV spring-run Chinook salmon may be present in the Delta during the tail end of their upstream migration in late June (and early July). If transfers originate from upstream reservoirs or other forms of water storage in the Sacramento River or San Joaquin River basin tributaries, there is the potential for all life stages to be exposed to the effects of water released for transfers during the July through November transfer window. CV spring-run Chinook migration into the upper Sacramento River and tributaries extends from mid-March through the end of July with a peak in late May and early June. From July 1 to September 30, adult CV spring-run Chinook salmon are present. CV spring-run Chinook salmon spawning occurs during the first half of September and thus some eggs are present in the gravel during this earlier portion ofthe water transfer window. Eggs are laid in similarly cool-water reaches of the upper Sacramento as winter-run Chinook salmon. CV spring-run Chinook salmon fry will emerge in mid- to late November, when they are first observed at RBDD. During the period of the water transfer extension (October and November) the majority of spring-run will still be found as incubating eggs in the gravel in the river reaches below Keswick, although some fish have already hatched and emerged from the gravel during the later portion of tis transfer window extension. 2.5.5.6.1.3 CCV Steelhead There is the potential for both adult and juvenile CCV steelhead life stages to be present in the Delta during the proposed water transfer window of July through November. Juvenile CCV stcclhcad may continue to out migrate through June and! into July, based on monitoring data from the Sacramento trawl. Juveniles can also start to be seen again in early fall (October and November) as they migrate downstream into the Delta. This portion of their migration timing represents a small fraction of the population as most juveniles migrate into the Delta in winter. In contrast, most of the annual adult spawning migration into the Sacramento River basin occurs from August through November and would have a large overlap with the water transfer window. Adult CCV steelhead migrating into the San Joaquin River basin would be present in the Delta starting in September and overlap with at least the last 3 months of the transfer window (September through November). Juvenile CCV steelhead rear in the upper Sacramento below Keswick Dam, and in the tailwater sections below the termjnal dams in Central Valley tributaries. These fish would be exposed to any water released for the purposes of water transfers. These upstream exposures would be the subject of their own consultation processes (see assumptions). 2.5.5.6.1.4 sDPS Green Sturgeon Both juvenile and adult sDPS green sturgeon are expected to be present in the Delta during the entire year. Therefore, they would overlap with the entire proposed period of water transfers (July through November). Likewise, adult and juvenile sDPS green sturgeon would be present in the upper Sacramento and potentially the lower Feather River during the July through November period. 367 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.6.2 Assess Response of Species to the Proposed Water Transfer Window For those fish present in the Delta during the water transfer window extension, there will be an increase in altered hydrodynamics in waters adjacent to the export facjlities as a result of any additional exports to implement a water transfer. The risk of entrainment into the export facilities, coupled with alterations in routing probabilities within the waterways of the central and southern Delta will become more pronounced. The additional level of exports required to divert water for transfer are over and above that which would be normally present without the extended transfer window, as the transfer of water can only occur when there is available export capacity that is not needed for authorized SWP or CVP purposes at the facilities. Additional risk of entrainment into the fish salvage facilities will increase the risk of mortality to exposed fish. Likewise, alterations in routing paths may increase the travel time or transit distance that a fish must travel to complete its migration behavior. Increases in either of these factors can lead to decreased survival rates through exposure to more predators for a greater distance or for more time (see DCC Operations Section 2.5.5.3.4 and references therein). These risks are more pronounced for juvenile fish than they are for adult fish. In contrast to the negative effects of increased export levels upon fish in the vicinity of the CVP and SWP export facilities in the south Delta, changes in flows in the Sacramento and San Joaquin rivers will be generally beneficial to listed fish present during the water transfers. Water released for transfers will augment flows coming into the Delta, providing a shorter transit time in riverine sections of the river channels due to higher flows and velocities. This will decrease the exposure to predators by decreasing the time exposed to the ambient predator field. In addition, higher flows may increase the probability of staying in the "better route" for migration rather than diverting into channels that lead into the Delta interior with their associated lower survival rates. This can be accomplished by offsetting tidal influence in the transition areas between riverine and tidal habitat. Furthermore, additional flows are expected to enhance water quality in the lower reaches of the Sacramento and San Joaquin rivers prior to entering the Delta. Finally, increased flows due to water being released for transfers can provide better migratory cues for adult fish returning on their spawning migrations. These higher flows from tributary watersheds may reduce straying by providing stronger olfactory cues for returning salmonids to fmd their natal rivers. In upper Sacramento River sections above the Delta, increased flows during the water transfer window will occur while winter-run and CV spring-run Chinook salmon eggs are still in the gravel incubating, and thus reduce the likelihood of redd dewatering. For those winter-run and CV springrun Chinook salmon that have emerged from the gravel during the water transfer window, fry and juvenile salmonids will likely move to areas of the river that are inundated by the increased flows, utilizing the increased habitat area for rearing. The flow augmentation for the water transfers from Shasta Reservoir is likely to maintain flows between 3,250 and 6,000 cfs during the fall. Thus, the water transfer releases will not exceed flow thresholds(> 12,000 cfs at Wilkins Slough) observed to trigger outmigration of winter-run Chinook salmon past Knights Landing (del Rosario et at. 2013). There is a risk to rearing and migrating fry of stranding in side channels and pools on the inundated streamside bench during ramp down of the reservoir releases. However adherence to the ramping rates required for Keswick Reservoir should minimize or avoid the risk of stranding. Adult CCV steelhead wiH be exposed to augmented flows which should improve their upstream migratory movements into the reaches below the dams, this is particularly true for the 368 Biological Opinion for the Long-Term Operation of the CVP and SWP American and StanisEaus rivers. The augmented flows should also increase the rearing area for juvenile CCV steelhead in these rivers, and will also likely improve water temperatures, provided that releases are conducted to maintain or improve water temperatures conditions in the river reaches downstream of the dams. A summary of the effects of the proposed water transfer window is provided in Table 2.5.5-64 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. 2.5.5.6.3 Risk to Listed Salmonids For winter-run Chinook salmon and CV spring-run Chinook salmon, the overall risk of additional mortality associated with entrainment at the fish salvage facilities or routing into inferior migratory routes due to the water transfer window extension is low. This is primarily due to the lack of temporal overlap with the period of water transfers for most of their life history phases in the Delta (i.e., migrating adult and juvenile life stages)(Tables 2.5.5-17, 2.5.5-18, and 2.5.5-19). For those winter-run Chinook salmon and CV spring-run Chinook salmon that are present in the Delta during the water transfer window, they are expected to see some benefit from the increased in-river flows created by the release of water for transfer. Adult CCV steelhead should experience positive effects of increased flows for attracting fish upstream on their migratory spawning runs. During the period from August through November when Sacramento River basin CCV steelhead are moving upstream into the Sacramento River basin, typical river flows are low. Increasing flows will provide stronger migratory cues and stronger olfactory signals to fish moving upriver. Juvenile CCV steelhead, if present, will have a greater risk of entrainment and re-routing into different migratory paths due to export actions. This has the potential to increase mortality within the Delta waterways. In the upper river reaches, augmented flows during the water transfer window (July- November) will reduce the risk of redd dewatering for winter-run and CV spring-run Chinook salmon by maintaining flows in the river for a longer period. Augmented flows will also improve rearing habitat area size for winter-run and CV spring-run Chinook salmon fry as well as CCV steelhead juveniles, which ultimately may improve juvenile productivity. Flows are not expected to reach levels where downstream migration ofwinter-run Chinook salmon fry is stimulated after hatching. There is a risk to rearing and migrating fry of stranding in side channels and pools on the inundated streamside bench during ramp down of the reservoir releases. However adherence to the ramping rates required for Keswick Reservoir should minimize or avoid the ri sk of strandjng. 2.5.5.6.4 Risk to Listed sDPS Green Sturgeon As previously described in Section 2.5.5.1.4 , adult, sub-adult, and juvenile sDPS gr,een sturgeon are found within the waters of the Delta year-round. Juvenile sDPS green sturgeon have been observed in salvage at both the TFCF and the SDFPF during most months of the year (Figure 2.5.5-25 and Table 2.5.5-8) and would overlap with the proposed period of water transfers (July through November). Increased levels of exports to accommodate water transfers would elevate the risk of entraining juvenile sDPS green sturgeon present in the channels of Old and Middle rivers leading to the export facilities. It is unlikely that the levels of increased exports would increase the risk of entrainment of sub-adult or adult sDPS green sturgeon into the facilities due to the physical barrier created by the trash racks entering the primary louver bays, however, sturgeon may be temporarily detained in front of the trash racks due to the velocity of the water 369 Biological Opinion for the Long-Term Operation of the CVP and SWP flowing into the facility. At the TFCF, the trash rack is located directly adjacent to the Old River channel, and fish can escape to other parts of the river channel when necessary by swimming against the current. At the SWP, the CCF is a -2,500 acre waterbody that functions as a regulating forebay, and sturgeon are first entrained into this waterbody when the radial gates are opened to the Old River channel prior to encountering the trash racks at the SDFPF. Adult, subadult, and juvenile fish may have long resident times in this forebay after being entrained into CCF. Inflow velocities at the radial gates are typically quite strong depending on the difference in water surface elevation between Old River and the CCF, and egress from the forebay is difficult until the flow velocity diminishes as water surface elevations become similar between the two sides of the gate. Any sDPS green sturgeon within CCF would need to swim through the radial gate structure to escape CCF and reenter the Delta via Old River when inflow velocities are sufficiently low to permit their upcurrent movement, and before the gates are closed at the end of the tidal cycle. In other parts of the Delta, adult, sub-adult, and juvenile sDPS green sturgeon may benefit from the increased flow of water into the Delta from upstream releases for water transfers. Higher flows will help transport adults downstream after spawning in the upstream Sacramento River reaches. Likewise, juvenile sDPS green sturgeon migrating downstream will benefit from the enhanced flows. Water quality conditions in the lower river reaches should improve with the additional flow, incr,easing circulation in these areas and also improving water quality conditions within the Delta. In the upper river sections of the Sacramento River, the augmented flows are not anticipated to create conditions that stimulate downstream movements of adult and sub adult sDPS green sturgeon beyond the baseline flows without transfers. Migratory behavior in adult and sub adult sDPS green sturgeon is typically stimulated by fall and early winter precipitation events that substantially increas,e the river flows and decrease ambient water temperatures. It is unlikely that the rei ease of transfer water will be of sufficient volume to increase flows and reduce water temperatures to the degree necessary to stimulate migratory behavior. Furthermore, early movement of adult or sub adult sDPS green sturgeon downstream into the Delta due to augmented flows from water transfers is not anticipated to cause any negative effects to these fish. Juvenile sturgeon typically hold in upriver locations during their first year before migrating downstream into the Delta. These fish hold in upriver locations during flows of much higher magnitude than would be anticipated from the water transfer releases. Thus, there is no anticipated negative impacts from the water transfer releases during the extension period. 2.5.5.7 Suisun Marsh 2.5.5.7.1 Suisun Marsh Salinity Control Gates Operation 2.5.5.7.1.1 Physical Description of the Suisun Marsh Salinity Control Gates Operation The Suisun Marsh Salinity Control Gates (SMSCG) are located on Montezuma Slough about 2 miles downstream of the confluence of the Sacramento and San Joaquin rivers, near Collinsville, California. The SMSCG span the 465-foot width of Montezuma Slough. The facility consists of three radial gates, a boat lock structure, and a maintenance channel that is equipped with removable flashboards. When the SMSCG are in operation, the flashboards are installed at the maintenance channel and the gates are operated tidally. 370 Biological Opinion for the Long-Term Operation of the CVP and SWP To evaluate the potential effects of the SMSCG operations on adult salmonid passage, telemetry studies were conducted on adult Chinook salmon starting in 1993. In seven different years (1993, 1994, 1998, 2001,2002,2003, and 2004), migrating adult fall-run Chinook salmon were tagged and tracked by telemetry in the vicinity of the SMSCG. These studies showed that the operation of the SMSCG delays passage of some adult Chinook salmon, while other adult Chinook salmon never pass through the SMSCG and instead swim downstream for approximately 30 miles to Suisun Bay and then access their natal Central Valley streams via Honker Bay. Based on the results of studies, the CDFG (now CDFW) recommended modifications to the structure to improve passage (Edwards et al. 1996, Tillman et al. 1996). In 1998, modifications were made to the flashboards at the SMSCG maintenance channel to include two horizontal openings, but telemetry monitoring indicated that the modified flashboards did not improve Chinook salmon passage (Vincik et al. 2003). Telemetry studies conducted in 2001, 2002, 2003, and 2004, evaluated the use of the existing boat lock as a fish passageway. These results indicated that fish passage improved when the boat lock was opened. Successful passage rates improved by 9, 16, and 20 percent in 2001 , 2003, and 2004, respectively, when compared to full SMSCG operation with the boat lock closed. In addition, opening of the boat lock reduced mean passage time by 19 hours, 3 hours, and 33 hours in 2001, 2003, and 2004, respectively. The 2002 results did not confirm these fmdings, but equipment problems at the structure during the 2002 season likely confounded the 2002 fish passage studies (Vincik et al. 2003). The purpose of gate operation is to decrease the salinity of the water in Montezuma Slough to meet salinity standards set by the SWRCB and Suisun Marsh Preservation Agreement. The SMSCG control salinity by lowering gates during flood tides to prevent flow of higher salinity water from Grizzly Bay into Montezuma Slough and opening gates during ebb tides to retain the lower salinity Sacramento River water that entered the marsh during the previous ebb (outgoing) tide. Currently, SMSCG operation occurs from October to May (- 10-20 days) where radial gates are lowered during the flood tides and opened during the ebb tides, flashboards are in place through September, and a boat lock is operated as-needed for passing vessels. The boat lock portion of the gate is held open at all times during SMSCG operation to allow for continuous Chinook salmon passage opportunity. However, the boat lock gates may be closed temporarily to stabilize flows to facilitate safe passage of watercraft through the facility. Outside of the period, the radial gates remain open, flashboards are removed, and operation of the boat lock is not needed. As of 2018, gates are operated during August in "below normal" or "above normal" water years in addition to October to May operation. 2.5.5.7.1.2 Deconstruct the Action- Proposed Suisun Marsh Salinity Control Gates Operation In addition to the October through May operation to meet Suisun Marsh water quality standards, Reclamation proposes operating the SMSCG on the tidal cycle in below-normal and abovenormal years in June through September for 60 days, not necessarily consecutive, to improve Delta Smelt critical habitat. Under the PA (February 5, 2019; Appendix AI) component, Reclamation and DWR would increase tidal operations of the SMSCG to direct more fresh water in Suisun Marsh to reduce salinity, increase food, and improve habitat conditions for Delta smelt. This would be combined with Roaring River Distribution System management for food production and flushing freshwater through the Roaring River Distribution System to increase 371 Biological Opinion for the Long-Term Operation of the CVP and SWP the low salinity habitat in Grizzly and Honker bays. Reclamation and DWR will continue to meet existing D-1641 salinity requirements in the Delta and Suisun Marsh. 2.5.5.7.1.3 Assess Species Exposure to Proposed Suisun Marsh Salinity Control Gates Operation The boat lock portion of SMSCG its held open at all times during SMSCG operation to allow for continuous salmonid passage opportunities. With increased understanding of the effectiveness of the gates at lowering salinity levels in Montezuma Slough, salinity standards have been met with less frequent gate operation compared to the early years of operations. The PA component would continue SMSCG operation for up to 20 days in October to May, plus an additional 60 days during June to September in above normal and below normal years. During the summer and early fall months, listed fish species are less likely to be present. However, adult and juvenile CCV steelhead and sDPS green sturgeon are known to be present in the Delta during some or all ofthese months. A summary of the effe.cts of the proposed SMSCG operation is provided in Table 2.5.5-65 in Section 2.5.5.14 Summary Tables of Stressors for each Project Component. 2.5.5.7.1.4 Risk to Salmonids The principal poten6al effect of the SMSCG being closed for up to 20 days per year from October through May, plus an additional60 days per year from June to September, is delay of upstream-migrating adult winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead that have entered Montezuma Slough from its westward end, and are seeking to exit the slough at its eastward end. del Rosario et al. (2013) found some evidence that opening of the boat lock improved passage rates of acoustically tagged adult Chinook salmon, and that even with the gates opened, -30-40 percent offish returned downstream. Adult salmonids that do not continue upstream past the SMSCG are expected to return downstream by backtracking through Montezuma Slough to Suisun Bay, and they likely find the alternative upstream route to their natal Central Valley streams through Suisun and Honker bays(Califomia Department of Water Resources and California Department ofFish and Game 2005). During the majority of the period from October to May, the SMSCG will not be operated and no fish passage delays due to the gates are anticipated. However, during the annual 10-20 days of periodic operation, individual adult salmonids and sDPS green sturgeon may be delayed in their spawning migration from a few hours to several days. The effect of this delay is not well understood. Winter-run Chinook salmon are typically several weeks or months away from spawning and, thus, they may be less affected by a migration delay in the estuary. CCV steelhead migrate upstream as their gonads are sexually maturing and a delay in migration may negatively impact their reproductive viability. CV spring-run Chinook salmon are typically migrating through the estuary several months before spawning, bU!t an extended delay in the estuary may affect their ability to access their natal spawning streams. CV spring-run Chinook salmon generally utilize high stream flow conditions during the spring snowmelt to assist their upstream migration. Rapid upstream movement may be needed to take advantage of a short duration high stream flow event, particular in dry years when high flow events may be uncommon. If the destination of a pre-spawning adult salmon or CCV steelhead is among the smaller tributaries of the Central Valley, it may be important for migration to be unimpeded, since access to a spawning area could diminish with receding flows. 372 Biological Opinion for the Long-Term Operation of the CVP and SWP Under the PA relative to current operations, operation of the SMSCG would increase by 60 days per year during the months of June to September in above normal and below normal years. This additional gate operation during the summer and early fall months is expected to have a minimal impact on adult and juvenile CCV steelhead that may be present during that time. However, the boat lock portion of SMSCG is held open at all times during SMSCG operation to allow for continuous salmonid passage opportunities. Therefore, the potential for negative near-field effects on downstream-migrating juvenile salmonids would be limited. Adult salmonids are at risk of delay if encountering closed SMSCG while the boat lock is closed for vessel passage, but salmonids could backtrack around the structure. The proportion of individuals that would do so is uncertain, and as described above, CV spring-run Chinook salmon and CCV steelhead would likely experience greater negative effects than winter-run Chinook salmon, because CV springrun Chinook salmon and CCV steelhead are more reliant on short-term high flow events in smaller tributaries to provide access to suitable spawning habitat. Salmonid smolt predation by striped bass and pikeminnow could be exacerbated by operation of the SMSCG. These predatory fish are known to congregate in areas where prey species can be easily ambushed. Pikeminnow are not typically major predators of juvenile salmonids (Brown and Moyle 1981 ), but both pikeminnow and striped bass are opportunistic predators that will take advantage of localized, unnatural circumstances. The SMSCG provides an enhanced opportunity for predation because fish passage is blocked or restricted when the structure is operating. However, DWR proposes to limit the operation of the SMSCG to only periods required for compliance with salinity control standards, and this operational frequency is expected to be 10-20 days per year. Therefore, the SMSCG will not provide the stable environment which favors the establishment of a local predatory fish population and the facility is not expected to support conditions for an unusually large population of striped bass and pikeminnow. In addition, most list,ed Central Valley salmonid smolts reach the Delta as yearlings or older fish. Since the size and type of prey taken by pikeminnow varies with the size and age of the fish (Brown and Moyle 1981), the relatively large body size and strong swimming ability of listed salmon and steelhead smolts, reduce the likelihood of being preyed upon. 2.5.5.7.1.5 Risk to sDPS Green Sturgeon Little is known about adult sDPS green sturgeon upstream passage at il:he SMSCG, with existing studies suggesting that Suisun and Honker bays are more utilized than Montezuma Slough where the SMSCG are located. NMFS anticipates that adult sDPS green sturgeon would have the opportunity to pass the SMSCG through the boat lock or gates (when open), as adult salmonids do, but that they could be delayed. sDPS green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River, and spring stream flows in the mainstem Sacramento River are generally not limiting their upstream migration. It is also common for sDPS green sturgeon to linger for several days in the Delta prior to initiating their active directed migration to the upper Sacramento River. Thus, any delays would not affect access to spawning habitat in the upper Sacramento River because adult sDPS green sturgeon tend to spawn in deeper water (Poytress et at. 2015) that would not be affected by temporary changes in flow. In addition, previous concerns regarding potentially delaying arrival at RBDD (where passage was previously restricted) no longer apply, because the RBDD gates are up year-round, allowing unimpeded passage. The potential for predation near the SMSCG that was previously discussed for juvenile salmonids would be of minimal concern for juvenile sDPS green sturgeon because 373 Biological Opinion for the Long-Term Operation of the CVP and SWP they are relatively large and unlikely prey for striped bass and Sacramento pikeminnow. In addition, the multi-year estuarine residence of juvenile sDPS green sturgeon often includes long periods of localized, non-directional movement interspersed with occasional long-distance movements (Kelly et al. 2007), and such movements are unlikely to be negatively affected by periodic delays ranging from a few hours to a few days at the SMSCG. 2.5.5.8 South Delta Export Operations In the analysis ofthis PA (February 5, 2019; Appendix Al) component, NMFS considers two primary categories of effects in the south Delta due to water export: ( 1) entrainment and loss at the south Delta export facilities, and (2) water-project-related changes to south Delta hydrodynamics that may reduce the suitability of the south Delta for supporting successful rearing or migration of salmonids and sturgeon from increased predation probability and exposure to poor water quality conditions. The effects from the PA components with regard to entrainment and loss at the south Delta export faci lities are described in Section 2.5.5.8.3.1 South Delta Salvage and Entrainment. The effects related to water-project-related changes to south Delta ]hydrodynamics that may reduce the suitability of the south Delta for supporting successful rearing or migration of salmonids and sturgeon, include the impacts to listed fish travel time, outrnigration, behavior changes, and juvenile survival from south Delta hydrodynamics. Water is diverted at two main facilities in the South Delta for export to regions south of the Delta and to the areas immediately adjacent to the Delta, including portions ofthe Bay area. The CVP operates the Jones Pumping Plant, the Delta Mendota Canal, and the TFCF. The SWP operates CCF, the SDFPF and the Harvey 0. Banks Pumping Plant. Key water-project-related drivers of south Delta hydrodynamics are Vernalis inflow, CVP and SWP exports from the south Delta export facilities, and the presence or absence of the Head of Old River (HOR) Barrier; these drivers interact with tidal influences over much of the central and southern Delta. [n day-to-day operations, these drivers are often correlated with one another (for example, exports tend to be higher at higher San Joaquin River in·flows) and regulatory constraints on multiple drivers may simultaneously be in effect. The modeling ofthe PA and COS conditions reflects those realities and, while those scenarios are appropriate for project analysis, they have hmited value for evaluating the isolated effects of one driver vs. another. Recently, the Salmonid Scoping Team, a technical team associated with the Collaborative Adaptive Management Team (CAMT) process, evaluated how the relative influence ofthese drivers on hydrodynamic conditions varied temporally and spatially throughout the south Delta, [(Salmonid Scoping Team 2017a): Appendix B: Effects of Water Project Operations on Delta Hydrodynamics). In order to describe the driver-specific effects on south Delta hydrodynamics which are relevant to the types of operations anticipated! in the PA, highlights of that report are provided below. While the specific combinations of drivers in the Salmonid Scoping Team (20 17a) analysis are not necessarily representative of any specific P A scenario, these scenarios cross factor individual drivers in a way that allows the evaluation of trends that are relevant to the PA. Key findings, with examples of relevance to effects of south Delta operations under the PA, include: • The major river channel distributaries in the south Delta (San Joaquin, Old, and Middle rivers) transition from a riverine environment to a tidally-dominated environment in the Delta. The effect of tides decreases with increasing distance upstream on the main stem 374 Biological Opinion for the Long-Term Operation of the CVP and SWP river channels, and the tidally dominated region varies with Delta inflow, exports, and tidal phase. • The hydrodynamic effect of increases in Delta inflow on flow and velocity in the south Delta is greatest at the upstream reaches of the major river channels; diminishes with distance downstream through the Delta or away from the main stem rivers (i.e., into the interior Delta); and is affe.cted by barriers, tidal phase, and exports. The hydrodynamic effect of exports on flow and velocity in the south Delta is strongest in Old River near the export facilities, in Middle River at Victoria Canal, and the downstream ends of Turner Cut, and Columbia Cut; and it is affected by tidal phase, Delta inflow, distance from the exports, and barriers. South Delta exports in the PA are expected to have the stronger effects in DSM2 channels 89 (Old River downstream of the south Delta export facilities) and DSM2 channe1143 (Middle River near Woodward Island) compared to locations on the main stem San Joaquin River (DSM2 channels 45 and 49), as shown in the velocity density overlap plots (Figure 2.5.5-29, Figure 2.5.5-30, and Figure 2.5.5-31). The Delta flow regime can have effects on a wide range of factors, such as productivity, food webs, or invasive species, and management actions related to CVP and SWP operations, which are just a few of many interacting drivers (Monismith et al. 2014, Delta Independent Science Board 2015) (Figure 2.5.5-32). The effects of south Delta export operations on listed winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon are described below. Export effects in the south Delta are expected to reduce the probability that juvenile salmonids in the south Delta will s.uccessfully migrate out past Chipps Island, either via entrainment or mortality in the export facilities, or via changes to migration rates or routes that increase residence time of juvenile salmonids in the south Delta and thus increase exposure time to agents of mortality such as predators, contaminants, and impaired water quality parameters (such as dissolved oxygen or water temperature). Export effects of ongoing diversions from the south Delta export facilities negatively impact hydrodynamic conditions in the south Delta, and impacts are modelled to increase in the PA compared to the COS as exports are increased, particularly in April and May, and less reductions in exports for fishery protections are anticipated under the PA. Much uncertainty remains about how reach-scale hydrodynamic effects link to salmonid migration behavior in the south Delta. More data are available on both. through-Delta survival and reach-scale survival for Chinook salmon and CCV steelhead. Salmonid Scoping Team (2017a, 2017b) summarize select data relevant to water-project-related effects on juvenile salmonid migration and survival in the south Delta [see in particular Appendices D and E of Volume 1 (Salmonid Scoping Team 2017a)]. While those reports did not evaluate specific elements of the PA, they were designed to summarize the latest information on salmonid behavior and survival in the south Delta in the context of water project operations and so offer relevant information to understanding effects of south Delta operations in the PA. Some overarching findings, summarized in the Executive Summary from Volume I (Salmonid Scoping Team 2017a), are: 375 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • • • "Spatial variability in the relative influence of Delta inflow and exports on hydrodynamic conditions means that any given set of operational conditions may differentially affect fish routing and survival in different Delta regions." "Gates and barriers influence fish routing away from specific migration corridors." "The relationship between San Joaquin River inflow and survival is variable, and depends on barrier status and region of the Delta." "Juvenile salmonid migration rates tend to be higher in the riverine reaches and lower in the tidal reaches." "The extent to which management actions such as reduced negative OMR reverse flows, ratio of San Joaquin River inflow to exports, and ratio of exports to Delta inflow affect through-Delta survival is uncertain." "Uncertainty in the relationships between south Delta hydrodynamics and through-Delta survival may be caused by the concurrent and confounding influence of correlated variables, overall low survival, and low power to detect differences." The first four fmdings highlight that effects on routing and survival differ across the Delta and are sensitive to inflow and barrier status. The final two findings relate to uncertainties and highlight the need for continued evaluation and testing of hypotheses linking project-related effects on hydrodynamics to biological responses, ideally in a formal adaptive management program. 2.5.5.8.1 Facility Descriptions 2.5.5.8.1.1 Tracy Fish Collection Facility The TFCF is located in the southwest portion of the Sacramento-San Joaquin Delta near the Cities of Tracy and Byron. It uses behavioral barriers consisting of primary and secondary louvers to guide entrained fish into holding tanks before transport by truck to release sites within the Delta. The original design of the TFCF focused on smaller fish (<200 mm) that would have difficulty fighting the strong pumping plant-induced flows, since the intake is essentially open to the Delta and also impacted by tidal action. The primary louvers are located in the primary channel just downstream of the trash rack structure. The secondary travelling screens (hydrolox screens) are located in the secondary channel just downstream of the primary bypasses. The primary louvers allow water to pass through into the main Delta-Mendota intake channel and continue towards the Bill Jones Pumping Plant located several miles downstream. However, the openings between the louver slats are tight enough and angled against the flow of water in such a way as to prevent most fish from passing between them and, instead, guide them into one of four bypass entrances positioned along the louver arrays. The efficiency of the louver guidance array is dependent on the ratio of the water velocity flowing into the bypass mouth and the average velocity in the main channel sweeping along the face of the louver panels. When south Delta hydraulic conditions allow, and within the original design criteria for the TFCF, the louvers are operated with the D-1485 objectives of achieving water approach velocities for striped bass of approximately 1 foot per second (fps) from May 15 through October 31, and for salmon of approximately 3 fps from November 1 through May 14. Channel velocity criteria are a function of bypass ratios through the facility. Louver efficiency at the TFCF is 376 Biological Opinion for the Long-Term Operation of the CVP and SWP dependent on the flow and velocities, fish species, and the fish size (life stage). The number of pumps (units) running at the Jones Pumping Plant (JPP) dictates the flow and velocity at the TFCF. There are 6 units at JPP but a maximum of 5 can used; each unit increases the velocity through the TFCF primary channel about 0.5 ftlsec. For juvenile Chinook salmon, the most recent whole facility efficiency evaluations completed using acoustic tag telemetry suggests that primary louver efficiency ranges from 50-100 percent with an average of approximately 88.7 percent (Karp et al. 2017, Wu and Fullard 2018). At higher pumping regimes of 4-5 JPP units, for juvenile Chinook salmon, louver efficiency was high at 71.4-100 percent (Karp et al. 20 17). Sutphin and Bridges (2008) has indicated that under the low pumping regimen required by the Vernalis Adaptive Management Plan (VAMP) experiment, primary louver efficiencies (termed capture efficiencies in the report since only one bypass was tested) can drop to less than 35 percent at the TFCF. The reductions in pumping create low velocities in the primary channel, and the necessary primary bypass ratios (> 1) cannot be maintained simultaneously with the secondary channel velocities (3.0 to 3.5 fps February 1 through May 31) required under D-1485. These study results indicate that loss offish can potentially increase throughout the entire louver system if the entire system behaves in a similar way as the test section performed in the experiments. Screening efficiency for juvenile green sturgeon is unknown, although apparently somewhat effective given that green sturgeon, as well as white sturgeon, have been collected during fish salvage operations. Studies by Kynard and Horgan (200 1) tested the efficiency of louvers at guiding yearling shortnose sturgeon (A cipenser brevirostrum) and pallid sturgeon (Scaphirhynchus a/bus) under laboratory conditions. They found that louvers were 96 to 100 percent efficient at guiding these sturgeon species past the experimental array and to the flume bypass. However, both sturgeon species made frequent contacts with the louver array with their bodies while transiting the louver array. The authors also found that sturgeon would rest at the junction between the louver array and the tank bottom for extended periods. This behavior may degrade the effectiveness of the louver array to guide fish towards the bypass. Current studies at the University of California at Davis are testing louver screening efficiencies for sturgeon using sections of louver panels from the south Delta facilities. "Pre-screen loss rate" is defined as "the rate ofloss to entrained salmon during movement from the trash racks to the primary louvers" (Aasen 2013). In essence, the "pre-screen loss rate" is the predation rate within the primary channel. Although Chinook salmon mortality have been observed in front ofthe TFCF trash rack (Vogel 2010), this mortality is not included in the prescreen loss calculation since this is outside of the area between the trash rack and primary louvers. Currently, a 15 percent pre-screen loss rate due to predation is an agreed upon placeholder value but has yet to be fully verified. For this placeholder, the predation rate within the primary channel is currently being verified with the use of Predation Detection Acoustic Tags (PDAT). Prescreen loss at the TFCF is dependent on fish species, fish size (life-stage), and predator load within the primary channel. In addition, it appears that prescreen loss may be inversely correlated with pumping rates (water velocity) and/or turbidity, although more data need to be collected to adequately determine these relationships. Data from Karp et al. (2017) and Wu and Fullard (20 18) suggest that prescreen loss ranges from 0- 40 percent for juvenile Chinook salmon. Low estimates of pre-screen loss (assuming all unknown fates in the primary channel are non377 Biological Opinion for the Long-Term Operation of the CVP and SWP participants) from these studies average approximately 14.0 percent, while high estimates of prescreen loss (assuming all unknown fates in the primary channel are losses to predation) average approximately 15.9 percent. Therefore, preliminary results indicate that the predation rate (or prescreen loss) may be close to the 15 percent placeholder value mentioned above (Karp et al. 2017, Wu and Fullard 20 18). Loss due to cleaning is not quantified in the current loss calculation, and therefore, tihe reported loss is chronically underestimated. Reclamation estimates that approximately 6. 7 percent of juvenile Chinook salmon that encounter the louvers are lost through the louvers when they are lifted for cleaning, and approximately 33.3 percent of louver loss occurs during louver cleaning activity (Karp et al. 2017). This value, however, is preliminary and needs further verification. There is a Tracy Fish Facility Improvement Plan (TFFIJ>) study plan being developed to study the amount of loss occurring during louver cleaning. The current primary louver cleaning procedures and operations involve lifting each individual louver panel, 36 total, out of the water in order to spray wash the debris. Generally, each primary louver panel is lifted and lowered back into place three times per day (generally at 600-0800, 1400-1600, and 2300-0100 hours), although frequency of cleaning may be increased or decreased according to pumping rate and debris loads. It takes approximately 3-7 minutes to lift, spray clean, and lower each louver panel back into place. While export pumping may be reduced to address damaged louver panels, issues during cleaning, or other maintenance scenarios where facilities are not capable of effectively salvaging fish, complete shutdown of pumping usually does not occur due to issues related to the primary louvers. At a minimum, all 36 louver panels are cleaned 2-3 times a day but during heavy debris loads, operators dean 3-6 times a day. The 2018 louver cleaning data (see below) suggests less frequent cleaning is required in early summer (low averages of 60 minutes per day) and much higher during the winter months (high averages of 440 minutes per day). This means that there is a gap in the louver panels ranging from l to 7.5 hours per day depending on season, pumping rates, and debris loads. Data from Cleaning Primary Louvers (20 18) Month Average daily (minutes) January 240 February 131 March 112 April 64 May 76 June 138 July 274 August 310 September 200 October 440 378 Biological Opinion for the Long-Term Operation of the CVP and SWP November 270 December 370 Secondary bypasses are not cleaned, although they are shut during the cleaning of the primary louvers to prevent excessive debris from entering the holding tanks. Fish salvage occurs at the TFCF 24 hours per day, 365 days per year. Fish are salvaged in flowthrough holding tanks (6.1-m diameter, 4.7-m deep) that provide continuous flows ofwater (Sutph.in and Wu 2008). Fish are maintained in these holding tanks for 8-24 hours depending on the species of fish that are being salvaged, the number of fish salvaged, and debris load. The number of fish that are salvaged in TFCF holding tanks is generally estimated by performing a 30-minute fish-count subsample every 120 minutes. The number of each species of fish collected in the subsample is determined and then multiplied by 4 (120 pumping minutes/30-minute fishcount subsample = expansion factor of 4) to estimate the total number of each species of fish, as well as the total number of fish, that were salvaged in TFCF holding tanks during the 120-minute period. Pumping minutes and fish-count minutes could potentially deviate from 120 minutes and 30 minutes, respectively, which would change the expansion factor used to estimate total fish salvage. This is typically done when the numbers offish salvaged are high or there is heavy debris loading in the holding tanks. If no Chinook salmon, steelhead, or Delta smelt are salvaged, other species offish can be maintained in TFCF holding tank for up to 24 hours. If a Chinook salmon or steelhead is collected during fish-counts, fish can only be maintained in TFCF holding tanks for up to 12 hours. If a Delta smelt is collected during fish count, sa]vaged fish may only be held in TFCF holding tanks for up to 8 hours. When fish can be maintained in TFCF holding tanks for 24 hours, fish transport (fish-haul) generally occurs at approximately 0700 each day. When 2 fish hauls per day are necessary, fish hauls generally occur at 0700 and 2130 each day. When 3 fish hauls are necessary, they are usually completed at 0700, 1500, and 2130 each day. The frequency of fish hauls is also dictated by the Bates Tables which u ses size classes, species, and water temperature as indicators for when to conduct a fish haul. During normal operations, salvaged fish are transported approximately 49.9 km and released at one of two Reclamation release sites near the confluence of the Sacramento and San Joaquin rivers (Antioch Fish Release Site and Emmaton Fish Release Site). In general, the Emmaton Fish Release Site is used for fish hauls performed during daytime hours and the Antioch Fish Release Site is used for fish hauls performed during nighttime hours. This is done for safety and security reasons as the Antioch Fish Release Site has a gate that can be locked behind the operator after he/she enters the release site area. Upon arrival at release sites, operators measure certain important water quality parameters (dissolved oxygen, salinity, and temperature) prior to releasing fish. This is done to verify that water quality parameters remain acceptable during fish transport. Salmon loss due to handling and trucking are generally low and are based on CDFW trucking and handling studies. Salmon loss is < 2 percent for salmon < 100 mm and zero percent for salmon > 100 mm (Aasen 2013). Estimates of post-release survival and mortality are currently not available, although release site survival and mortality is being investigated by Reclamation (Fullard et al. 20 18) and results are anticipated within the next couple of years. It is anticipated that loss to predation is the main source of post release mortality. 379 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.1.2 Skinner Delta Fish Protection Facility The John E. Skinner Fish Protection Facility was built in the 1960s and designed to prevent fish from being entrained into the water flowing to the Harvey 0. Banks Pumping Facility, which lifts water from the inlet canal into the California Aqueduct. The fish screening facility was designed to screen a maximum flow of 10,300 cfs. Water from the Delta is first diverted into CCF, a large artificially flooded embayment that serves as a storage reservoir for the pumps, prior to flowing through the louver screens at the SDFPF. After water enters CCF through the radial gates, it first passes a floating debris boom before reaching the trashrack. The floating debris boom directs large floating material to the conveyor belt that removes the floating material for disposal in an upland area. Water and fish flow under the floating boom and through a trashrack (vertical steel grates with 2-inch spacing) before entering the primary screening bays. There are 7 bays, each equipped with a flow control gate so that the volume of water flowing through the screens can be adjusted to meet hydrodynamic criteria for screening. Each bay is shaped in a "V" with louver panels aligned along both sides of the bay. The louvers are comprised of steel slats that are aligned 90 degrees to the flow ofwater entering the bay with linch spacing between the slats. The turbulence created by the slats and water flowing through the slats guides fish to the apex of the "V" where bypass orifices are located. Fish entrained into the bypass orifice are carried through underground pipes to a secondary screening array. The older array uses the vertical louver design while the newer array uses a perforated fl at plate design. Screened fish are then passed through another set of pipes to the holding tanks. Fish may be held in the holding tanks for up to 8 hours, depending on the density of salvaged fish and the presence of listed species. Like the TFCF, the louvers are not I 00 percent efficient at screening fish from the water flowing past them. Louver efficiency is assumed to be approximately 75 percent [74 percent, (California Department of Water Resources 2005)] for calculating the loss through the system. Louver efficiency estimates for Chinook salmon developed in the past 10 years are largely consistent with the findings of the original testing program for the SDFPF (Skinner I974)]. More recent studies have examined louver efficiencies at the SDFPF. Clark et al. (2009) found louver efficiencies for steelhead using releases of PIT-tagged hatchery steelhead released at the SDFPF trash rack. The study reported two estimates of efficiency; 74 percent (range I7 to I 00 percent) and 82 percent (range 19 to 100 percent). The latter value incorporates an estimate of emigration from the study area (e.g., "swim out") which was documented in the study. Wunderlich (2015) used fall-run Chinook salmon tagged with PIT tags which were released in front of the SDFPF in April and May of2013. Louver efficiency was reported as 74 percent (ranging 71 to 76 percent). Miranda (20I9) utilized releases of PIT and acoustic tagged fall and late-fall run Chinook salmon released at the SDFPF trash rack. Efficiency was reported as 81.7 percent (range 77.9 to 86.2 percent) and 55.0 percent (range 54.3 and 55.7 percent) for "Salmon" and "Striped Bass" Operating Criteria, respectively. "Pre-screen loss" is the estimated loss offish from the radial gates at the entrance to the CCF to the trash rack in front ofthe primary louver bays at the SDFPF. The pre-screen loss estimates for Chinook salmon developed in the past 10 years are largely consistent with the historical studies outlined in Gingras (1997), which ranged from 63-99 percent. Clark et al. (2009) calculated prescreen loss rates from paired releases of PIT and acoustic tagged fish released at the CCF radial gates and at the SDFPF trash rack. Pre-screen loss was calculated as 82±3 percent and 78±4 percent (when adjusted for emigration of tagged fish from CCF). Wunderlich (2015) utilized 380 Biological Opinion for the Long-Term Operation of the CVP and SWP releases of PIT tagged, fall-run Chinook salmon released at the radial gates and the SDFPF in April and May of2013. A pre-screen loss rate of81.14 percent was reported, ranging from 41 to 100 percent. Miranda (2016) utilized PIT tagged late-fall and fall-run Chinook salmon released at the CCF radial gates from January through May of2016. Monthly estimates of mean prescreen loss ranged from 75 to 91 percent, with a season mean estimate of91 percent. Miranda (20 19) utilized releases of PIT and acoustic tagged fall and late-fall run Chinook salmon released at the CCF radial gates and at the head ofthe SDFPF. Pre-screen loss was estimated as 77.16 percent for all races combined. Pre-screen loss was estimated as 56.07 percent (26.1 to 88.5 percent) for late-fall run Chinook salmon, and 92.1 percent (92.1 to 98.5 percent) for fall-run Chinook salmon. Losses due to cleaning the primary louvers at the SDFPF are quite low compared to the TFCF. The SDFPF was built with a modular design including multiple primary louver bays that can be isolated, two secondary channels, and two holding tank buildings. Under most circumstances, this design effectively mitigates fish losses as a result of routine maintenance and cleaning, and mechanical breakdowns. Maintenance, cleaning, and breakdowns normally result in a reduction in overall available capacity rather than exports without salvage. However, in the event of an unplanned outage (e.g., a power loss), attempts are made to immediately rectify the issue through either changes in the configuration of the facility (e.g., changing bays) or backup systems (e.g., alternate power source) and CDFW is notified. In the event of an unplanned outage lasting greater than 1 hour, CDFW is immediately consulted and/or Banks pumping plant exports may be temporarily halted. Planned outages are typically scheduled to avoid periods of unscreened water export. For example, major maintenance activities are scheduled in the spring during a I week complete shutdown ofBanks Pumping Plant coinciding with NMFS 2009 Opinion RPA Action IV.2.1 (previously VAMP). During other periods, export capacity of the facility is reduced accordingly. The duration and frequency of louver cleaning operations fluctuates significantly due to a number of factors including pumping schedule, high fish counts, flow rates, debris loads, environmental factors, and staffing. In general: • • Cleaning of individual primary louver bays is performed weekly. It takes a minimum of 2 hours to clean each bay, and bays are isolated during cleaning to prevent fish losses. Cleaning is performed by lifting individual louver panels using a gantry crane and pressure washing them from both front and back. Cleaning of the secondary channels is performed twice weekly and is also used as a predator flush. It generally takes 30-60 minutes to clean each secondary bay. During cleaning, each channel is dewatered and the louver or screen panels are pressure washed from each side using a fire hose. After the panels have been washed, the primary bypass valve(s) at the head each bay are opened rapidly to flush predators and debris into a holding tank for removal. Salvage of fish occurs at the SDFPF up to 24 hours per day, 365 days per year. Fish are salvaged in flow-through holding tanks that provide continuous flows of water. The number of fish that are salvaged in SDFPF holding tanks is generally estimated by performing a 30 minute fishcount subsample every 120 minutes. However, this may change due to the number of fish salvaged or the level of debris in the holding tank. The fraction oftime sampled is used to 381 Biological Opinion for the Long-Term Operation of the CVP and SWP calculate the salvage expansion factor, as was done at the TFCF. Fish are transported to release sites on the San Joaquin River near Antioch, and on the Sacramento River near Horseshoe Bend. The effects of Collection, Handling, Trucking, and release operations have been evaluated in a number of studies at the SDFPF, as outlined below. No attempt has been made to quantify postrelease survival due to logistical challenges and because it likely fluctuates wildly based on a number of factors including, but not limited to, the number of fish being released, season, and frequency of release. Raquel ( 1989) found that survival rates for Chinook salmon were never less than 98 percent and, in most cases, was 100 percent. The loss equation used by CDFW to calculate SWP losses utilizes the 2 percent value. This study also found no detrimental effects to steelhead from the handling and trucking process. Miranda and Padilla (201 0) found that the survival of Chinook salmon exposed to a mock salvage release process was 99.2 percent, 97.4 percent, and 98.4 percent in trials with no debris, moderate debris, and heavy debris, respectively. There was no significantly detectable effect on survival from the release process. 2.5.5.8.2 OMR Flow Management Note that supplemental analysis based on PA revisions received June 14, 2019 is provided in Section 2.5.5.1 1. Reclamation and DWR propose to operate the CVP and SWP in a manner that maximizes exports while minimizing entrainment of fish and protecting critical habitat. Net OMR flow provides a surrogate indicator for how export pumping at Banks and Jones Pumping Plants influence hydrodynamics in the south Delta. Reclamation proposes to manage OMR, in combination with other environmental variables, to minimize the entrainment of fish in the south Delta and at CVP and SWP fish salvage facilities. Reclamation and DWR propose to maximize exports by incorporating real-time monitoring offish distribution, turbidity, temperature, hydrodynamic models, and entrainment models into the decision support for the management of OMR to focus protections for fish when necessary and provide flexibility where possible, consistent with the WIIN Act Sections 4002 and 4003, as described below. Estimates of species distribution will be described by multi-agency Delta-focused technical teams. Reclamation and DWR will make a change to exports within 3 days of a trigger when monitoring, modeling, and criteria indicate protection for fish is necessary. The following OMR Flow Management description is from the April 30, 2019 PA (Appendix A2); the primary difference from the February 5, 2019 PA (Appendix AI) is in the additional details for "Storm-related OMR Flexibility" and corrections ofOMR flow requirements in the Integrated Early Pulse Protection and Turbidity Bridge A voidance subsections. • • • Reclamation and DWR propose to operate to an OMR index computed using an equation. An OMR index allows for short-term operational planning and real-time adjustments. OMR Management: From the onset of OMR management to the end, Reclamation and DWR will operate to an OMR index no more negative than a 14-day moving average of -5,000 cfs unless a storm event occurs (see below for storm-related OMR flexibility). OMR could be more positive than -5000 cfs if additional real-time OMR restrictions are triggered as described below. Onset of OMR Management: Reclamation and DWR shall start OMR management when one or more of the following conditions have occurred: 382 Biological Opinion for the Long-Term Operation of the CVP and SWP o o • Integrated Early Winter Pulse Protection ("First Flush" Turbidity Event): When the running 3-day average of the daily flows at Freeport is greater than 25,000 cfs and the running 3-day average of the daily turbidity at Freeport is 50 NTU or greater for the period from December 1 through January 31, Reclamation and DWR propose to reduce exports for 14 consecutive days so that the 14-day averaged OMR index for the period shall not be more negative than -2,000 cfs. This "First Flush" action may only be initiated once during the December through January period to limit the CVP/SWP influence on delta smelt's population-scale migration/dispersal. The action will not be required if: 1) the Freeport flow and turbidity conditions are met after January 31, or 2) water temperature reaches 12 degrees Celsius based on a three station daily mean at Honker Bay, Antioch, and Rio Vista, or 3) when ripe or spent delta smelt are collected in a monitoring survey. Salmonids: After January 1, if more than 5 percent of any one or more salmonid species (wild young-of-year winter-run Chinook salmon, wild young-of-year CV spring-run Chinook salmon, or wild CCV steelhead) are estimated to be present in the Delta as determined by their appropriate monitoring working group based on available real-time data, historical information, and modeling. Additional Real-Time OMR Restrictions: Reclamation and DWR shall manage to a more positive OMR than -5,000 cfs based on the following conditions: Turbidity Bridge Avoidance ("South Delta Turbidity"): In years when a "First Flush" occurs, once Delta smelt have dispersed, there is no evidence that large, population-scale movements continue. This action begins after the completion of the Integrated Early Winter Pulse Protection (above) or February I , whichever comes first. The purpose of this action is to avoid the formation of a continuous turbidity bridge from the San Joaquin River shipping channel to the fish facilities, which historically has been associated with elevated salvage of Delta smelt. Reclamation and DWR propose to manage exports in order to maintain daily average turbidity in Old River at Bacon Island (OBI) at a level of less than 12 NTU. lfturbidity does not exceed 12 NTU at OBI, then there will be no explicit limit on OMR flow for the purposes of protecting Delta smelt. If daily average turbidity at OBI cannot be maintained at less than 12 NTU, the 3-day averaged OMR index shall not be more negative than -2,000 cfs, until the 3-day average turbidity at OBI drops below 12 NTU. The action is to be taken from February 1 through March 31 even if the Integrated Early Winter Pulse Protection action has not occurred earlier in the water year. The action will no longer be required on or after April 1. o Larval and Juvenile Delta Smelt: When Q-West is negative and larval or juvenile Delta smelt are within the entrainment zone of the pumps based on real-time sampling, Reclamation and/or DWR propose to run hydrodynamic models informed by the Enhance Delta Smelt Monitoring program (EDSM), 20 mm trawl survey (20 mm) or other relevant survey data to estimate the percentage of larval and juvenile Delta smelt that could be entrained, and operate to avoid no greater than 10 percent loss of modeled larval and juvenile cohort Delta Smelt (typically this would come into effect beginning the middle of March). o 383 Biological Opinion for the Long-Term Operation of the CVP and SWP o o Wild CCV steelhead Protection: Reclamation and DWR would operate to an OMR flow of -2,500 cfs for 5 days whenever more than 5 percent of steelhead are present in the Delta and the natural-origin steelhead loss trigger exceeds 10 steelhead per TAF (combined loss at the CVP and SWP). The timing of this action is intended to provide protections to San Joaquin origin CCV steelhead, but the loss-density trigger is based on loss of all steelhead since there is currently no protocol to distinguish San Joaquin-basin and Sacramento-basin steelhead in salvage. Reclamation would use the current loss equation for steelhead or a surrogate. This action will no longer be required after May 31. Salvage or Loss Thresholds: Reclamation and DWR propose a cumulative annual salvage loss threshold equal to 1 percent of the abundance estimate based on EDSM for adult Delta smelt; 1 percent of the winter-run Chinook salmon Juvenile production estimate (JPE) (genetically confirmed) or 2 percent of the winter-run Chinook salmon JPE (based on length at date); loss equal to 1 percent of the CV spring-run Chinook salmon JPE (or 0.5 percent of yearling CNFH late fall-run spring-run surrogates); the salvage of 3,000 unclipped juvenile CCV steelhead, and the salvage of ] 00 juvenile sDPS green sturgeon. Reclamation and DWR may operate to a more positive OMR when the daily salvage loss indicates that continued OMR of -5,000 cfs may exceed the cumulative salvage loss thresholds as described below: • • Restrict OMR to a 14-day moving average OMR index of -3,500 cfs when a species-specific cumulative salvage or loss threshold exceeds 50 percent of the threshold. The OMR restriction to -3,500 cfs will persist until the speciesspecific off ramp is met. Restrict OMR to a 14-day moving average OMR index of -2,500 cfs (or more positive if determined by Reclamation) when a cumulative salvage or loss threshold for any of the above species exceeds 75 percent of the specific threshold. The OMR restriction to -2,500 cfs will persist until the speciesspecific off ramp is met. Species specific OMR restrictions will end when the individual species-specific off ramp from "End of OMR management criteria," below, are met. • Storm-Related OMR Flexibility: If Reclamation and DWR are not implementing additional real-time OMR restrictions, consistent with other applicable legal requirements, Reclamation and DWR may operate to a more negative OMR up to a maximum (otherwise-permitted) export rate at Banks and Jones Pumping Plants of 14,900 cfs (which could result in a range ofOMR values) to capture peak flows during storm-related events. Reclamation and DWR will continue to monitor fish in real-time and will operate in accordance with "Additional Real-time OMR Restrictions," above. Under the following conditions, Reclamation and DWR would not cause OMR to be more negative for capturing peak flows from storm-related events. 384 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • Additional real-time OMR restrictions, above, are triggered, then Reclamation would operate in accordance with those additional real-time OMR restrictions and would not cause OMR to be more negative for capturing peak flows from storm-related events. Actual cumulative expanded salvage of Delta Smelt is greater than 50 percent of the average smelt index over the prior three years of non-zero FMWT surveys and a Cumulative Salvage Index of7.98 during December 1- January 20 or cumulative expanded salvage of Delta Smelt is greater than or equal to 75 percent of the average smelt index calculated described above. Predicted adult or juvenile Delta Smelt salvage would exceed 50 percent during December 1 - January 20 or cumulative expanded salvage is greater than or equal to 7 5 percent as determined above, based on the data sources in the Secretarial Memo dated January 17,2019. Measured cumulative loss to date since October 1 for winter-run Chinook salmon (based on length-at- date criteria) is greater than the percentage below of a loss threshold calculated as 2 percent of the JPE: o o o o o o o • • • January 1 - 15: 2 percent (0.04 percent of JPE) January 16 - 31 : 4 percent ( 0. 08 percent of JPE) February 1 - 14: 6 percent (0.12 percent of JPE) February 15-28: 9 percent (0.18 percent ofJPE) March 1- 15: 21 percent (0.42 percent of JPE) March 16 - 31: 26 percent (0.52 percent of JPE) April 1 -End of OMR: 30 percent (0.60 percent of JPE) Predicted cumulative loss for winter-run Chinook salmon is greater than 30 percent of the loss threshold described above in "Additional Real-Time OMR Restrictions" [1 percent of the Winter-Run Chinook Salmon JPE (genetically confirmed) or 2 percent of the Winter-Run Chinook Salmon JPE (based on length-at-date)] or salvage for steelhead is greater than 50 percent of the salvage threshold described above in "Additional Real-Time OMR Restrictions." Changes in spawning, rearing, foraging, sheltering, or migration behavior beyond those described in the forthcoming biological opinion for this project. End of OMR Management: OMR criteria may control operations until June 30, or when both of the following conditions have occurred, whichever is earlier: o o Delta smelt: when the daily mean water temperature at CCF reaches 25°C for 3 consecutive days. Salmonids: when more than 95 percent of listed salmonids have migrated past Chipps Island, as determined by the Delta monitoring working group, OR after daily average water temperatures at Mossdale exceed 72°F for 7 days during June (the 7 days do not have to be consecutive). 2.5.5.8.3 Assess Species Exposure to Proposed South Delta Operations- Exports and OMR Management Note that supplemental analysis based on PA revisions received June 14, 2019 (Appendix A3) is provided in Section 2. 5.5.11 385 Biological Opinion for the Long-Term Operation of the CVP and SWP The temporal and spatial occurrence of each run of Chinook salmon, CCV steelhead, and sDPS green sturgeon in the Delta is intrinsic to their natural history and summarized in Section 2.2 Status of the Species. A more detailed description of the presence of these species in the Delta is given in Section 2.5.6.1 Presence of the Species within the Bay-Delta Division. A summary of the effects of the proposed south Delta export operations is provided in Table 2.5.5-66 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. Old and Middle River Flows- The modelling conducted for the PA (February 5, 2019; Appendix AI) depicts that OMR flows will become substantially more negative in April and May under the PA as compared to the COS due to changes in the PA compared to the NMFS 2009 Opinion. In particular, the following RP A actions influenced OMR flow values in the COS: RPA Action IV.2.1: San Joaquin River flow requirements (I:E ratio) which restricted export rates to a ratio of the inflow of the San Joaquin River as measured at Vernalis during April and May, and RPA Action IV.2.3: Old and Middle River flow management which restricted exports to manage to more positive OMR flow values for specified periods of time for the protection of listed salmonids when the exceedance of certain threshold triggers of listed fish loss occurred at the CVP and SWP fish salvage facilities. In addition, the modelled OMR flow patterns depict more negative values for OMR in the months of January, February, March and June (Table 2.5.5-21). Furthermore, more negative OMR flows are modelled to occur in October of wet and above normal water year types with a difference of approximately 1,500 cfs under the PA as compared to the COS conditions. A similar response is modelled for January of above and below normal water year types in which the PA is approximately 700 cfs more negative than the modelled COS flows for OMR. In drier water year types, the modelling indicated that OMR flows in February and March are anticipated to be I ,000 to 1,600 cfs more negative (below normal to critical water year types) with the differences becoming greater as water year types become drier. The shift in April and May OMR flow values between the PA and COS, as modelled, indicated that differences of approximately 4,000 cfs more negative flows would occur in wetter years. In drier years (below normal and dry water year types) the differences between the PA and COS were less, but were still approximately I ,500 cfs more negative under the PA conditions as compared to the COS conditions. In critical water year types, the PA was modelled to be 600800 cfs more negative than the COS conditions. Seldom during the April and May period are modelled OMR flows predicted to be more positive/less negative under the PA than under the COS conditions, and positive OMR flow values occur in April and May less frequently under the PA (<10 percent ofyears) compared to the COS (approximately 50 percent of years). During June, the PA is modelled as being more negative by 1,000 to 1,600 cfs in drier water year types (below normal, dry, and critical). In summary, the modelled OMR flow values for the PA indicate that for most ofthe winter and spring months (25 of the 30 month and water year type combinations for January through June) flows will be more negative in the channels leading to the export facilities, creating conditions that, per NMFS's conceptual model, will be more negative to fish. Exports- In April and May, modelling indicated that combined exports would be almost twice as high for the PA as compared to the COS conditions (Table 2.5.5-22). Combined exports under the COS conditions were modelled to average 2,300 cfs in May and 2,500 cfs in April for the full simulation period. In contrast, combined exports under the PA were modelled to be 5,284 cfs in 386 Biological Opinion for the Long-Term Operation of the CVP and SWP May and 5,564 cfs in April. Differ·ences in the export flows during April ranged from approximately 4,500 cfs in wet years to 713 cfs in critical years, with the PA flows always modelled to be greater than the COS conditions. In May, a similar trend is also seen. Differences in export flows are modelled to be approximately 4,250 cfs in wet years and 761 cfs in critical years, with the PA always having greater export flows. Average monthly combined exports are consistently greater under the PA than the COS for all months except December and July. The differences between the PA and COS range from -548 cfs in December (COS > PA) to 2,977 cfs in May (P A> COS). In almost all water year types, exports modelled for the PA are greater than for the COS conditions in October, November, January, February, March, April, and May. In wet years, exports in the PA are substantially greater in October, November, April, and May. In drier years (below normal to critical water year types) the PA typically has flows that are 1,000 cfs or greater than the COS conditions for the January through June period. These increases in combined export flows mirror the trends seen in the modelling done for the OMR flows as would be expected. Velocity Density Modelling- The results of the velocity density modelling parallel the trends already exhibited for OMR and combined export modelling. In locations along the Old and Middle river routes, density plots show a shift to more negative velocities in the March through May periods for river reaches adjacent to the export facilities. Modelling for the velocity density comparisons used 3-month bins: December through February, March through May, June through August, and September through November. The 3-month bin for the modeling obscures the details of the effects of exports and reverse flows in Old and Middle rivers on a monthly basis as was presented earlier. The shift to more negative velocity values in the March through May period for the Old River and Middle River channel segments (89, 90, and 143) indicate the hydrodynamic effects of the increased combined exports and mirrors the resulting tr·ends seen in the OMR flow values for the modelled PA conditions. Greater exports would tend to create more negative OMR flows given the same inflow and tidal conditions, and given that the geometry of the channel segments used in the modelling should remain consistent, increased negative flow should result in more negative velocity values in those channels. For example, the velocity density plots for Old River at Highway 4, and just upstream towards the export facilities (channels 89 and 90) show a shift to more negative velocities in the March through May period for all water year types. Similar trends are seen for Middle River at Woodward Island (channel 143) and Old River near Woodward Island (channel 95). The percentage of overlap between the modeled PA and COS conditions is typically greater for drier years (conditions are more similar) than for wetter years (more dissimilar), which parallels the greater difference in total exports and OMR flows seen in the wetter years compared to drier years. 2.5.5.8.3.1 South Delta Salvage and Entrainment Entrainment of juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon at the south Delta export facilities may result in mortality. "Loss" is a term used to refer to the estimated number of fish that experience mortality within the fish collection facilities as they go through the salvage process, and is estimated based on the number of salvaged fish (fish observed within the fish collection facilities at the export facilities) and a number of components related to facility efficiency and handling. For example, at the SWP, the salvage process starts with fish entrainment into CCF, and proceeds with fish moving 387 Biological Opinion for the Long-Term Operation of the CVP and SWP across the CCF until they enter the SDFPF, where they are collected in holding tanks. After fish collection, a subsample is counted for determining the number of fish salvaged in a given period of time. This is usually represented by a 30-minute subsample of a 2-hour block of fish collections. After this stage, fish are transferred to tanker trucks and driven to releases sites in the western Delta and released back into the Sacramento or San Joaquin rivers. At the CVP, the fish salvage process is considered to start with fish encountering the trash rack on Old River in front of the primary channel, and then progressing through the salvage process until the salvaged fish are ultimately releases at the release sites, similar to the process at the SDFPF. In the following description, percentages refer to the percent of fish reaching a specific stage in the salvage process that are assumed to experience mortality during that stage. For example, the 75 percent loss associated with prescreen loss. at the SWP means that 75 percent of the fish entering CCF at the radial gates are assumed to die before reaching the primary louvers at the SDFPF. Of those fish that do reach the louvers, another 25 percent are lost, and so on. The total loss percentages represent the overall percent loss across all stages, that is, the percent of all fish entering the facility that die somewhere during the salvage process. • • SWP: (1) Prescreen loss (from CCF radial gates to primary louvers at the SDFPF): 75 percent loss, (2) Louver efficiency: 25 percent loss; (3) Collection, handling, trucking, and release: 2 percent loss; (4) Post release: 10 percent loss; and (5) Total loss (combination of the above): 83.5 percent. CVP: (1) Prescreen loss (in front of trash racks and primary louvers): 15 percent loss; (2) Louver efficiency: 53.2 percent loss; (3) Collection, handling, trucking, and release: 2 percent loss; (4) Post release: 10 percent loss; and (5) Total loss (combination of the above): 64.9 percent. For purposes of evaluating the effect of near-field south Delta exports on Chinook salmon, steelhead, and green sturgeon, NMFS presents juvenile loss data using: (1) historical salvage and loss data; and (2) salvage-density method as modelled. NMFS provides a quantitative analyses of entrainment differences between COS and PA using the salvage density methodology, and a qualitative discussion of potential predation differences between COS and P A. The salvage-density method (Appendix G) relies on historic export rates and observed loss of salmonids and sturgeon at the CVP and SWP collection facilities (for water years 1995-2009). This period represents a hydrologic regime that predates the 2009 Biological Opinion and does not reflect the -5,000 OMR restriction (or other operations) in either the PA or COS. This period was what was used in the equivalent modeling for the California WaterFix consultation and the accelerated timeframe of the current consultation didn't allow for the method to be updated to include more recent years. The method essentially functions as a description of changes in export flows weighted by seasonal changes in loss. While the model is designed as a comparative tool, NMFS does use the absolute estimates of loss to put the potential effect into a population context for CV spring-run Chinook salmon and CCV steelhead, but those results should be considered a coarse screening level analysis due to limitations of the salvagedensity method itself (limited historical time-frame ofloss; relatively simple weighting of loss by export changes and no other operational factors) and use of the average annual modeled loss rates (over the 15-year data period) scaled to both low and high population estimates. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the 388 Biological Opinion for the Long-Term Operation of the CVP and SWP average loss rate likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. 2.5.5.8.3.1.1 Sacramento River Winter-run Chinook salmon exposure Fish entrained at the state and Federal fish collection facilities that reach the salvage tanks are collected and transported back to the Delta from both the state and Federal water projects. A screened subsample of fish that reach the salvage tanks are sampled every 2 hours and the total fish salvage per each sampling period is calculated by expanding the number of fish salvaged by the fraction of time that diversions were sampled. Fish loss for that period of time is calculated based on the standard loss equations (CDFW 2013; available at the CDFW website: ftp://ftp.dfg.ca.gov/salvage/Salmon%20Loss%20Estimation/). Daily salvage and loss is the cumulative sum for those metrics for all of the sampling periods that occurred in that given day. Historical salvage and loss data analysis is presented in Table 2.5.5-24 and Table 2.5.5-25 to provide context for the loss estimates for the PA and COS based on the salvage density method. Using the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers, the average annual adipose fin clipped juvenile winter-run Chinook salmon (hatchery-produced fish) salvage and loss from brood years 1999 to 2017 were estimated to be 1,428 and 3,976 juveniles, respectively (Table 2.5.5-24). The average proportional loss, which is the annual total loss of clipped juvenile winter-run Chinook salmon divided by the annual number of hatchery-reared and released juvenile winter-run Chinook salmon, was 2.39 percent (Table 2.5.5-24). The average between 1999 and 2008 was 4.08% while the average from 2009-2017 was 0.52%. Using the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers, the average annual unclipped juvenile winter-run sized Chinook salmon salvage and loss from brood years 1992 to 2017 were estimated to be 1,205 and 3,201 juveniles, respectively (Table 2.5.5-25). The average proportional loss of unclipped juveniles, which is the annual total loss of unclipped juveniles divided by the annual juvenile production estimate (JPE) of juvenile winter-run Chinook salmon, was 1.01 percent (Table 2.5.5-25). The average between 1992 and 2008 was 1.35% while the average from 2009-2017 was 0.36%. 2.5.5.8.3.1.1.1 Juvenile Salvage Estimates using the Salvage-Density Method The salvage density method relies on historic exports and observed loss (for water years 19952009) of salmonids at the CVP and SWP fish salvage facilities and essentially functions as a description of changes in export flows weighted by seasonal changes in loss (see caveats in Section 2.5.5.8.3.1). The results of the salvage-density method showed that, based on modeled south Delta exports, annual loss of winter-run Chinook salmon at the south Delta export facilities would be 7 percent (in Above Normal water year types) to 38 percent (in Critical water year types) higher under the PA than the COS (Table 2.5.5-26). The monthly loss of winter-run Chinook salmon at the south Delta export facilities (Table 2.5.5-27) shows that while loss does increase by a high percentage in April and May, the historical pattern is that the majority of winter-run Chinook salmon salvage occurs before April. It is possible that some of the loss modeled to occur at the export facilities under the PA flow conditions might have occurred due to far-field effects in the south Delta under COS conditions, but no modeling tool is available 389 Biological Opinion for the Long-Term Operation of the CVP and SWP that allows estimation of and comparison of independent estimates of direct loss and far-field effects under the PA vs. COS. Fish that may have been predated upon or otherwise lost in far field areas under the influence of the Project operations in the COS scenario (i.e., migrational delay, increased transit time, increased predator exposure) may arrive at the fish salvage facilities under the PA scenario due to faster transit times in the adjacent river routes, thus having less exposure to predators, only to be lost in the salvage process at the fish facilities. While we do have information on reach-scale survivals and travel-times, our current understanding of subdaily, fine scale fish movement within a reach (and associated survival outcomes) is limited since no study has deployed sufficient instrumentation to track fine scale movement and fish survival outcomes. Tools such as the Delta Passage Model provide estimates of total throughDelta survival. While results of that model (described previously) show negligible changes in overall survival between the PA and COS, that model doesn't capture effects to San Joaquinorigin populations of listed salmonids. The absolute differences between the PA and the COS were greater in wetter water years, as a result of more south Delta export pumping, however a greater percentage difference between the estimated loss occurred in drier water year types (Table 2.5.5-28). For winter-run Chinook salmon, the differences ranged from 5.3 percent more under the PA at the SWP in above normal years to 45.3 percent more under the PA at the CVP in critical years (Table 2.5.5-28). Within years, the monthly estimated loss varied considerably. The estimated loss rates were typically higher from January through May for all water year types for the PA compared to the COS. However, February and March had lower loss values in wet years for the PA compared to the COS conditions, but higher values in drier years (Table 2.5.5-29, Table 2.5.5-30, Table 2.5.5-31, Table 2.5.5-32, and Table 2.5.5-33). The largest percentile differences between the PA and COS occurred in April, wlhere the PA loss rate could be as much as 238 percent higher than the COS conditions [above normal years at the SWP (Table 2.5.5-30)] and loss values were typically 100 percent higher for the other water year types. This difference reflects the substantial increase in exports during April under the PA compared to the COS conditions. Increased entrainment into the south Delta fish collection facilities would decrease migratory success for winter-run Chinook salmon that are exposed to the export facilities in the waterways immediately adjacent to the facility intakes and that do not migrate through the salvage facilities. An increased negative flow in the region immediately adjacent to the intakes to the CCF and the CVP would increase the probability of fish being unable to reverse course and successfully exit the Delta, although the magnitude of this effect is currently unknown due to a lack of data regarding fme scale, reach specific fish movement behavior and survival in those reaches under increased export conditions. Increased pumping has far-field migratory impacts as well, particularly in the Old and Middle River corridors which would negatively affect winter-run Chinook salmon in those corridors. Fish that are present in the Old River or Middle River corridors and their distributaries downstream of the south Delta export faci lities would experience increased net flows towards the export facilities. Increased exports would obscure more of the ebbing tjde signal that would normally cue fish to move out of those corridors and back into the main migratory corridor of the San Joaquin River before moving southwards into waters that are more heavily influenced by the effects of reverse flows due to exports. An important concept to note is that even though the numbers of fish lost in the drier water year types may be lower than during wetter water year types, this is a function of overall watershed survival differences between water year types. During wet water years, more juvenile salmonids 390 Biological Opinion for the Long-Term Operation of the CVP and SWP enter the south Delta from either basin and greater numbers are therefore exposed to the export facilities (Kjelson et al. 1982, Brandes and McLain 2001, Newman and Brandes 201 0). Lower numbers of fish salvaged in drier years, therefore, does not necessarily indicate that restrictions on pumping are impacting a smaller proportion offish. Often the OMR flows are more negative in dry years even if exports are reduced. In dry years, less water is flowing into the Delta from tributaries, and in particular the San Joaquin River basin. Less flow into the HOR will exacerbate the effects of exports since there is less flow moving downstream from the HOR towards the CVP and SWP intakes to offset the volume of water being diverted, and more water will have to come from alternative sources, such as the waters of the central Delta to supply the volume of water being exported. Conversely, it is possible to be exporting to full capacity in the wet years and OMR flows are still positive due to very high San Joaquin River and tributary flows, which can completely offset the volume of water being diverted by the CVP and SWP. Furthermore, NMFS does have concerns that in drier years, under lower flows in the Sacramento River, a greater proportion offish will enter the central Delta due to the greater effect of reverse flows created from tidal influence. This greater proportion of fish that enter the Delta interior are expected to have a lower survival rate and also have exposure to the effects of the south Delta exports. Conversely, in wetter years with more flow in the Sacramento River, the riverine reach of the mainstem Sacramento River extends farther downstream and less fish are routed into the central Delta, remaining in the mainstem instead. Regional flows in south Delta waterways are expected to remain strongly affected by any export actions in drier water year types, which in tum increases the likelihood that out-migrating juvenile winter-run Chinook salmon will be negatively affected by exports. 2.5.5.8.3.1.2 CV Spring-Run Chinook Salmon Exposure Using the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers, the estimate of average annual adipose fin clipped CV spring-nun Chinook salmon juvenile salvage and loss from brood year 1999 to 2017 were 667 and 1,406 juveniles (Table 2.5.5-34), respectively, for the SWP and CVP combined. The estimated average proportional loss, which is the estimated annual total loss divided by the annual number of hatchery-reared and released CV spring-run Chinook salmon juveniles, was 0.63 percent (Table 2.5.5-34). The estimated cumulative SWP and CVP average annual unclipped CV spring-run sized Chinook salmon juvenile salvage and loss from brood year 1992 to 2017 using the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers, were 14,062 and 26,241 juveniles (Table 2.5.5-35), respectively. 2.5.5.8.3. 1.2. 1 Juvenile Salvage Estimates using the Salvage-Density Method The salvage density method relies on historic exports and observed loss (for water years 19952009) of salmonids at the CVP and SWP fish salvage facilities and essentially functions as a description of changes in export flows weighted by seasonal changes in loss (see caveats in Section 2.5.5.8.3.1 ). The historical loss pattern used in the Salvage-Density modeling identified fish to run based on length-at-date (LAD) criteria. Because of run-assignment error associated with the LAD criteria, much of projected spring-run-sized loss may not represent genetic CV 391 Biological Opinion for the Long-Term Operation of the CVP and SWP spring-run Chinook salmon loss, but rather represent loss of (primarily) unmarked hatchery fallrun. Harvey and Stroble (2013) reported that 98 percent of the spring-run-sized fish in their sample were not genetic spring-run (95 percent genetic fall-run, 1 percent genetic winter-run, and 2 percent genetic late-fall-run). In order to generate a loss estimate more representative of genetic CV spring-run Chinook salmon, we multiplied the projected loss numbers by 0.02 and refer to the outcome as "adjusted loss." The results of the salvage-density method showed that, ibased on modeled south Delta exports, annual adjusted loss of CV spring-run Chinook salmon at the south Delta export facilities would be 64 percent (in Critical years) to 159 percent (in Above Normal years) higher under the PA than the COS (Table 2.5.5-36). The monthly loss of CV spring-run Chinook salmon at the south Delta export facilities (Table 2.5.5-36) shows that the largest increases in loss occur in April (143 p ercent), and May (128 percent). The majority ofCV spring-run Chinook salmon outmigration occurs during the April-May period, so the risk of increased loss during April and May will affect the majority of CV spring-run Chinook salmon outmigrants. It is possible that some of the loss modeled to occur at the export facilities under the PA flow conditions might have occurred due to far-field effects in the south Delta under COS conditions before fish arrived at the CVP or SWP facilities. Some of this far-field loss may be attributable to the effects of the SWP and CVP export operations, but no modeling tool is available that quantifies that loss and allows comparison of both direct loss and far-field effects under PA vs. COS conditions associated with the SWP and CVP export operations. NMFS put the combined CV spring-run Chinook salmon loss in a population context (see full caveats in Section 2.5.5.8.3.1) by expressing the estimated annual combined loss as a percentage of the juvenile CV spring-run Chinook salmon entering the Delta. These results should be considered a coarse screening level analysis due to limitations of the salvage-density method itself (limited historical time-frame of loss; relatively simple weighting of loss by export changes and no other operational factors) and use of the average annual modeled loss rates (over the 15year data period) scaled to both low and high population estimates. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the average loss rate likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. Assuming that the relationship between spring-run escapement and number ofjuveniles entering the Delta is similar to that for winter-run Chinook salmon 14 (Table 2.5.5-38), the observed Brood Year 2010-2018 tributary CV spring-run Chinook salmon escapement range of 1,059 to 19,516 is estimated to produce 35,334 to 3,837,720 juvenile CV spring-run Chinook salmon entering the Delta. The estimated annual combined loss from the COS is 851 juveniles, and estimated annual combined loss from the PA is 1,73 2. Applying the estimated annual combined loss to the lowest and highest juvenile population estimates provides ranges of < 1 (851 + 3,837,720) to 2 (851 + 35,334) percent loss of the juvenile CV spring-run Chinook salmon population in the Delta for the COS, and < 1 (1 ,732 + 3,837,720) to 5 (1,732 + 35,334) percent loss of thejuvenile CV spring-run Chinook salmon population in the Delta for the PA. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the average loss rate 14 Mortality during spawning, egg incubation, and juvenile rearing and migration may differ between spring-run and winter-run Chinook salmon since the seasonal timing of those life history stages don't fully overlap, but we used this assumption since winter-run Chinook salmon is the only salmonid for which there is an estimate of juveniles entering the Delta. 392 Biological Opinion for the Long-Term Operation of the CVP and SWP likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. The results of the salvage-density method showed that, based on modeled south Delta exports, mean Ross at the south Delta export facilities would be substantially higher under the PA than the COS in all water year types for CV spring-run Chinook salmon. The absolute differences and percentile differences between the PA and the COS were greater in wetter water years, as a result of more south Delta export pumping (Table 2.5.5-39). For CV spring-run Chinook salmon, the differences ranged from 28.2 percent more under the PA at the CVP in critical years to 167.5 percent more under the PA at the SWP in above normal years (Table 2.5.5-39). Within years, the monthly estimated loss varied considerably. The estimated loss rates were typically higher from March through May for drier year types for the PA compared to the COS. However, March had lower loss values in wet years for the PA compared to the COS conditions, but higher values in drier years (Table 2.5.5-40, Table 2.5.5-41, Table 2.5.5-42, Table 2.5.5-43, and Table 2.5.5-44). The largest percentile differences between the PA and COS occurred in April, where the PA loss rate could be as much as 238 percent higher than the COS conditions [above normal years (Table 2.5.5-45)] and loss values were typically 80 percent higher for the other water year types. This difference reflects the substantial increase in exports during April under the PA compared to the COS conditions. As discussed previously for winter-run Chinook salmon juveniles, there are many issues that influence the movement and vulnerability of juvenile CV spring-run Chinook salmon to entrainment, salvage, and loss at the fish collection facilities for the CVP and SWP. Like winterrun Chinook salmon, the majority of CV spring-run Chinook salmon originate in the Sacramento River basin and, thus, follow a common emigration pathway to the Delta through the main stem of the Sacramento River. Factors which influence the routing and survival of winter-run Chinook salmon juveniles will also influence the routing and survival of juvenile CV spring-run Chinook salmon. A further issue, that does not apply to juvenile winter-run Chinook salmon is the emigration of juvenile CV spring-run Chinook salmon out ofthe San Joaquin River basin (originating from the experimental population) and the necessity of surmounting obstacles unique to the San Joaquin River basin, including the actions of the south delta agricultural barriers, and migrating through the waterways of the south Delta as the primary route to the ocean and not as a secondary route as seen for the Sacramento River basin fish. Increased entrainment into the south Delta facilities is expected to decrease migratory success for CV spring-run Chinook salmon that are exposed to the pumping plants in the waterways immediately adjacent to the facility intakes. A more negative flow environment in the region immediately adjacent to the intakes of the CCF and the CVP would decrease the probability of fish being able to alter course and successfully exit the Delta, although the magnitude of this effect is currently unknown due to a lack of data regarding fme scale fish movement behavior and survival in those reaches under export conditions. This is particularly important for CV spring-run Chinook salmon that originate in the San Joaquin River basin and enter the Old River channel when there is no HOR barrier present as proposed under the PA. These fish would migrate downstream in either the Old River, Middle River, or Grant Line/ Fabian- Bell channels. All three channels have considerable exposure to the effects of exports. The Old River and Grant Line/ Fabian -Bell channels pass directly in front of or in very close proximity to the intakes for the CVP and SWP, and a large proportion of fish moving through these channels are expected to be entrained into the fish collection facilities where high levels of mortality are 393 Biological Opinion for the Long-Term Operation of the CVP and SWP expected. The Middle River channel joins with the man-made Victoria CanaV North Canal, a large dredged channel directly leading to the export facilities, and net flows move towards the export facility intakes under most conditions. Increased export has negative far-field migratory impacts as well, particularly in the Old and Middle River corridors which would negatively affect CV spring-run Chinook salmon in those corridors. Fish that are present in the Old River or Middle River corridors and their distributaries downstream of the south Delta export facilities would experience increased net flows towards the export facilities. Increased exports would mute the ebbing tide signal to cue fish to move out of those corridors and back into the main migratory corridor of the San Joaquin River rather than moving farther southwards into waters that are more heavily influenced by the effects of reverse flows due to exports. This would affect both juvenile CV spring-run Chinook salmon originating in the Sacramento River basin as well as those CV spring-run Chinook salmon originating in the San Joaquin River basin and migrating downstream within the main s1tem channel of the San Joaquin River from upstream locations. The PA does not include installation of the HOR barrier, which will result in keeping less flow in the San Joaquin River corridor, thereby decreasing survival for CV spring-run Chinook salmon originating in the San Joaquin River basin and entering the South Delta and interior Delta through this route. There are two main reasons for these impacts. Less downstream flow in the San Joaquin River channel downstream of the confluence with the HOR in conjunction with increased exports was modeled to slightly shift the velocity density to more negative velocities (more upstream flows), potentially indicating more tidal effect in this reach under the PA (Figure 2.5.5-30). This shift in tidal influence tends to direct more flow (and migrating fish) into Old River due to the tidal forcing of the flood tide moving upriver in the main stem of the San Joaquin River. The modeling of the velocity density indicated that within the main stem San Joaquin River near its junction with the Mokelumne River and farther downstream at Jersey Point, there was a high degree of overlap between the PA and COS due to the overwhelming tidal influence. Ther,efore, in this portion of the main stem San Joaquin River, there is little difference between the PA and the COS. However, survival in these reaches are considered to be low due to the influence of the tides prolonging migration transit times and increasing exposure to predators along the route. As discussed in the winter-run Chinook salmon section above, it is an important concept to note that even though the absolute numbers of fish lost in the drier water year types under current conditions are lower than during wetter water year types, this is also a function of overall watershed survival differences between water year types as well as the magnitude of exports. During wet water years, more juvenile salmonids enter the south Delta from either basin and greater numbers are, therefore, exposed to the export facilities (Kjelson et al. 1982, Brandes and McLain 2001, Newman and Brandes 2010). Lower numbers offish lost in drier years, therefore, does not necessarily indicate that restrictions on pumping are impacting a smaller proportion of fish, but that there is potentially a smaller pool of fish present to be entrained. The effects of more negative OMR flows have already been discussed for winter-run Chinook salmon and NMFS expects that they will have similar impacts upon CV spring-run Chinook salmon. 394 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.3.1.3 CCV Steelhead Exposure Using the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers, the estimated average annual cumulative clipped juvenile CCV steelhead salvage and loss from brood year 1999 to 2017 for the SWP and CVP were 2,798 and 6,990 juveniles, respectively (Table 2.5.5-45). The average proportional loss for the years 1999-2014 (incomplete hatchery release data were available for 2015-20 17), which is the annual cumulative total loss divided by the annual number of hatchery-reared and released steelhead juveniles, was 0.50 percent (Table 2.5.5-45). Since 1998, all hatcheryproduced steelhead that are released into the waters of the Central Valley are adipose fin clipped to allow them to be distinguished from natural fish. The average annual cumulative unclipped (natural) juvenile CCV steelhead salvage and loss from brood year 1999 to 2017 for the SWP and CVP were 1,324 and 3,110 juveniles, respectively (Table 2.5.5-46). As discussed previously for juvenile winter-run Chinook salmon and CV spring-run Chinook salmon, there are many issues that influence the movement and vulnerability ofjuvenile CCV steelhead to entrainment, salvage, and loss at the fish collection facilities for the CVP and SWP. Comparable to the winter-run Chinook salmon and CV spring-run Chinook salmon populations, the majority of CCV steelhead originate in the Sacramento River basin and, thus, follow a common emigration pathway to the Delta through the main stem of the Sacramento River. Factors which influence the routing and survival of Chinook salmon juveniles will also influence the routing and survival of juvenile CCV steelhead. Like juvenile spring-run originating from the experimental population in the San Joaquin River basin, juvenile CCV steelhead emjgrating out of the San Joaquin River basin (Southern Sierra diversity group) face the necessity of surmounting obstades unique to the San Joaquin River basin, including the actions of the south Delta agricultural barriers, and migrating through the waterways of the south Delta as the primary route to the ocean and not as a secondary route as seen for the Sacramento River basin fish. The discussion of the effects of south Delta export facilities operations that has already been described for winter-run Chinook salmon and CV spring-run Chinook salmon would be applicable to CCV steelhead. Juvenile CCV steelhead migration through the Delta overlaps with both the migration timing of winter-run Chinook salmon and CV spring-run Chinook salmon, and, therefore, the discussion from both Chinook salmon races would be expected to apply to CCV steelhead, too. In the San Joaquin River basin, comparisons to CV spring-run Chinook salmon are especially appropriate, as NMFS expects juveniles from both salmonid groups will be migrating out of the San Joaquin River basin at the same time and wil[ experience the same hydrologic and operational effects during their movements. 2.5.5.8.3.1.3. 1 Juvenile Salvage Estimates using the Salvage-Density Method The salvage density method relies on historic exports and observed loss (for water years 19952009) of salmonids at the CVP and SWP collection facilities and essentially functions as a description of changes in export flows weighted by seasonal changes in loss (see caveats in Section 2.5.5.8.3.1). The results of the salvage-density method showed that, based on modeled south Delta exports, annual loss of CCV steelhead at the south Delta export facilities would be 15 percent (in Above Normal years) to 38 percent (in Critical years) higher under the PA than the COS (Table 2.5.5-47). The monthly loss of CCV steelhead at the south Delta export facilities 395 Biological Opinion for the Long-Term Operation of the CVP and SWP (Table 2.5.5-48) shows that the largest increases in loss occur in April (153 percent), and May (132 percent). The majority of steelhead outrnigration from the San Joaquin Basin occurs during the April-May period, so while much overall steelhead salvage occurs prior to April, the risk of increased loss during April and May will affect the majority of San Joaquin-origin steelhead outmigrants. It is possible that some of the loss modeled to occur at the export facilities under the PA flow conditions might have occurred due to far-field effects in the south Delta under COS conditions before fish arrived at the CVP or SWP facilities. Some of this far-field loss may be attributable to the effects of the SWP and CVP export operations, but no modeling tool is available that quantifies that loss and allows comparison ofboth direct loss and far-field effects under PA vs. COS conditions associated with the SWP and CVP export operations. NMFS put the combined CCV steelhead loss in a population context (see full caveats in Section 2.5.5.8.3.1) by expressing the estimated annual combined loss as a percentage of the steelhead population in the Delta. These results should be considered a coarse screening level analysis due to limitations of the salvage-density method itself (limited historical time-frame of loss; relatively simple weighting of loss. by export changes and no other operational factors) and use of the average annual modeled loss rates (over the 15-year data period) scaled to both low and high population estimates. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the average loss rate likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. Estimated annual combined loss from the COS is 6,560 juveniles, and estimated annual combined loss from the PA is 7 ,988. Good et al. (2005) estimated the CCV steelhead population at approximately 94,000-336,000 juveniles, and Nobriga and Cadrett (2001) estimated the CCV steelhead population at 413,069-658,453 juveniles. Applying the estimated annual combined loss to the lowest and highest juvenile population estimates provides ranges of I (6,560 -:- 658,453) to 7 (6,560 -:- 94,000) percent loss of the juvenile CCV steelhead population in the Delta for the COS, and 1 (7,988 -:- 658,453) to 8 (7,988 -:- 94,000) percent loss of the juvenile CCV steelhead population in the Delta for the PA. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the average loss rate likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. The results of the salvage-density method showed that, based on modeled south Delta exports, mean [oss at the south Delta export facilities would be higher under the PA than the COS in all water year types for CCV steelhead. The absolute differences between the PA and the COS were similar in most water year types (1 ,250 to 1,600 fish), except in dry years when the difference between the PA and COS was estimated as 2,249 fish for the SWP and 486 for the CVP (Table 2.5.5-49). For CCV steelhead, the differences ranged from 13.3 percent more under the PA at the CVP in below normal years to 38.8 percent more under the PA at the SWP in critical years (Table 2.5.5-49). Within years, the monthly estimated loss varied considerably. The estimated loss rates were typically higher in April and May for all water year types for the PA compared to the COS. However, March had lower loss values in wet years for the PA compared to the COS conditions, but higher values in drier years (Table 2.5.5-50, Table 2.5.5-51, Table 2.5.5-52, Table 2.5.5-53, and Table 2.5.5-54). The largest percentile differences between the PA and COS occurred in April and May, where the PA loss rate could be as much as 238 percent higher than the COS conditions (April, above normal years and below normal years [Table 2.5.5-51 and 396 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-52]) and loss values were typically at least 75 percent higher for the other water year types. This difference reflects the substantial increase in exports during April and May under the PA compared to the COS conditions. 2.5.5.8.3.1.4 sDPS Green Sturgeon Exposure In recent years (2011-2018) only 8 green sturgeon have been observed in salvage, 4 at the SWP (2016) and 4 at the CVP (2017). For the period from 1981 to 2018, the estimated annual cumulative expanded salvage of green sturgeon between the CVP and SWP has ranged between 0 and 1,476 fish, with a mean annual cumulative salvage of200 fish using current methods for expanding salvage counts. However, since the late 1980s, annual salvage has been substantially less than this. 2.5.5.8.3.1.4.1 Juvenile Salvage Estimates using the Salvage-Density Method The salvage density method relies on historic exports and observed salvage (for water years 1995-2009) of sturgeon at the CVP and SWP fish salvage facilities and essentially functions as a description of changes in export flows weighted by seasonal changes in salvage (see caveats in Section 2.5.5.8.3.1). The results of the salvage-density method showed that, based on modeled south Delta exports, average sDPS green sturgeon salvage at the south Delta export facilities would be slightly higher under the PA than the COS. The biggest differences would occur in wet years with the PA modelled as having between 4.4 percent (SWP) and 9.3 percent (CVP) more fish salvaged during wet water year types. Due to the rarity of sDPS green sturgeon in salvage, these numbers are typically represented by only a very small numbers offish (Table 2.5.5-55, Table 2.5.5-56, Table 2.5.5-57, Table 2.5.5-58, Table 2.5.5-59, and Table 2.5.5-60). 2.5.5.8.4 Species responses to OMR Flow Management Note that supplemental analysis based on PA revisions received June 14, 2019 (Appendix A3) is provided in Section 2. 5.5.11 The following discussion addresses the potential responses oflisted salmonids and sDPS green sturgeon to the proposed OMR flow management plan. As previously stated, increasing exports increases the probability of fish entrainment into the fish salvage facihties through alterations in the near- and far-field hydrodynamics of the south Delta. Measuring OMR flows is a proxy for determining the influence of exports and Vernalis inflow on the local hydrodynamic field surrounding the export facilities in the south Delta waterways. 2.5.5.8.4.1 Onset of OMR Flow Management The OMR flow management PA (April 30, 20 19; Appendix A2) component requires several assumptions to be made for its implementation. The foiJowing assumptions are made regarding the implementation of this PA component: • • The Delta monitoring group assesses the percentage of population present in the Delta in a manner similar to the current DOSS group. Similar or better information is available to the Delta monitoring group. 397 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.4.1.1 Integrated Early Water Pulse Protection (First Flush) Turbidity Event Although this PA component is specifically designed to protect Delta smelt during their upstream movements prior to spawning, it may provide protective benefits to emigrating juvenile salmonids. This PA component will be implemented following a "First Flush" event in the Delta that is triggered when there are flows greater than 25,000 cfs on the Sacramento River, as measured at Freeport on a 3-day running average coupled with a 3-day running daily average turbidity of 50 NTU at Freeport during the period ofDecember 1 through January 31. The PA component may only occur once during this period. If the required conditions exist, Reclamation and DWR will reduce exports for 14 consecutive days to achieve an OMR index flow that will be no more negative than -2,000 cfs 15 over the 14-day averaged flow. The reduced export environment will be beneficial to any listed salmonids or sDPS green sturgeon in the vicinity of the export facilities that could encounter near-field or far-field effects of the exports. A more positive OMR would be expected to change the local hydrodynamics resulting in reduced entrainment into the facilities, and reduced alterations to the routing of migrating fish into the south delta region from the north. As previously stated in this document, during the period of the "First Flush" PA component from December 1 through January 31, juvenile winter-run Chinook salmon and yearling CV springrun Chinook salmon would be expected to initiate their emigration into the Delta when precipitation events in the upper Sacramento River watershed cause flows in the main stem to increase substantially. Flows in excess of approximately 14,000 cfs on the Sacramento River (as measured at Wilkins Slough) have been shown to be an indication that emigration ofjuvenile winter-run Chinook salmon will occur (del Rosario et al. 2013). Similarly, increases in flows in Sacramento River tributaries such as Deer Creek and Mill Creek over 95 cfs have been correlated with emigration of yearling CV spring-run Chinook salmon juveniles from those watersheds. The triggers described for the "First Flush" protective P A component would also indicate that environmental conditions are present that would stimulate emigration of listed salmonids (winter-run Chinook salmon and yearling CV spring-run Chinook salmon) into the Delta. The amount of overlap between the initiation of salmonid emigration and the "First Flush" PA component would depend upon the timing of storm events and flows in the Sacramento River. If the first major storm event of the winter rainy season occurred during the December through January implementation period, and produced the appropriate flow and turbidity conditions to trigger the "First Flush" PA component, then there would be a high level of overlap between winter-run Chinook salmon and yearling CV spring-run Chinook salmon emigration and the protective PA component. On the other hand, if smaller storms came through earlier in the season that did not create the conditions necessary to trigger the "First Flush" PA component, but were sufficient to raise Sacramento River flows over 14,000 cfs at Wilkins Slough, then the expectation is that salmonid emigration will have already started and the overlap with the "First Flush" PA component will not occur to the same extent if conditions eventually occur later in the season that trigger the action. It is also possible that the conditions to initiate the "First Flush" will not occur in a given year, and thus there is no protective P A component taken and no benefits to listed salmonids of the reduced exports. 15 At a May 21 , 2019, consultation meeting on the Delta, Reclamation con:f"trmed the OMR limit during a " First F lush" event should be -2,000 cfs. 398 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.4.1.2 Salmonid Onset Triiggers Reclamation and DWR proposed that OMR flows will be no more negative than -5,000 cfs after January 1 if more than 5 percent of any one or more unclipped listed salmonid species (winterrun Chinook salmon, CV spring-run Chinook salmon, CCV steelhead) are estimated to be present in the Delta as determined by "real-time" monitoring data and the advice of a Deltaspecific working group. The PA component incorporates a percentage of listed salmonid population in the Delta metric to initiate OMR management and that management of OMR flows cannot start any earlier than January 1. It is possible under this new metric that management of OMR flow levels may not start on January 1, if none of the listed salmonid species has at least 5 percent of the population in the Delta by January 1. Ifthis condition exists, these listed fish in the Delta would not hav,e any of the protections afforded by an OMR management action that maintains flows at no more negative than -5,000 cfs. The Salmonid Scoping Team was asked to evaluate the effectiveness of the OMR onset criteria in the NMFS 2009 CVP/SWP Operations opinion whicln is reflected in the COS scenario. Since January 1 plays a role in both the COS and the PA, NMFS considers tlhat evaluation relevant for understanding the potential effects of the PA on salmonids and reviews those results here. The Salmonid Scoping Team (20 17b) concluded that the "January I onset ofOMR reverse flow management coincides with the presence of protected salmonids in the Delta in almost all years, but an earlier onset would often be more effective for some listed salmonids. The January 1 trigger date provides a general approximation of a date by which juvenile winter-run Chinook have hkely entered the Delta and, based on its simplicity for triggering management actions, has utility." Furthermore, the Salmonid Scoping Team (2017b) reported that "while initiating OMR flow restrictions on January I each year provided protection, initiating the restrictions prior to January 1 would have provided better protection for winter-nm Chinook salmon. This is because these fish were detected prior to January I in the Delta in all but one year from 1995 to 2015." The Salmon Scoping Team concluded that "in most years, improved protection of Sacramento River salmonid populations from export effects would be provided if the onset date ofOMR reverse flow management were triggered by detection of migrants at monitoring stations located on the Sacramento River upstream of distributary junctions leading toward the San Joaquin River." Based on the historical record, winter-run Chinook salmon are the listed salmonid species most likely to be in the Delta on January 1 with more than 5 percent of its brood year population present. Using the information from the retrospective compilation of data from Sacramento trawls at Sherwood Harbor, the average date by which 5 percent of the population passes Sherwood Harbor (site of the Sacramento trawls) is December 17 (median date December 11). On average, 25 percent of the winter-run population is in the Delta by January 9 (median date December 29) which indicates that for the endangered w inter-run Chinook salmon population, approximately 20-25 percent of the population is already in the Delta prior to any protective OMR flow management actions being implemented on January 1 (Table 2.5.5-1 1). The timing of CV spring-run Chinook salmon and CCV steelhead emigrations indicate that these populations do not enter the Delta (based on the Sacramento trawl data) until the end of January and into early February (Table 2.5.5-12 and Table 2.5.5-13). OMR flow management actions are not taken for any life stage of sDPS green sturgeon, as they are assumed to be present in the Delta year-round. Real time estimates of listed salmonid presence in the Delta by the DOSS working group only includes natural juvenile winter-run Chinook salmon and CV spring-run Chinook salmon. The DOSS working group currently does not make any estimates of the distribution of 399 Biological Opinion for the Long-Term Operation of the CVP and SWP the wild juvenile CCV steelhead population, given the difficulty of monitoring for this species. Juvenile CCV steelhead are difficult to capture in the trawls and RSTs used in the Central Valley monitoring programs as they can easily avoid them, thus making any assessment to population distribution uncertain. The proposed onset of OMR based on salmonid triggers, for the most part, would not often be different than current operations under the COS conditions, with OMR flow management restrictions likely starting on January 1 except in the driest of years when juvenile migration occurs after January 1. Listed salmonids entering the Delta prior to January 1 would not have any protection from elevated exports, and may be exposed to OMR flows more negative than -5,000 cfs unless first flush conditions have triggered an OMR action that targets protecting Delta Smelt In those infrequent years when emigration of winter-run Chinook salmon is delayed by upstream flow conditions, the entry of the bulk of the juvenile winter-run Chinook salmon population into the Delta would be delayed until precipitation events create the right conditions to stimulate emigration. However, a proportion of the winter-run Chinook salmon population (and likely yearling spring-run Chinook salmon too) would continll!e to trickle into the Delta in low numbers under these low flow conditions prior to the main migration movement. This would place up to 5 percent of early migrants at risk of entrainment or having their migratory routes altered as discussed previously for export impacts in this document. This would potentially decrease the diversity of the life history strategies of the Chinook salmon and steelhead populations by not protecting these early emigrants to the Delta, and exposing them to high export conditions with more negative OMR flows. 2.5.5.8.4.2 End of OMR Flow Management Reclamation and DWR proposed to end OMR flow management actions on June 30 at the latest, or when both of the following conditions are met, whichever is earlier: • • For Delta smelt protection, the condition for endling OMR flow management is when the mean water temperature in CCF reaches 25°C (77°F) for 3 consecutive days. For listed salmonid protections, the conditions for ending OMR flow management is when 95 percent of the listed population has migrated past Chipps Island as determined by the Delta monitoring work group, or, the daily average water temperature at Mossdale has exceeded 72°F (22.2°C) for 7 days during June. The water temperature days in June do not need to be consecutive. In most years, the conditions for Delta smelt are likely to be the limiting factor, as water temperatures of 25°C (77°F) for 3 consecutive days in CCF typically occurs after water temperatures at Mossdale exceed 72°F and both conditions must be met to end OMR flow management. The criteria requiring 95 percent of a given listed salmonid population to have migrated past Chipps Island before ending the OMR flow management actions will typically be driven by the distribution of CV spring-run Chinook salmon, based on Chipps Island monitoring. Typically, at least 95 percent of winter-run Chinook salmon and CV spring-run Chinook salmon have left the Delta prior to the beginning of June (Figure 2.5.5-19 and Figure 2.5.5-20). On average, the date of all winter-run Chinook salmon passing Chipps Island is April 28. The average date for 95 percent of the annual CV spring-run Chinook salmon brood year passing Chipps Island is May 8. For CCV steelhead, the average date by which 95 percent of the annual population has past Chipps Island is April 28, based on information from the SacPas website 400 Biological Opinion for the Long-Term Operation of the CVP and SWP (www.cbr.washington.edu/sacramento/). These dates are derived from retrospective analysis of the Chipps Island trawl data. While the current DOSS working group does make estimates of CV spring-run Chinook salmon distribution in the Delta, DOSS does note that those estimates are very uncertain once hatchery fall-run Chinook salmon are present in tlhe system. Since most monitoring locations use length-at-date criteria to assign fish to run, and many of the unmarked 75 percent of the hatchery releases may fall into the CV spring-run Chinook salmon size class, it becomes more difficult to interpret the data on spring-run-sized fish. Since the current DOSS working group does not make any assessments of CCV steelhead distribution in the Delta, there is no existing information to use for how the group will assess late season steelhead distribution and w!hether it will track with the data in the website in real time. The current management of OMR flows, with the cap on OMR flows not being more negative than -5,000 cfs during the salmonid migratory period, continues through June 15, with an offi·amp if there are 7 consecutive days of water temperatures exceeding 72°F (22°C) after June 1). This restriction on OMR flows was designed in part to protect late emigrating salmonids, particularly CCV steelhead from the San Joaquin River basin that typically migrate out of the system in April and May. The Chipps Island trawl data for CCV steelhead are heavily biased by the much larger population of CCV steelhead originating in the Sacramento River basin. Thus, the earlier date of April 28 for the time when 95 percent of the current year's juvenile CCV steelhead population having passed Chipps Island is skewed by the differences in the Sacramento and San Joaquin river basins CCV steelhead populations. The date reflects the dominate size of the Sacramento River basin population and its migratory patterns, and not necessarily the migratory behavior of the smaller San Joaquin River basin steelhead population. Therefore, the proposed end ofOMR management poses a greater risk to San Joaquin River CCV steelhead than the current management of OMR flows under the COS if CCF temperatures are not controlling. There is the potential to end OMR flow management prior to the completion ofthe San Joaquin River basin's steelhead outmigration, and place these fish at greater risk of entrainment at the export facilities or alterations of their migratory routing, leading to increased transit times and distance, resulting in reduced survival. 2.5.5.8.4.3 Additional Real-time OMR Management Actions 2.5.5.8.4.3.1 Turbidity Bridge Avoidance Reclamation and DWR propose to implement PA components designed to avoid creating a turbidity bridge between the main stem of the San Joaquin River to the north, and the export facilities to the south to protect adult Delta smelt that may be present iin the main stem ofthe San Joaquin River from moving southwards towards the export facilities. This PA component will be implemented after the completion ofthe integrated early winter pulse protection action (First Flush) or by February 1, whichever comes first. Exports will be managed to maintain a daily turbidity average at the Old River at Bacon Island (OBI) monitoring site at a level less than 12 NTU. If turbidity does not exceed 12 NTU, there is no explicit OMR hmits for protecting Delta smelt. If daily turbidity levels exceed 12 NTU, the 3-day average OMR index values will not be more negative than -2,000 cfs until the 3-day average twrbidity at OBI falls below the 12 NTU threshold. This PA component will be implemented from February 1 to March 31, even ifthe first flush action has not occurred earlier in the year. This PA component will not be required on or after April 1. 401 Biological Opinion for the Long-Term Operation of the CVP and SWP This P A component has the potential to be beneficial to listed salmonids or sDPS green sturgeon if the turbidity criteria are exceeded and the OMR flows are capped at being no more negative than -2,000 cfs during the turbidity bridge event. However, if the turbidity criteria for protecting Delta smelt has not been met and if the criteria for protecting salmonids during this period has not occurred (i.e., more than 5 percent of any listed salmonid population is in the Delta after January 1), then any listed salmonids or sDPS green sturgeon present in the Delta would be vulnerable to the effects of the elevated exports allowed! under this proposal, since there are no explicit OMR limits required for protecting Delta smelt. However, it would be unlikely that there would not be at least one population of listed salmonids that would have at least 5 percent of their population in the Delta at this time (likely winter-run Chinook salmon) and, thus, there would already be the requirement that OMR flows be no more negative than -5,000 cfs to protect listed salmonids from the effects ofhigh exports. 2.5.5.8.4.3.2 Larval and Juvenile Delta Smelt Protections Reclamation and DWR propose to protect larval and juvenile Delta smelt be changing operations when the flows in the western Delta, as measured by Q-West, are negative, and real-time Delta smelt monitoring indicates that Delta smelt larvae and juveniles are wjthin the entrainment zone of the export pumps. The PA component will depend on hydrodynamic modelling that will estimate the percentage of the larval and juvenile smelt population that are at risk of entrainment, and operate to avoid a loss of no greater than 10 percent of the population. The description of the PA component does not explain what actions will be taken, or to what degree exports will be modified, so our assessment of impacts on listed salmonids is qualitative. Reductions in export pumping are typically beneficial to listed salmonids and sDPS green sturgeon and reduce the risk of entrainment and the alterations in routing and transit times associated with the effects of exports on local hydrodynamic conditions. During the period that actions would be taken to protect larval and juvenile Delta smelt (mid-March through June), actions to protect listed salmonids would most likely already be restricting the OMR flows to no more negative than -5,000 cfs. 2.5.5.8.4.3.3 Natural CCV Steelhead Protection Reclamation and DWR propose under the PA (April30, 2019; Appendix A2) to protect CCV steelhead by operating to an OMR flow of -2,500 cfs for 5 days whenever more than 5 percent of the annual population of CCV steelhead is determined to be in the Delta by the Delta specific working group and that the daily cumulative loss of natural (unclipped) steelhead at the CVP and SWP fish salvage facilities exceeds 10 fish per a thousand acre feet of water exported (10 fish!TAF. Reclamation and DWR intend for this PA component to protect San Joaquin River basin steelhead, but acknowledge that it is not feasible to discern which basin the observed CCV steelhead in salvage are coming from. This PA component will end on May 31 of each season. Currently there is no assessment of when 5 percent of the population has entered the Delta, and no assessment of the size of the steelhead cohort each year to base it on. It is unclear how any new Delta specific working group will do this assessment due to the difficulty of monitoring for steelhead and their ability to avoid most monitoring gear. Furthermore, most CCV steelhead salvaged at the CVP and SWP fish salvage facilities are believed to be from the Sacramento River basin due to the greater population size originating in that basin. The San Joaquin River 402 Biological Opinion for the Long-Term Operation of the CVP and SWP basin is believed to have a substantially smaller population size that would be overwhelmed by the signal generated by Sacramento River basin fish in salvage. The disparity in population sizes is just one factor making detection, and therefore protection of San Joaquin River basin fish difficult with this PA component. Another factor is the apparent differences in out migration timing. Sacramento River basin fish tend to emigrate earlier in the season than do San Joaquin River basin fish. Most Sacramento River basin CCV stee1head emigrate earlier in the season as indicated by the Sacramento trawl data (February and March, Figure 2.5.5-22) compared to the April and May period for the San Joaquin River basin population, and are likely the majority of CCV steelhead that are salvaged by the end of April (90 percent of salvage by May 1; Table 2.5.5-19). It is unlikely that the size ofthe San Joaquin River basin CCV steelhead population would be sufficient to trigger the 10 steelhead/TAF threshold that Reclamation and DWR are proposing. NMFS expects that in most instances when the loss density of natural CCV steelhead has exceeded the I 0 fish/TAF threshold that these fish belonged to the Sacramento River basin population and not to the San Joaquin River basin population. Currently export reductions are taken at two different levels of steelhead loss density; 8 fish/TAF and 12 fish/TAF. If the first level is exceeded, OMR is held at no more negative than -3,500 cfs for a minimum of 5 days. If the second level is exceeded, than OMR is held at no more negative than -2,500 cfs for a minimum of 5 days. Furthermore, NMFS assessed the frequency of steelhead loss density trigger exceedances since water year 2010 (the year that the RPA actions from the NMFS2009 Opinon were first implemented) and found that incorporation of the proposed loss density trigger would reduce the implementation of OMR protective actions, based on steelhead loss density triggers, by 26 percent over all of the years in the period (2010-2018) and 46 percent in the years in which loss density triggers were actually exceeded (Table 2.5.5-23). In contrast, OMR flows in April and May are approximately 4,000 cfs more positive under the COS than the PAin wetter years. In drier years (below normal and dry water year types) the differences between the PA and COS were less, but were still approximately 1,500 cfs more positive under the COS conditions as compared to the P A conditions. In critical water year types, the COS was modelled to be 600-800 cfs more positive than the PA conditions. Seldom during the April and May period are modelled OMR flows predicted to be more positive/less negative under the P A than under the COS conditions, and positive OMR flow values occur in April and May less frequently under the PA (<10 percent ofyears) compared to the COS (approximately 50 percent ofyears). During June, the PAis modelled as being more negative by 1,000 to 1,600 cfs in drier water year types (below normal, dry, and critical). Therefore, The COS is more protective of San Joaquin River basin CCV steelhead due to lower exports and more positive OMR flows than the proposed CCV steelhead loss density trigger. Under the PA, not only are OMR flows in April and May considerably more negative, but reductions in OMR flows (typically linked to reductions in exports) due to CCV steelhead loss density trigger exceedances will be less frequent. Thus, the loss density trigger proposed by Reclamation and DWR is considerably less protective of CCV steelhead in general and particularly for the populations originating in the San Joaquin River basin. The triggers will be dominated by CCV steelhead from the Sacramento River basin and typically occur earlier in the season when these fish are present in the Delta system. The higher threshold for the loss density trigger means that the implementation of the OMR protective actions will only occur about half as frequently (54 percent) as compared to the current protective actions implemented in the COS conditions. A fmal exacerbation of the risk to 403 Biological Opinion for the Long-Term Operation of the CVP and SWP San Joaquin River CCV steelhead is the proposed elimination of the installation of the HOR barrier in the spring. This allows a greater opportunity for CCV steelhead from the San Joaquin River basin to migrate downstream through the Old River route and be exposed to the agricultural barriers as well as the export facilities with their associated reductions of survival, typically associated with migratory delays and increased predator exposure. Since it is unlikely that any reductions in exports will occur due to the proposed loss density trigger for CCV steelhead, exports are likely to continue at a rate that manages to an OMR of no more negative than -5,000 cfs during the spring. It is unlikely that at the export rates typical of this OMR level, that any fish arriving at the export facilities via Old River will escape the influence of the exports, and will be ,entrained into the fish salvage facilities. Its survival is then linked to the efficiency of the fish salvage operations and the predator field in front of the fish salvage facilities. 2.5.5.8.4.3.4 Salvage or Loss Thresholds Reclamation and DWR propose under the PA (April 30, 2019; Appendix A2) to set annual cumulative loss or salvage thresholds to modify export operations rather than the current real time actions under the COS related to the NMFS 2009 Opinion RP A actions (National Marine Fisheries Service 2009b). The PA component sets the winter-run Chinook salmon threshold as equal il:o loss of 1 percent of the annual winter-run JPE for unclipped (natural) fish (genetically confirmed) or 2 percent of the JPE if length-at-date (LAD) identification is used. For unclipped CV spring-run Chinook salmon, a threshold of 1 percent loss of an annual spring-run JPE (or a loss threshold of 0.5 percent of the yearling CV spring-run Chinook salmon surrogate releases -late fall-run Chinook salmon from Coleman National Fish Hatchery) is proposed. NMFS assumes that the proposal would use the current methodology for calculating salvage and loss, based on expansion of observed salvaged fish and using the current loss multipliers. A threshold of 3,000 unclipped juvenile CCV steelhead in salvage is proposed for the PA. For green sturgeon, an annual salvage threshold of 100 fish is proposed. Reclamation and DWR intend to operate to -5000 cfs OMR flows until the annual cumulative loss or salvage reaches 50 percent of any of the threshold limits for a given species, at which point it will reduce exports and manage to an OMR limit of no more than -3,500 cfs on a 14-day moving average. If cumulative annual loss or salvage exceeds 75 percent of any annual threshold limii.t for a given species, then exports will be reduced to achieve an OMR flow of no more negative than -2,500 cfs on a 14-day movmg average. There are several factors which make this proposal difficult or unworkable. First, there is no CV spring-run Chinook salmon JPE currently calculated that could serve as the basis for the proposed limit, so presumably the threshold based on the yearling CV spring-run Chinook salmon surrogate releases would be implemented until a CV spring-run Chinook salmon JPE has been developed that would meet the objectives of this proposal. Secondly, based on historical salvage and loss data from the SWP and CVP facilities, it is unlikely that the 50 percent and 75 percent triggers would ever be exceeded. For unclipped winter-run Chinook salmon, the proposed 50 percent exceedance threshold (1 percent of JPE using LAD criteria) occurred six times since 1992, but only twice since the implementation of the COS starting with brood year 2009. These most recent events occurred in 2 years when the JPE was very low compared to other years (Table 2.5.5-25). There are no proposed loss threshold triggers for hatchery produced winter-run Chinook salmon. This leaves hatchery winter-run Chinook salmon vulnerable to 404 Biological Opinion for the Long-Term Operation of the CVP and SWP excessive entrainment. There is no CV spring-run Chinook salmon JPE, as previously mentioned, so there is no historical reference of proportional take to guide the impacts of the implementation of the proposed limit. In regards to the proposed limits for unclipped CCV steelhead, the historical record for unclipped steelhead s ince 1998 when all hatchery-produced CCV steelhead began to be adipose fm-clipped, the annual salvage of unclipped CCV steelhead exceeded 1,500 fish seven times. However since brood year 2009 when the COS was implemented, the trigger threshold has not been exceeded (Table 2.5.5-37). Since 2000, the annual salvage of sDPS green sturgeon has been less than 100 fish in any given year except for 2006, when 363 green sturgeon were salvaged. In recent years since 2010, only twice have sDPS green sturgeon been salvaged, and both times it was for a total of 4 fish annually, substantially below the 50 percent threshold of 50 fish required to initiate any export reductions to manage OMR flows. Based on the above information, it is unlikely that the thresholds proposed by Reclamation and DWR will be exceeded, except on rare occasion. Thus, reductions in exports and changes to make OMR more positive are unlikely to occur and the OMR flows will stay at -5000 cfs for the entire period of implementation of OMR flow management (January 1 through late spring). This is considerably less protective than the current COS conditions which provide substantial export reductions in the April and May periods to protect San Joaquin River basin CCV steelhead. Furthermore, the proposed OMR flow management actions do not include real-time reductions based on daily trigger thresholds in the NMFS 2009 Opinion for RPA Action IV.2.3 (National Marine Fisheries Service 2009b). This places an additional risk on listed fish populations that are already experiencing difficult conditions in the Delta and have low overall population viability. 2.5.5.8.4.4 Storm-Related OMR Flexibility Reclamation and DWR are also proposing to incorporate storm-related flexibility in OMR flow management by proposing combined exports to increase up to potentially full capacity (14,900 cfs) to capture any excess water in the Delta system that is available through storm-related increases in river inflows and export that water south of the Delta. The full description of the PA component is provided in Section 2.5.5.8.2 "OMR Flow Management." Storm-related increases in exports will not be allowed if any of the previous additional real-time OMR restrictions already discussed are triggered, and in that case, Reclamation would operate in accordance with those additional real-time OMR restrictions and would not cause OMR to be more negative for capturing peak flows from storm-related events. The PA component also includes measures to off ramp from the storm flex exports if natural winter-run Chinook salmon are entrained and their calculated loss exceeds the percentages of cumulative loss thresholds tied to the annual JPE provided in Section 2.5.5.8.2. These percentages increase with the progression into the winter-run Chinook salmon migratory season and extend through the end of the OMR flow management period. The Salmonid Scoping Team (Management Question #3 in Volume 2, 2017b) summarized the conceptual model for export-related effects on salmonids as follows: "Export effects that incrementally increase the routing ofjuvenile salmonids (either from the Sacramento River orfrom the San Joaquin River) into the Interior Delta will incrementally reduce overall survival .. .In addition to the predicted effects ofexport on 405 Biological Opinion for the Long-Term Operation of the CVP and SWP routing, the conceptual model predicts that OMR reverse flow management will decrease mortality by increasing the probability that juveniles that enter the South Delta (San Joaquin River mainstem and channels to the south and west ofthe San Joaquin River mainstem) will successfully migrate out of the South Delta to Chipps Island. Mechanisms by which this might occur include: 1) reducing entrainment at the export facilities ... ; 2) reducing confusing navigational cues caused by OMR reverse flow; and 3) increasing the duration and magnitude ofebb tide flows and velocities, relative to flood tides, which is expected to reduce the residence time ofjuveniles in the South Delta and, therefore, reduce exposure time to agents ofmortality. " Key conclusions in the SST report were: • • • • For junctions on both the Sacramento River and San Joaquin River," ... a -5,000 cfs OMR reverse flow limit provides protection compared to more negative OMR reverse flow levels that would exert a larger influence on flow routing at distributary junctions and, thus, on juvenile routing and survival." However, the SST "did not conclude at what precise level of OMR flow more negative than -5,000 cfs exports would begin to affect distributary flows, juvenile routing, and survival", and also noted some technical disagreement on this point. Within the interior channels of the South Delta," .. .the -5,000 cfs OMR flow is predicted to be less effective at preventing or minimizing export effects on juvenile routing at junctions and residence times within the interior channels of the South Delta than in the mainstems of the Sacramento River and San Joaquin River...because the export-driven influence on hydrodynamic conditions at a given OMR flow level increase with proximity to the export facilities. The SST noted that there is "inadequate empirical evidence from fish tracking studies to more precisely evaluate junction-specific relationship between distributary flow changes and changes in fish routing and survival. As a results there is uncertainty in relating specific OMR reverse flow thresholds to overall through-Delta survival. The SST concluded that " . .. route selection is generally proportional to the flow split at channel junctions, and the effect of exports on route selection is strongest at the junction leading directly to the export facilities (i.e., Head of Old River)." We can evaluate some ofthe conceptual model mechanisms described above based on modeling provided in the ROC on LTO BA. The salvage density modeling shows that salvage and associated loss increases with exports during months when listed salmonids are present in the Delta. Therefore, if fish are present in the vicinity of the export facilities in the south Delta during a time that storm flex export operations are implemented, NMFS concludes there will be an increase in the number offish entrained into the salvage facilities above that which would have been seen with no increases in exports. Furthermore, since listed salmonids tend to start migrating downstream in response to elevated flows in the Sacramento River basin and San Joaquin River basin waterways, there is a high probability that more fish will be present in the Delta exactly when the CVP and S WP increase their exports. Besides the fish entering the Delta on the elevated storm flows, listed salmonids (especially winter-run Chinook salmon) may already be present in the Delta due to migration earlier in the year. This overlap in fish presence and the potential for combined exports to reach 14,900 cfs can result in increased entrainment 406 Biological Opinion for the Long-Term Operation of the CVP and SWP risk as a result of the potentially very negative OMR flows. Reclamation has committed to a risk assessment before implementing a storm flex export operation which could limit risks. The Salmonid Scoping Team (2017a) concluded that" ... roU!te selection is generally proportional to the flow split at channel junctions, and the effect of exports on route selection is strongest at the junction leading directly to the export facilities (i.e., Head of Old River)." Any fish that originates in the San Joaquin River basin will be at a high risk of entrainment due to the routing of fish through Old River from the HOR. The fish that stay within the main stem San Joaquin River channel at the Head of Old River may enter the interior Delta at other junctions and be exposed to the increased foot print of the altered hydrodynamics created by the high level of exports in the channels leading to the pumps. Triggers based on loss density for unclipped steelhead are less likely to happen under the high export condition as greater volumes of water are present to be diverted, compared to the number of fish present to he entrained in the surrounding waterways. The hydraulic conditions created by the high export rates have a high probability of creating more adverse conditions in the south Delta waterways than are currently observed for migrating fish. The severity will depend on which basin has the high storm flows and to what extent the exports are increased. Assuming the worst case scenario, combined exports of 14,900 cfs, with flows originating only in the Sacramento River basin, the footprint of the export effects will encompass much of the south and central Delta up to and including the main stem San Joaquin River downstream to at least Jersey Point. If the storms are present only in the Sacramento River basin and river flows are increased only for that basin, then elevated exports will exaggerate the effects of OMR as water is predominately coming from the north across the Delta to supply the high exports. Low flows in the San Joaquin River basin at the same time would exacerbate this condition, as they would not offset the source of export water being diverted by the pumps. Conversely, if storms are centered over the San Joaquin River basin and high delta inflows are confined to the main stem of the San Joaquin River, the high export rates will pull in mostly water from this source. Flow through Old River via the HOR will offset the effects of exports on OMR flows to some extent, depending on the magnitude of combined exports, and the volume of flow coming through the HOR. Because there is less unregulated flow in the San Joaquin River compared to the Sacramento River, "storm" events that trigger an OMR storm flex are more likely to be dominated by Sacramento River flow. 2.5.5.8.5 South Delta Export Facilities 2.5.5.8.5.1 Minimum Export Rate Reclamation and DWR propose to have a minimum combined export rate of 1,500 cfs for human health and safety. This level of exports would meet the minimum level of water supplies obligated to senior water rights holders and minimum deliveries to wildlife refuges. This low level of exports is not expected to substantially impact OMR flows or alter hydrodynamics in the South Delta except under the very lowest of river inflow conditions. At an export level of 1,500 cfs however, the efficiency of the louvers that make up the primary fish screens at both the SWP and CVP decreases, and more fish that encounter the louvers are lost to the system through the louvers, or fail to enter the bypasses that lead to the secondary screens and the holding tanks. This risk is reduced by the reduction in the effects of the export pumping in the near-field and far-field areas ofthe south Delta adjacent to the location of the CVP and SWP. Reduced exports 407 Biological Opinion for the Long-Term Operation of the CVP and SWP of 1,500 cfs are expected to produce more positive OMR flows and reduce the extent of the export's zone of influence in channels leading towards the pumps. 2.5.5.8.5.2 Tracy Fish Facility Improvements 2.5.5.8.5.2.1 Predator Removal (C02 injection) A number of conservation measures are proposed to improve salvage efficiency at the Tracy Fish Collection Facility (TFCF), including installing a carbon dioxide (C02) injection device to allow remote controlled anesthetization of predators in the secondary channels of the TFCF by elevating the dissolved C02 concentration in the secondary channels. These PA components could potentially benefit juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sOPS green sturgeon through greater salvage efficiency and reduced mortality related to predation. 2.5.5.8.5.2.1.1 Deconstruction of the Action Reclamation proposes to construct a C02 injection device within the secondary channel of the TFCF. The device will diffuse C02 gas into the water column of water moving into the secondary channel when removal of predators is warranted. The device has not been explicitly described in the BA. but is likely to consist of a manifold with diffuser pipes through which C02 gas is diffused into the water column of the secondary channel. Construction of such a device will require that the secondary channels be dewatered for periods of time to install the infrastructure. Construction of the device will occur during the August through October in-water construction period. Operations of the device will, at a minimum, occur during the period in which listed salmonids and sOPS green sturgeon are present, and may occur year-round. 2.5.5.8.5.2.1.2 Exposure of Listed Salmonids to Construction During construction of the C02 injection system, winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead are not expected to be exposed to the effects of construction, based on the timing of in-water construction (August-October) and the typical seasonal occurrence and salvage timing in the Delta of listed salmonids. Although the construction window avoids the majority of the juvenile salmonid migration period in the Delta, a few migrating juvenile salmonids could still occur during the in-water work window. To minimize or avoid adverse effects to these few fish due to construction activities, Reclamation proposes to minimize risk by incorporating the appropriate avoidance and minimization measmes (AMMs) (Reclamation [2019], Appendix E, Avoidance and Minimization Measures) into the construction protocol. 2.5.5.8.5.2.1.3 Exposure of sDPS Green Sturgeon to Construction Juvenile sOPS green sturgeon can occur in the Delta year-round and, therefore, have the potential to be exposed to the effects of construction of the C02 injection device proposed for the TFCF improvements. If construction impacts the efficiency of green sturgeon salvage, there could be a minor effect to a small number of individual fish, although risk would be minimized through the incorporation of appropriate AMMs. As with other proposed construction in the Delta under the PA, the timing of early out-migrating adult sDPS green sturgeon occurrence in the Delta could overlap with C02 injection device construction as part of TFCF improvements. 408 Biological Opinion for the Long-Term Operation of the CVP and SWP Application of AMMs and the small scale of the in-water construction would minimize the potential for any effects to individual adult sDPS green sturgeon. 2.5.5.8.5.2. t.4 Risk to Listed Salmonids during Construction The risk to listed salmonids should be minimal as the construction of the COz injector occurs during the in-water work window of August through October when listed salmonids are least likely to be present. Incorporation of the AMMs will further reduce the potential of any risk to listed salmonids. Furthermore, installation of the injector will occur in the dewatered secondary channel. The secondary is typically dewatered to work on the secondary travelling screens or to remove predators, and flushes all fish in the secondary channel into the holding tanks where they are held until release. During any dewatering of the secondary channel, salvage operations are suspended, and any listed salmonid present may pass through the primary louvers into the intake channel leading to the export pumps where it is lost to the system. 2.5.5.8.5.2.1.5 Risk to sDPS Green Sturgeon during Construction The risk to sDPS green sturgeon is considered to be low. Although green sturgeon are present year-round in the Delta, the incorporation of the AMMs will further reduce the risk of exposure to construction effects. As described for the listed salmonids, the secondary channel will be dewatered, and any sDPS green sturgeon present will be flushed into one of the holding tanks for future release. There is the potential that during the period that the secondary channel is dewatered and salvage operations are halted, that any individual sDPS green sturgeon present in the primary channel may pass through the primary louvers into the intake channel and be lost to the system. This is considered unlikely as the probability of any sDPS green sturgeon being present in the primary at the time of dewatering is low, given their rarity in salvage at any time. 2.5.5.8.5.2.1.6 Exposure of Listed Salmonids and sDPS Green Sturgeon during Operations The COz injection system is intended to be used to remove predators during the periods of the year when listed salmonids are present in salvage. Therefore, winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead have the potential to be present during the use of the injector system during predator removals. Any listed salmonid present in the secondary channel at the time of the predator removal will be exposed to the effects of the elevated dissolved COz concentrations in the water of the secondlary channels. 2.5.5.8.5.2.1.7 Risk to Listed Salmonids and sDPS Green Sturgeon during Operations Once installed, Reclamation proposes to use the COz injection device to clear predators from the secondary channel on a regular basis. Reducing the predator density within the secondary channels will enhance survival through the TFCF by reducing predation on listed salmonids and sDPS green sturgeon passing through the secondary channel to the holding tanks. Predator removal targets those predators that are present in the secondary channel and bypass system, many ofwhich are resident or semi-resident within the system. Removal of these predators reduces the standing population of predators within the TFCF. During a predator clean out of the secondary channel, water is directed into the holding tank used for salvage counts while the COz is injected into the secondary channel. Predators that are anesthetized by the COz are drawn into the holding tanks by the water fl ow where they can be removed from the system during regular salvage counts and potentially relocated to waters outside of the Delta (e.g., Delta Mendota 409 Biological Opinion for the Long-Term Operation of the CVP and SWP Canal, Bethany Reservoir). Listed salmonids may be exposed to the effects of the increased dissolved C02 (hypercapnia) during predator removals and also become anesthetized. A proportion of these fish, due to their smaller size, may dlie due to the effects of the increased C02 levels in their blood stream. However, the reduction in predation loss within the TFCF resulting in greater salvage efficiency and higher overall survival will offset the number of fish lost through the exposure to the elevated C02 concentrations in the secondary channels during a predator clean out. 2.5.5.8.5.2.2 Tracy Fish Collection Facility Release Sites Improvements In addition to incorporating the C02 injection system into the secondary channels to reduce predator density, Reclamation is also proposing to modify its procedure for releasing salvaged fish back into the Delta. Currently, Reclamation manages two release sites in the Delta, one on the Sacramento River near Horseshoe Bend, and the other on the San Joaquin River immediately upstream of the Antioch Bridge. Reclamation is proposing to add additional release sites in the western Delta outside the influence of the export operations. Additional release sites, coupled with a rotating release schedule between sites, is believed to reduce the potential for predators to habituate to a given release site as a source of food. In theory, if the number of release sites is low, and the release of salvaged fish occurs frequently (up to several times a week per site) then predators will associate the release locations and the release site pipe as a source of food in the form of released fish from the salvage operations exiting from the end of the pipe, including listed salmonids. Although some loss will occur due to predation at the additional sites, the current belief is that the cumulative loss due to predation from all release sites should be reduced due to lower predator density at each release site. However, the lack of information regarding the locations of the alternative release sites, and the intended construction actions and their impacts do not permit a complete effects analysis to be done for this P A component, thus it w ill be considered as a programmatic consultation. 2.5.5.8.5.2.3 Tracy Fish Collection Facility Infrastructure Improvements Reclamation proposes to improve the infrastructure of the TFCF to reduce the loss of entrained fish by: (1) incorporating additional fish exclusion barrier technology into the primary fish removal barriers, (2) incorporating additional debris removal systems at each trash removal barrier, screen, and fish barrier, (3) Constructing additional channels to distribute the fish collection and debris removal among redundant paths through the facility, (4) Construct additional fish handling systems and holding tanks to improve system reliability; and (5) Incorporate remote operation into the design and construction of the facility. These physical infrastructure improvements are likely to enhance the overall efficiency of the salvage facility while ultimately reducing the level of loss of entrained fish. In particular, the construction of additional channels to distribute the fish collection and debris removal among several redundant pathways has the potential to reduce or eliminate the issue of open louver bays during the cleaning process, as is the case at the SDFPF with its multiple primary inlet channels that can be operated independently from each other. However, the lack of details and specificity of design and construction schedule do not allow for the analysis of project effects for this PA component. The scope of this PA component will likely require several years to complete infrastructure improvements and testing, and may require 410 Biological Opinion for the Long-Term Operation of the CVP and SWP numerous construction actions, all of which have not been described. Therefore, this PA component will be considered as a programmatic consultation. 2.5.5.8.5.3 Skinner Delta Fish Protection Facility Improvements The PA components associated with Skinner Delta Fish Protection Facility improvements involve predator control efforts and are intended to reduce predation on listed fish species following their entrainment into CCF. This improvement could benefit juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon entrained into CCF by reducing predation and pre-screen loss (mortality). DWR proposes to continue the implementation of projects to reduce mortality of listed salmonids and sDPS green sturgeon at the SWP facilities. These projects include studies to reduce the predation of listed fish in the CCF and operational changes that have the potential to benefit listed fish and reduce mortality. Specifically, DWR propose to continue studies regarding: (1) the electro-fishing of predatory fish and their relocation from CCF (the Predator Reduction Electrofishing Study [PRES]); (2) controlling aquatic weeds that provide habitat for predatory fish; (3) a predatory fish relocation study (PFRS) that uses commercial fishing techniques to capture predators and relocating them away from CCF; and (4) developing operational changes (i.e., preferential pumping through the Federal Jones Pumping Plant) that provide additional protection to listed fish when they are present. 2.5.5.8.5.3.1 Deconstruct the Action - Predator Reduction Electrofishing Study (PRES) DWR has already completed a 3-year study of the PRES, but is proposing to continue the study for an additional2 years (California Department of Water Resources 2018a). The PRES study will take place within CCF and will collect and relocate predatory fish in order to study the effects of the predator removal on survival of listed salmonids. The PRES will use three electrofishing boats that will be fished concurrently within CCF to capture target predatory fish species (striped bass [Morone saxatilis], largemouth bass [Micropterus salmoides], spotted bass [M punctulatus], channel catfish [Jctalurus punctatus], white catfish [Ameiurus. catus], black bullhead [A. melas], and brown bullhead [A. nebulosus]). These species (or other predatory species collected but not listed) will be re-located to Bethany Reservojr. The three electrofishing boats will make syst,ematic sweeps through CCF. The proposed fish collections will occur 4 days a week from January to June, as conditions allow. No collection will occur once temperatures in the CCF exceed °C. This schedule may be altered for safety reasons (weather or boating conditions), staffing, CCF hunting events or environmental conditions (presence of aquatic vegetation), or other unforeseen variables. If listed fish are incidentally collected during the electrofishing, crews will recover them, identify them, take and archive genetic tissue samples as permitted, and release the species back into CCF. 2.5.5.8.5.3.1.1 Exposure of Listed Fish to the PRES Listed fish are expected to be present within the CCF during the implementation of the PRES. From January to June, winter-run and CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon are expected to be present and potentially exposed to the effects ofthe electrofishing operations within the confines ofCCF. 411 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.5.3.1.2 Response of Listed Salmonids to the PRES Listed salmonids that are present in the vicinity of the electrofishing boats will be exposed to the electrical current within the water column when the boats are actively fishing. Since the boats are targeting larger fish species that would be capable of predating on juvenile Chinook salmon or CCV steelhead, less voltage is required to stun these fish. The greater length of the predatory fish creates a greater voltage gradient along the length of the fish, and thus less voltage is needed to anesthetize the fish in the electric field. However, larger fish such as sDPS green sturgeon, adult salmonids, or even larger CCV steelhead smolts may be susceptible to the electric field and become stunned. As evidence of this risk, the cumulative incidental take of Chinook salmon and steelhead from the previous 3 years of study is 152 Chinook salmon and 50 steelhead observed moving into the vicinity of the electrofishing boats in response to the electric field. The protocol for the electrofishing crews is to stop fishing if they observe salmonids entering the electric field of the boats, and move to another Eocation. All of the salmonids observed during the first 3 years of study immediately recovered when the electrofishing equipment was turned off. 2.5.5.8.5.3.1.3 Response of sDPS Green Sturgeon to the PRES As discussed above, larger fish are more susceptible to the effects of electrofishing due to their greater length and the larger voltage gradient across their body. During the previous 3 years of the PRES, no sDPS green sturgeon were reported in the incidental catch of listed fish. This could be due to several factors. sDPS green sturgeon are benthic oriented and prefer deeper waters to hold in. It is possible that the electric field used in the PRES did not reach deep enough into the water column to affect sDPS green sturgeon, or that the habitats that were sampled did not contain any sDPS green sturgeon to begin with. However, iflarger sDPS green sturgeon were exposed to the electric field, there is the potential for notochord injury due to the reflexive muscle contractions caused by the electric field. The larger the fish, or the greater the voltage gradient, the more violent and forceful the contractions can be, and the higher the probability of injury (McMichael et at. 1998, Holliman and Reynolds 2002). 2.5.5.8.5.3.1.4 Risk to Listed Salmonids There is an inherent risk to listed salmonids associated with the proposed use of electrofishing in the PRES. However, due to the targeting of larger predatory fish, most of the listed salmonids in the CCF will be much smaller than the size of the predators, and, therefore, the effects of the electric field generated by the electrofishing equipment should not physically harm them. As stated above, the protocols used by the electrofishing teams require them to tum off the equipment if they observe any salmonids being drawn to the electric field. This prevents the fish from becoming incapacitated, and vulnerable to predation, either by avian predators or by predatory fish. 2.5.5.8.5.3.1 .5 Risk to sDPS Green Sturgeon Like listed salmonids, there is an inherent risk associated with the use of electrofishing in the PRES. Due to the larger size of sDPS green sturgeon, the risk of injury is greater than to the smaller salmonids. Water depth and protocols that require the turning off of the equipment if listed :fish are observed will reduce the risk to sDPS green sturgeon. 412 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.8.5.3.2 Deconstruct the Action - Predator F ish Relocation Study (PFRS) The PFRS proposes to use commercial fishing techniques to capture predatory fish within the CCF. These techniques will include both passive and active fishing methods. The methods include beach seines, purse seines, fyke traps, hoop nets, and trawls. The size of the net mesh will be no smaller than 2 inches stretched. Each fish collection method is expected to sample different habitats in CCF and target different predatory species. The specific habitats sampled by collection methods include the Scour Hole, deep habitat (> 60 ft. deep) immediately downstream of the Radial Gates, the Intake Channel leading to the SDFPF, shoreline habitat, and shallow mudflat areas (< 6 ft. deep) throughout CCF. The details of each method and the frequency of sampling are described in a separate BA developed for this study (California Department of Water Resources 20 18a). The PFRS was proposed as an additional study to be implemented by DWR to reduce predation in CCF during the ROC on L TO consultation, replacing the fishing incen6ve program originally proposed. Proposed fish collection will take place Monday through Thursday each week from October through June, as conditions allow. No collection will occur once temperatures in the CCF exceed -21°C. This may follow the same general schedule as PRES, but could be altered for safety reasons (weather or boating conditions), staffing, CCF hunting events or environmental conditions (presence of aquatic vegetation), or other unforeseen variables. Any predator fish collected will be transported to Bethany Reservoir and released. There is no access from Bethany Reservoir back into the Delta. During fish collection, listed species including CV spring-run Chinook salmon, winter-run Chinook salmon, sDPS green sturgeon, and CCV steelhead could be captured. Each crew will identify and enumerate all ESA-listed fish species captured as incidental bycatch, take tissue samples and archive with CDFW, as appropriate, and release the species back into CCF. 2.5.5.8.5.3.2.1 Exposure of Listed Fish to the PFRS Listed fish are expected to be present within the CCF during the implementation of the PFRS. From January to June, winter-run Chinook salmon and CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon are expected to be present and potentially exposed to the effects of the fishing operations within the confines ofCCF. From October through December, only sDPS green sturgeon are expected to be present. 2.5.5.8.5.3.2.2 Response of Listed Salmonids to the PFRS Although most juvenile Chinook salmon should be small enough to escape through the mesh of the nets, some of the larger fish may become entangled when they try to swim through the net. When fish entangle themselves in the net, they risk damaging their sensitive gill structures or injuring their eyes. Furthermore, abrasions along the body may become infected. These injuries will reduce the fitness ofthe fish and may lead to death or predation in its weakened state. In addition, listed salmonids that are entrapped in the fyke, traps or hoop nets with predators may be predated upon if they cannot escape through the mesh. During each set of the nets, study personnel are on hand to monitor the nets. For beach seines, purse seines, and trawls, the duration of the net set is short and most listed fish should be recovered alive and released back into the waters of CCF. The fyke traps and hoop nets are fished overnight and the risk to fish increases due to the longer soak time. For all fishing techniques, there are protective fish handling and recovery protocols that are designed to minimize the stress of capture of any listed 413 Biological Opinion for the Long-Term Operation of the CVP and SWP salmonid. Listed fish are removed from the nets or traps first and processed. Fish will be allowed to recover in holding units and will only be released when they regain fully normal behavior and function. 2.5.5.8.5.3.2.3 Response of sDPS green sturgeon to the PFRS Entanglement of sDPS green sturgeon in the mesh of the nets is likely due to their behavior of rolling in the nets when captured. As described above for listed salmonids, fish are immediately removed from the nets when the haul is completed and processed. The fish handling and recovery protocols are designed to minimize the stress of capture and fish are allowed to recover fully before being released back into the waters of CCF. 2.5.5.8.5.3.2.4 Risk to listed salmonids to the PFRS The PFRS will be conducted during the period when juvenile listed salmonids are present in CCF and they will be vulnerable to capture by the different commercial fishing techniques employed. Capture in the beach seine, purse seine, or trawl should have a relatively low risk of mortality due to the short time of each fishing event and the proposed fish handling and recovery protocols. In contrast, the fyke trap and hoop nets pose a greater risk due to the longer soak times overnight. Captured salmonids will be exposed to predation in the traps if they cannot escape through the mesh, or may die or be eaten if they become ensnared in the mesh trying to escape. 2.5.5.8.5.3.2.5 Risk to sDPS green sturgeon to the PFRS Some sDPS green sturgeon are likely to be present in CCF during the study and will be vulnerable to the fishing techniques employed. Like the listed salmonids, risk to sDPS green sturgeon is low for the beach seines, purse seines, and trawls due to the short time of the fishing events and the lower probability that they will be present in the areas available for beach seining or within the portion of the water column vulnerable to the purse seines or surface trawls. Benthic trawls that target deeper water are more likely to capture sDPS green sturgeon, but the short duration of the trawl will allow any captured sDPS green sturgeon to be quickly processed and released. Capture of sDPS green sturgeon in the fyke trap or hoop nets will result in longer periods of time in which the fish may be entangled in the nets before processing. However, based on other studies in the Delta, the overnight soak time should not create sufficient stress to result in death of the captured fish. 2.5.5.8.5.3.3 Deconstruct the Action- Aquatic Weed Control for Predator Habitat DWR proposes to control aquatic weeds that provide habitat for predatory fish. Most of this weed control will be focused on specific areas and may only require spot removal or use of a mechanical harvester to remove the floating or shallow submerged aquatic vegetation. These actions will typically take place in the summer and will coincide with the larger aquatic weed control program in CCF. 2.5.5.8.5.3.3. 1 Exposure of Listed Fish to Aquatic Weed Control for Predator Habitat Listed salmonids are not expected to be present within the CCF during the implementation of the weed control program to reduce habitat for predatory fish during the summer, however sDPS green sturgeon may be present at this time. From January to June, winter-run and CV spring-run 414 Biological Opinion for the Long-Term Operation of the CVP and SWP Chinook salmon, CCV steelhead, and sDPS green sturgeon are expected to be present and potentially exposed to the effects of the reduced vegetation cover for predators. 2.5.5.8.5.3.3.2 Response of Listed Salmonids to Aquatic Weed Control for Predator Habitat Listed salmonids should benefit from the removal of submerged and floating vegetation that serves as habitat for ambush predators. With less habitat to hide in, ambush predators will have to move away from the cleared areas, thus reducing the potential exposure of listed salmonids to ambush attacks in a greater area of CCF. 2.5.5.8.5.3.3.3 Response of sDPS Green Sturgeon to Aquatic Weed Control for Predator Habitat There is likely little response to the cleared habitat from sDPS green sturgeon. sDPS green sturgeon are probably not as vulnerable to ambush predators as salmonids since they inhabit deeper portions of CCF and are likely to congregate in areas devoid of any vegetation (i.e., deep scour lhole). 2.5.5.8.5.3.3.4 Risk to ESA-Listed Salmonids to Aquatic Weed Control for Predator Habitat Since the action is likely to occur during the summer, no listed salmonids are expected to be present. Therefore the risk is considered to be minimal. 2.5.5.8.5.3.3.5 Risk to sDPS Green Sturgeon to Aquatic Weed Control for Predator Habitat The risk to sDPS green sturgeon is minimal due to the area in which tlhe sDPS green sturgeon are likely to be found. The areas in which aquatic weed control of floating and shallow submerged weeds is not the type of habitat that sDPS green sturgeon are likely to be found in. 2.5.5.8.5.3.4 Deconstruct the Action - Operational Changes when ESA-Listed Fish are Present DWR proposes to shift exports from the SWP to the CVP under the new addendum to the COA provisions signed on December 12, 2018, when it would benefit listed fish species. An "Operational Changes Summary" document (DWR, March 1, 2019) from DWR indicates that in order to reduce pre-screen loss in CCF, the SWP will shift some of its "pumping at Banks Pumping Plant to the Central Valley Project at Jones Pumping Plant when listed species are present. The amount of shifted pumping under Stage 1 Joint Point of Diversion will be limited by the operational or available physical capacity at Jones Pumping Plant. Any SWP pumping greater than what can be shifted to the CVP would still be exported through CCF and Banks Pumping Plant. A minimum SWP pumping amount of approximately 300 cfs is required to support Byron-Bethany and South Bay Aqueduct water needs. This action could occur anytime between January 1 and June 15." 2.5.5.8.5.3.4.1 Exposure of ESA-Listed Fish to the Operational Changes when ESA-Listed Fish are Present Listed salmonids are typically present in salvage from December through June of each year at the south Delta export facilities. The salvage of juvenile winter-run Chinook salmon typically 415 Biological Opinion for the Long-Term Operation of the CVP and SWP occurs from December through March. Salvage of CV spring-run Chinook salmon may occur as early as December and January (yearling life history phase) and extends through May and early June for young-of-the-year juveniles. CCV steelhead may be salvaged in any month of the year, but primarily from December through June. The salvage of sDPS green sturgeon may occur during any month of the year based on their year-round presence in the Delta. Listed salmonids and sDPS green sturgeon will be present during the periods when this shift in exports is likely to occur. The shifting of exports is predicated on the presence of listed fish in salvage at the SWP, and the availability of capacity at the CVP. 2.5.5.8.5.3.4.2 Response of Listed Salmonids to the Operational Changes when ESA-Listed Fish are Present This P A component is designed to reduce the number of listed salmonids lost through the SDFPF. However, shifting exports to the CVP may result in more fish being entrained into the TFCF, but the combined loss between the two faci lities should be reduced, as the loss expansion for salvaged fish is less at the CVP than it is at the SWP. This difference is due to the much higher pre-screen loss associated with CCF that influences the magnitude ofloss at the SWP. 2.5.5.8.5.3.4.3 Response of sDPS Green Sturgeon to the Operational Changes when ESAListed Fish are Present sDPS green sturgeon should have a similar positive response to the shifting of exports to the CVP. Although the rate of loss for sDPS green sturgeon is unknown, lower entrainment into CCF would benefit sDPS green sturgeon by keeping them out of CCF where they can become trapped behind the radial gates. 2.5.5.8.5.3.4.4 Risk to ESA-Listed Salmonids to the Operational Changes when ESA-Listed Fish are Present The risk of predation to listed salmon ids is likely to be reduced by reducing entrainment into CCF and shifting exports to the CVP. By reducing the likelihood of entrainment into CCF, the exposure of listed salmonids to the predator field in CCF is reduced and overall combined survival between the two facilities is expected to increase. 2.5.5.8.5.3.4.5 Risk to sDPS Green Sturgeon to the Operational Changes when ESA-Listed Fish are Present The risk of entrainment into CCF should be reduced for sDPS green sturgeon. Remaining outside of CCF should be a benefit to individual fish and the overall population as fish will be free to migrate without having their movements delayed by being trapped behind the radial gates leading into CCF. 2.5.5.8.5.3.5 Clifton Court Forebay Aquatic Weed and Algal Bloom Management 2.5.5.8.5.3.5.1 Deconstruct the Action- CCF Aquatic Weed and Algal Bloom Management DWR has proposed to apply herbicides and use mechanical harvesters on an as-needed basis to control aquatic weeds and algal blooms in CCF. Herbicides may include Aquathol® K, chelated copper herbicides (copper-ethylenediamine complex and copper sulfate pentahydrate) and 416 Biological Opinion for the Long-Term Operation of the CVP and SWP copper carbonate compounds, or other copper-based herbicides; and algaecides may include peroxygen-based algaecides (e.g. PAK 27) to reduce the standing crop of the invasive aquatic weeds or algal blooms growing in the water body. The dominant species of aquatic weeds in the forebay change from year-to-year and can include Egeria densa, curly-leaf pondweed, sago pondweed, and southern naiad; however, other native and invasive aquatic weeds are present as well. Excessive weeds fragment and clog the trashracks and fish screens of the Skinner Delta Fish Protection Facility, reducing operating efficiency and creating conditions in which the screens fail to comply with the appropriate flow and velocity criteria for the safe screening of listed fish. In addition, the weeds create sufficient blockage to the flow of water through the trashracks and louver array, that the pumps at the Banks Pumping Facility begin to reduce the water level downstream of the SDFPF and the loss of hydraulic head creates conditions that lead to cavitation of the impeller blades on the pumps if pumping rates are not quickly reduced. The algal blooms do not affect the pumps, but rather reduce the quality of the pumped water by imparting a noxious taste and odor to the water, rendering it unsuitable for drinking water. In addition, dense stands of aquatic weeds provide cover for unwanted predators that prey on listed species within the CCF. Aquatic weed control is included as a conservation measure to reduce mortality ofESA-listed fish species within the CCF. DWR has applied herbicides in CCF since 1995, typically during the spring or early summer when listed salmonids have been present in CCF. From 1995 to 2006, complex copper herbicide was applied once or twice annually usually during May or June to target early plant growth when the herbicide has greatest efficacy; though applications have occurred as early as May 3rd and as late as September 101h. Copper-based herbicides are very effective at controlling Egeria, the predominant aquatic weed in CCF at that time. DWR temporarily stopped applying herbicides in CCF after the 2006 season when sDPS green sturgeon was listed as a threatened species. New operational procedures for aquatic herbicide applications in CCF were identified in the Modified 2011 Project Description for the CVP and SWP as part of Reclamation' s Biological Assessment. The procedures, which limited herbicide applications to July 1 through August 31 (or as authorized by NMFS or USFWS), were developed to allow resumption of aquatic herbicide applications in CCF while avoiding potential toxicity from exposure to copper to salmon, steelhead, and sturgeon. Copper-based herbicides present toxicity issues to salmonids and sDPS green sturgeon due to their high sensitivity to copper at both sublethal and lethal concentrations. In response to an increasing abundance of aquatic weeds that culminated in the failure of several fish louvers of the SDFPF in September 2014, treatments resumed in 2015. As documented in the 20 14 California Department ofFood and Agriculture (CDFA) aquatic plant survey, the aquatic weed community in CCF shifted from Egeria densa-dominant to pondweed dominant. In August 2015, DWR received approval from NMFS to use endothall, a fast-acting contact herbicide that is effective at controlling aquatic weeds in CCF. DWR selects endothall-based herbicides when aquatic plant surveys indicate that pondweeds are the dominant species, and copper-based herbicides when Egeria spp. are the dominant species (Department of Water Resources 2016). Additionally, DWR's 2016 Aquatic Pesticides Application Plan states that since 2006 a mechanical harvester has been used to remove weeds near the outlet from CCF into the approach canal leading to the trash racks in front of the SDFPF. The harvester is used for regular removal of pondweeds to help maintain flows to the SDFPF and Banks Pumping Plant (Department of Water Resources 2016). 417 Biological Opinion for the Long-Term Operation of the CVP and SWP Aquatic weed and algae treatments is proposed to occur on an as-needed basis depending upon the level ofvegetation biomass, the cyanotoxin concentration from the harmful algal blooms (HAB), or concentration of taste and odor compounds. The frequency of aquatic herbicide applications to control aquatic weeds is not expected to occur more than twice per year, as demonstrated by the history of past applications. Aquatic herbicides are ideally applied early in the growing season when plants are susceptible to them during rapid growth and formation of plant tissues; or later in the season, when plants are mobilizing energy stores from their leaves towards their roots for overwintering senescence. The frequency of algaecide applications to control HABs is not expected to occur more than once every few years, as indicated by monitoring data and demonstrated by the history of past applications. Treatment areas are typically about 900 acres, and no more than 50 percent of the 2,180 total surface acres. DWR proposes to conduct the following operational procedures: • • Apply Aquathol® K and copper-based aquatic pesticides, and use mechanical harvesters, as needed, from June 28 to August 31. Apply Aquathol®K and copper-based aquatic pesticides, as needed, prior to June 28 or after August 31 if the average daily water temperature within CCF is at or above 25°C and if Delta Smelt, salmonids and sDPS green sturgeon are not at additional risk from the treatment as conferred by NMFS and USFWS. o • Apply Aquathol® K and copper-based aquatic pesticides, as needed, during periods of activated Delta Smelt and salmonid protective measures and when average daily water temperature in CCF is below 25°C if the following conditions are met: o o o • • Prior to treatment outside of the June 28 to August 31 timeframe, DWR will notify and confer w ith NMFS and USFWS on whether ESA-listed fish species are present and at risk from the proposed treatment. The herbicide application does not begin until after the radial gates have been closed for 24 hours or after the period ofpredicted Delta Smelt and salmonid survival within CCF (e.g. after predicted mortality has occurred due to predation or other factors) has been exceeded, and The radial gates remain closed for 24 hours after the completion of the application, unless it is conferred that rapid dilution of the herbicide would be beneficial to reduce the exposure duration to listed fishes present within the CCF. Apply peroxygen-based aquatic algaecides, as needed, year-round. o • Prior to treatment outside of the June 28 to August 31 timeframe, DWR will notify and confer with NMFS and USFWS on whether ESA-listed fish species are present and at risk from the proposed treatment. There are no anticipated impacts on fish with the use o:f peroxygen-based aquatic algaecides in CCF during or following treatment. Monitor the salvage of listed fish at the SDFPF prior to the application of the aquatic herbicides and algaecides in CCF. For Aquathol® K and copper compounds, the radial intake gates will be closed at the entrance to CCF prior to the application of pesticides to allow ·fish to move out of the 418 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • targeted treatment areas and toward the salvage facility and to prevent any possibility of aquatic pesticide diffusing into the Delta. For Aquathol® K and copper compounds, the radial gates will remain closed for a minimum of 12 and up to 24 hours after treatment to allow for the recommended duration of contact time between the aquatic pesticide and the treated vegetation or cyanobacteria in CCF, and to reduce residual endothall concentrations for drinking water compliance purposes. (Contact time is dependent upon pesticide type, applied concentration, and weed or algae assemblage).. Radial gates would be reopened after a minimum of 36 hours (24 hours pre-treatment closure plus 12 hours post-treatment closure). For peroxide-based algaecides, the radial gates will be closed prior to the application of the algaecide to prevent any possibility of the algaecide diffusing into the Delta. The radial gates may reopen immediately after the treatment as the required contact time is less than 1 minute and there is no residual by-product of concern. Application will be made by a licensed applicator under the supervision of a California Certified Pest Control Advisor. Aquatic herbicides and algaecides will be applied by boat or by aircraft. o • • • • Boat applications will be by subsurface injection system for liquid formulations and boat-mounted hopper dispensing system for granular formulations. Applications would start at the shoreline and move systematically farther offshore, enabling fish to move out of the treatment area. Aerial applications of granular and liquid formulations will be by helicopter or aircraft. No aerial spray applications will occur during wind speeds above 15 mph to prevent spray drift. Application would be to the smallest area possible that provides relief to SWP operations or water quality. No more than 50 percent of CCF will be treated at one time. Water quality samples to monitor copper and endothall concentrations within or adjacent to the treatment area, per NPDES permit requirements, will be collected before, during and after application. Additional water quality samples may be collected during and following treatment for drinking water compliance purposes. No monitoring of copper or endothall concentrations in the sediment or detritus is proposed. No monitoring of peroxide concentration in the water column will occur during and after application as the reaction is immediate and there is no residual. Dissolved oxygen concentration will be measured prior to and immediately following application within and adjacent to the treatment zone. A spill prevention plan will be implemented in the event of an accidental spill. DWR proposes to implement additional protective measures to prevent or minimize adverse effects from herbicide applications. As described above, applications of aquatic herbicides and algaecides will be contained within CCF. Additionally, prior to aquatic herbicide applications following gate closures, the water will be drawn down in the CCF via the Banks Pumping Plant. This drawdown helps faci litate the movement of fish in the CCF toward the fish diversion screens and into the fish protection facility, and lowers the water level in the CCF to decrease the total amount of herbicide need to be applied, per volume of water, and aides in the dilution of any residual pesticide post-treatment. Following reopening ofthe gates and refilling ofCCF, the rapid dilution of any residual pesticide and the downstream dispersal of the treated water into the 419 Biological Opinion for the Long-Term Operation of the CVP and SWP California Aquaduct via Banks Pumping Plant reduces the exposure time of any fish species present in CCF. 2.5.5.8.5.3.5.2 Assess the Species Exposure The timing of the application of the aquatic herbicides (Aquathol®K, chelated copper herbicides, and copper carbonate compounds) and mechanical harvesting in the waters ofCCF will occur normally during the summer months beginning June 28 through August 31. Some exceptions outside of this time frame are proposed on an "as needed basis" after DWR confers with NMFS and USFWS and it is determined that listed fish are not present in CCF. The probability of exposing salmonids to the endothall- or copper-based herbicides or harvesters during the normal summer application period is very low due to the life history of Chinook salmon and CCV steelhead in the Delta region. Migrations of juvenile winter-run Chinook salmon and CV springrun Chinook salmon primarily occur outside of the summer period in the Delta. CCV steelhead have a very low probability of being in the South Delta during the period proposed for herbicide treatments. Historical salvage data indicate that in wet years, a few CCV steelhead may be salvaged as late as early July, but this is uncommon and the numbers are based on a few individuals in the salvage collections. Based on typical water temperatures in the vicinity ofthe salvage facilities during this period, the temperatures would be incompatible with salmonid life history preferences. M igrations of juvenile winter-run Chinook salmon and spring-nun Chinook salmon primarily occur outside of the summer period in the Delta. CCV steelhead have a low probability of being in the south Delta during late June when temperatures exceed 25°C through August (Grimaldo et al. 2009). In contrast, juvenile and sub-adult sDPS green sturgeon are recovered year-round at the CVP/SWP fish salvage facilities, and have higher levels of salvage during the months of July and August compared to the other months of the year. The reason for this distribution is unknown at present. Therefore, juvenile and sub-adult sDPS green sturgeon are likely to be present during the application of the herbicides or mechanical harvesting. 2.5.5.8.5.3.5.3 Assess Species Response to the Application of Herbicides and Algaecides for the Aquatic Weed Control Program in Clifton Court Forebay 2.5.5.8.5.3.5.3.1 Copper-Based Herbicides and Algaecides When aquatic plant survey results indicate that E. densa is the dominant species, copper-based compounds will be selected due to their effectiveness in controlling this species. Previous applications of copper-based herbicides (Komeen® and Nautique®) have followed the label directions of the product, which limits copper concentration in the water to 1,000 f.lg/L (1 part per million [ppm] or 1,000 parts per billion [ppb]). The copper in some of the copper-based herbicides is chelated, meaning that it is sequestered within the molecule and is not fully dissociated into the water upon application. Therefore, not all of the copper measured in the water column is biologically available at the time of application. DWR proposes to apply copper herbicides and algaecides in a manner consistent with the label instructions, with a target concentration dependent upon target species and biomass, water volume and the depth of CCF. Applications of copper herbicides for aquatic weed control will be applied at a concentration of I ppm with an expected dilution to 0.75 ppm upon dispersal in the water column. Applications for algal control will be applied at a concentration of0.2 to 1 ppm with expected dilution within the water column. DWR will monitor dissolved copper concentration levels during and after 420 Biological Opinion for the Long-Term Operation of the CVP and SWP treatment to ensure levels do not exceed the application limit of 1 ppm, per NPDES permit required procedures. Treatment contact time will be up to 24 hours. Ifthe dissolved copper concentration falls below 0.25 ppm during an aquatic weed treatment, DWR may opt to open the radial gates after 12 hours but before 24 hours to resume operations. Opening the radial gates prior to 24 hours would enable the rapid dilution of residual copper and thereby shorten the exposure duration ofESA-Iisted fish to the treatment. No more than 50 percent of the surface area of CCF will be treated at one time. Toxicity studies conducted by the California Department ofFish and Game (2004) measured the concentrations of a chelated copper herbicide (Komeen®) that killed 50 percent of the exposed population over 96 hours (96hr-LC50) and 7 days (7d LC50) as well as determining the maximum acceptable toxicant concentration level (MATC) to exposed organisms. CDFG found that the 96hr-LC50 for fathead minnows (Pimephales promelas) was 0.31 ppm (0.18- 0.53 ppm 95 percent confidence limit) and the 7d- LC50 was 0.19 ppm. The MATC was calculated as 0.11 ppm Komeen®in the water column. Splittail (Pogonichthys macrolepidotus), a native cyprinid minnow, was also tested by CDFG. The 96hr-LC50 for splittail was 0.5 1 ppm. Toxicity studies by Wagner et al. (2017) measured concentrations of a copper carbonate compound (Nautique®) that negatively affected 50 percent of the exposed population over 96 hours (96hr-EC50) and 96hr-LC50. Wagner et al. (2017) found that for brook trout (Salvelinus fontinalis), the 96hr-EC50 was 26.2 ppm and the 96hr-LC50 was 28.2 ppm. The same study found that for fathead minnows, the 96hr-EC50 and 96hr-LC50 were 23.0 ppm and 24.4 ppm at 22°C, and 19.6 and 19.7 ppm at 28°C respectively. These values indicate that certain copper carbonate compounds may have higher toxicity at elevated water temperatures (Wagner et al. 2017). NMFS did not fmd toxicity data for exposure of sDPS green sturgeon to copper-based herbicides; however, exposure to other compounds including pesticides and copper were found in the literature (Dwyer et al. 2000, Dwyer et al. 2005a, Dwyer et al. 2005b). From these studies, sturgeon species appeared to have sensitivities to contaminants comparable to salmonids and other highly sensitive fish species. Therefore, NMFS will assume that SDPS green sturgeon will respond to copper-based herbicides in a fashion similar to that of salmonids and should have similar mortality and morbidity responses. Pacific salmonids (Oncorhynchus spp.) are very susceptible to copper toxicity, having the lowest LC50 threshold of any group of freshwater fish species tested by the EPA in their Biotic Ligand Model (BLM) (U.S. Environmental Protection Agency 2003) with a Genus Mean Acute Value (GMAV) of29.11 ppb of copper. In comparison, fathead minnows, the standard EPA test fish for aquatic toxicity tests, have a GMAV of 72.07 ppb of copper. Therefore, salmonids are approximately 3 times more sensitive to copper than fathead minnows. NMFS assumes that sDPS green sturgeon will have a similar level of sensitivity. Hansen et al. (2002) exposed rainbow trout to sub-chronic levels of copper in water with nominal water hardness of 100 mg/1 (as CaC03). Growth, whole body copper concentrations, and mortality were measured over an 8-week trial period. Significant mortality occurred in fish exposed to 54.1 ppb copper (47.8 percent mortality) and 35.7 ppb copper (11.7 percent mortality). Growth and body burden of copper were also dose dependent with a 50 percent depression of growth occurring at 54.0 ppb, but with significant depressions in growth still occurring at copper doses as low as 14.5 ppb after the 8-week exposure (Hansen et al. 2002). 421 Biological Opinion for the Long-Term Operation of the CVP and SWP In a separate series of studies, Hansen et al. (1999a) and Hansen et al. (1999b) examined the effects of low dose copper exposure to the electrophysiological and histological responses of rainbow trout and Chinook salmon olfactory bulbs, and the two fish species behavioral avoidance response to low dose copper(Hansen et al. 1999a, Hansen et al. 1999b). Chinook salmon were shown to be more sensitive to dissolved copper than rainbow trout and avoided copper levels as low as 0.7 ppb copper (water hardness of25 mg/1), while the rainbow trout avoided copper at 1.6 ppb. Diminished olfactory (i.e., taste and smell) sensitivity reduces the ability of the exposed fish to detect predators and to respond to chemical cues from the environment, including the imprinting of smolts to their home waters, avoidance of chemical contaminants, and diminished foraging behavior (Hansen et al. 1999b). The olfactory bulb electroencephalogram (EEG) responses to the stimulant odor, L-serine (10-3M), were completely eliminated in Chinook salmon exposed to 50 ppb copper and in rainbow trout exposed to 200 ppb copper within 1 hour of exposure. Following copper exposure, the EEG response recovery to the stimulus odor were slower in fish exposed to higher copper concentrations. Histological examination of Chinook salmon exposed to 25 ppb copper for 1 and 4 hours indicated a substantial decrease in the number of receptors in the olfactory bulb due to cellular necrosis. Similar receptor declines were seen in rainbow trout at higher copper concentrations during the one-hour exposure, and were nearly identical after four hours of exposure. A more recent olfactory experiment (Baldwin et al. 2003) examined the effects of low dose copper exposure on coho salmon (0. kisutch) and their neurophysiological response to natural odorants. The inhibitory effects of copper ( 1.0 to 20.0 ppb) were dose dependent and were not influenced by water hardness. Declines in sensitivity were apparent within 10 minutes of the initiation of copper exposure and maximal inhibition was reached in 30 minutes. The experimental results from the multiple odorants tested indicated that multiple olfactory pathways arc inhibited and that the thresholds of sublethal toxicity were only 2.3 to 3.0 ppb above the background dissolved copper concentration. The results of these experiments indicate that even when copper concentrations are below lethal levels, substantial negative effects occur to salmonids exposed to these low levels. Reduction in olfactory response is expected to increase the likelihood of morbidity and mortality in exposed fish by impairing their homing ability and consequently migration success, as well as by impairing their ability to detect food and predators. In addition, NMFS issued a technical white paper on copper toxicology (Hecht et al. 2007). Given that sDPS green sturgeon use their sense of smell and tactile stimulus to find food w ithin the bottom substrate, degradation of their olfactory senses could diminish their effectiveness at foraging and compromise their physiological condition through decreases in caloric intake following copper exposure. In addition to these physiological responses to copper in the water, Sloman et al. (2002) found that the negative effect of copper exposure was also linked to the social interactions of salmonids. Subordinate rainbow trout in experimental systems had elevated accumulations of copper in both their gill and liver tissues, and the level of adverse physiological effects were related to their social rank in the hierarchy of the tank. The increased stress levels of subordinate fish, as indicated by stress hormone levels, is presumed to lead to increased copper uptake across the gills due to elevated ion transport rates in chloride cells. Furthermore, excretion rates of copper may also be inhibited, thus increasing the body burden of copper. Sloman et al. (2002) concluded that not aU individuals within a given population will be affected equally by the presence of waterborne copper, and that the interaction between dominant and subordinate fish 422 Biological Opinion for the Long-Term Operation of the CVP and SWP will determine, in part, the physiological response to the copper exposure (Sloman et al. 2002). It is unknown how social interactions affect juvenile and sub-adult green sturgeon in the wild. Current EPA National Recommended Water Quality Criteria and the California Toxics Rule standards promulgate a chronic maximum concentration (CMC) of 5.9 J.tg/1 and a continuous concentration criteria of 4.3 J.tg/1 for copper in its ionized form. The dissociation rates for the chelated copper molecules in the copper-based herbicide formulations were unknown at the time of this consultation, so that NMFS staff could not calculate the free ionic concentration of the copper constituent following exposure to water. However, the data from the toxicity studies mentioned above indicates that a maximum working concentration of 1.0 ppm metallic copper will be toxic to salmonids if they are present, either causing death or severe physiological degradation, and therefore, sDPS green sturgeon would likely be similarly affected based on their similar sensitivities to copper toxicity. 2.5.5.8.5.3.5.3.2 Aquathol® K Aquathol® K is registered for use in California and has effectively controlled pondweeds and southern naiad in CCF and in other lakes. It is available in both liquid and granular formulations. Aquathol® K, the liquid formulation of dipotassium salt of endothall, consists of 40.3 percent of 7 -oxabicyclo [2.2.1] heptane-2, 3-dicarboxylic acid equivalent 28.6 percent, which is equivalent to 4.23 pounds of active ingredient per gallon of product. The active ingredient in AquathoJ® K is Dipotassium salt of endothall. Endothall is an herbicide in the dicarboxylic acid chemical class (Endothall 1995). While its exact mode of action is unknown, hypotheses include cellular disruption, possibly including interference with protein or lipid synthesis or disrupting the transport of nutrients across cell membranes (Tresch et al. 20 II). The potential for bioaccumulation is not fully known. The Forest Service estimates that endothall may have a modest potential for mammalian bioaccumulation (Syracuse Environmental Research Associates Inc. (SERA) 2009), but studies indicate that bioaccumulation in fish is unlikely (Wisconsin Department ofNatural Resources (WI DNR) 2012). The Aquathol® K label recommends application concentrations between 0.75 and 5.0 ppm depending on target plant species, with a maximum of 30 ppm over the course of a treatment season. The EPA maximum concentration allowed for Aquathol® K is 5 ppm. The label requires a 7-day wait period between 5 ppm applications. There are no wind, temperature, or irrigation restrictions on the AquathoJ® K label. The concentrated product should not be permitted to contact crops. The endothall concentration in potable water must be less than 0.1 ppm, and application requires a minimum setback of 600 feet from an active potable water intake unless the intake is shut off during treatment. The label states that Aquathol® K should not be used in brackish or saltwater. The NPDES receiving waters limit is I 00 ppb. USEP A approved endothall as a reduced risk herbicide. DWR is proposing to use the dipotassium salt formulation of endothall (as Aquathol® K) and not the amine salt (Hydrothol) formulations, which are highly toxic to fish and invertebrates bioaccumulation (Syracuse Environmental Research Associates Inc. (SERA) 2009). The fish acute and chronic toxicity endpoints for endothall relevant to ESA listed species include: LC50s for Chinook salmon range from 23 ppm to > 150 ppm and > 100 ppm for coho salmon. One study (Courter et al. 20 12) of the effect of Cascade®, an herbicide with the same endothall formulation as Aquathol® K, on salmon and steelhead smolts showed no sublethal effects until exposed to 9-12 ppm. A study on the 423 Biological Opinion for the Long-Term Operation of the CVP and SWP ecotoxicity of endothall commissioned by CDBW from 2014 to 2017 reported a wide range of acute effects to fish species ranging from No Observable Effect Concentration (NOEC) for growth and survival effects at the highest concentration tested (NOEC > 500 ppm) for rainbow trout. Figure 2.5.5-33 provides an illustration of endothall estimated Effects Concentration (EC), Lethal Concentration for 50 percent of the organisms (LC50), No Observable Effect Concentration (NOEC), and Lowest Observable Effect Concentration (LOEC) levels for reptile surrogate and fish species. The NPDES permit limit for endothall in receiving waters is 100 ppb. The lowest chronic fish endpoint observed is impaired weight for the fathead minnow at 3.1 ppm and NOEC for Chinook salmon at approximately 3.5 ppm. When aquatic plant survey results indicate that pondweeds are the dominant species in CCF, Aquathol® K will be selected due to its effectiveness in controlling these species. Aquathol® K will be applied according to the label instructions, with a target concentration dependent upon plant biomass, water volume, and CCF depth- Aquathol® labeling (Aquathol SDS) recommends 0.75 ppm to 3.0 ppm for Pondweeds (Potamogeton spp.) (United Phosphorus 2016). The target concentration of treatments DWR proposes is 2 to 3 ppm. Additionally, the duration of exposure to endothall for listed fish will be approximately 12-24 hours. A minimum contact time of 12 hours is needed for biological uptake and treatment effectiveness, but the contact time may be extended up to 24 hours to reduce the residual endothall concentration for NPDES compliance purposes. DWR will monitor herbicide concentration levels during and after treatment to ensure levels do not exceed the AquathoJ®K application limit of 5 ppm. Additional water quality testing may occur following treatment for drinking water intake purposes. Samples are submitted to a laboratory for analysis. No more than 50 percent ofthe surface area ofCCF will be treated at one time. Due to the lack of data on effects of Aquatihol®K to surrogates for sDPS green sturgeon, NMFS will assume that sDPS green sturgeon will respond to Aquathol®K in a fashion similar to that of salmonids and should have similar mortality and morbidity responses. Chinook salmon are affected at low concentrations by endothall and display acute and chronic effects to endpoints at various life stages (juvenile growth and survival are within the range of maximum application concentration). NMFS assumes that sDPS green sturgeon will have a similar level of sensitivity, and are likely to experience negative physiological effects (i.e., reduced growth and survival), and vulnerability to predation as a result of endothall exposure. 2.5.5.8.5.3.5.3.3 Peroxygen-Based Algaecides PAK 27 algaecide active ingredient is sodium carbonate peroxyhydrate. An oxidation reaction occurs immediately upon contact with the water destroying algal cell membranes and chlorophyll. There is no contact or holding time requirement, as the oxidation reaction occurs immediately and the byproducts are hydrogen peroxide and oxygen. There are no fishing, drinking, swimming, or irrigation restrictions following the use of this product. P AK 27 has NSF/ ANSI Standard 60 Certification for use in drinking water supplies at maximum-labeled rates and is certified for organic use by the Organic Materials Reviews Institute (OMRI). PAK 27, or equivalent product, will be applied in a manner consistent with the label instructions, with permissible concentrations in the range of 0.3 to 10.2 ppm hydrogen peroxide. NMFS did not find toxicity data for exposure of salmonids or sturgeon to peroxygen-based algaecides. In a single study, for fathead minnows the 96hr-NOEC was 7.4 ppm and the LC50 was 71 ppm (United Phosphorus 20 15). These data reflect low toxicity effects on fish. Due to the 424 Biological Opinion for the Long-Term Operation of the CVP and SWP lack of data on effects of peroxygen-based algaecides to surrogates for ESA-listed salmonids or green sturgeon, NMFS will assume that they will respond to peroxygen-based algaecides in a fashion similar to that of fathead minnows and should have similar mortality and morbidity responses. Fathead minnows are only affected at very high concentrations by peroxygen-based algaecides. NMFS assumes that salmonids and sturgeon will have a similar level of sensitivity, and are not likely to experience negative physiological effects as a result of exposure. Therefore, there are no anticipated direct impacts on ESA-listed fish with the use ofperoxygen-based aquatic algaecides in CCF. However, it should be noted that decaying algae, killed by peroxygen-based algaecides, can deplete dissolved oxygen levels in the water, which could result in fish mortality. Because the frequency of algaecide applications to control HABs is not expected to occur more than once every few years, and no more than 50 percent of the surface area of CCF will be treated at one time, it is unlikely that algal decomposition will lead to sufficient oxygen depletion to result in fish mortality. 2.5.5.8.5.3.5.4 Assess Species Response to the Mechanical Harvesting for the Aquatic Weed Control Program in Clifton Court Forebay DWR proposes to continue using mechanical methods to manually remove aquatic weeds. A debris boom and an automated weed rake system continuously remove weeds entrained on the trashracks. During high weed load periods such as late summer and fall when the plants senesce and fragment or during periods of hyacinth entrainment, boat-mounted harvesters are operated on an as-needed basis to remove aquatic weeds in CCF and the intake channel upstream of the trashracks and louvers. The objective is to decrease the weed load on the trashracks and to improve flows in the channel. Effectiveness is limited due to the sheer volume of aquatic weeds and the limited capacity and speed of the harvesters. Harvesting rate for a typical weed harvester ranges from 0.5 to 1.5 acres per hour or 4 to 12 acres per day. Actual harvest rates may be lower due to travel time to off-loading sites, unsafe field conditions such as high winds, and equipment maintenance. Mechanical aquatic weed control activities associated with the use of harvesters, booms, and automated rakes are likely to result in various stressors (e.g., conveyor mechanism and bycatch, increased turbidity, and low DO) which could increase the likelihood of negative effects to salmonids and green sturgeon in the form of injury, mortality, avoidance activity, gi11 fouling, and reduced forging capability. The potential for direct and indirect effects to listed species as a result of mechanical removal methods depends on the magnitude (duration and frequency of exposure) of disturbance, the type of method used, and the presence and proximity of listed species in the treatment site. Potential effects of the operation of automated rakes include mortality or injury from contact with the rake, entrapment, removal from water, and temporary disturbance. Automated rakes have the potential to indirectly and directly affect (i.e., injure or kill) listed species if the species are collected along with the aquatic weeds. The operation of a hydraulic rake cleanjng system has been shown to trap and kill adult Chinook salmon and other non-listed fish (U.S. Bureau of Reclamation 2016b). Harvesters, cutters, and shredders have the potential to indirectly (i.e., alter feeding behavior and foraging of prey items) and directly affect (i.e., injure or kill) listed species due to the mechanics of the cutting equipment and, for harvesters, the conveyor belt systems that will be used to remove biomass (and any potential bycatch) from the water. Engel (1995) found that harvesting also has the potential for direct and indirect effects by removing macroinvertebrates, aquatic 425 Biological Opinion for the Long-Term Operation of the CVP and SWP vertebrates, forage fishes, young-of-the-year fishes and game fishes (Engel 1995). Additionally, fragmentation caused by cutting may spread invasive plant infestations, and both harvesting and cutting may suspend sediments, temporarily increasing turbidity (Madsen 2000). Madsen (2000) showed that these methods may release nutrients. This finding is supported by a USACE study that determined that shredding had mixed effects on nutrients and dissolved oxygen - plant decomposition tended to increase biochemical oxygen demand and nutrient cycling, but this was offset by increases in algal productivity and the increase in oxygen caused by the shredding machine's mixing of the water (James et al. 2000). 2.5.5.8.5.3.5.5 Assess Risks to Listed Salmonids and sDPS Green Sturgeon The proposed mechanical harvest and herbicide application program's normal period of application (June 28 through August 31) will substantially avoid the presence of listed salmonids in the CCF due to the run timing of the juveniles through the Delta. As described earlier, CCV steelhead smolts may arrive during any month of the year in the delta, but their likelihood of occurrence is considered very low during the proposed treatment period. It is also highly unlikely that any winter-run Chinook salmon or CV spring-run Chinook salmon will be present during this time period in the South Delta. Unlike the salmonidls, however, sDPS green sturgeon have been salvaged during the summer at both the CVP and SWP fish salvage facilities. This is related to their year round residency in the Delta during their first 3 years of life. It is, therefore, likely that individuals from the sDPS green sturgeon will be exposed to the endothall and/or copper herbicides and mechanical harvesting activity, and based on the comparative sensitivities of sturgeon species wit!h salmonids, some of these fish are likely to be kiHed or otherwise negatively affected. The exact number offish exposed is impossible to quantify, since the density of sDPS green sturgeon residing or present in CCF at any given time is unknown. The short duration of treatment and rapid flushing of the system will help to ameliorate the adverse conditions created by the herbicide treatment. The application of herbicides and mechanical harvesting in CCF under the Aquatic Weed Control Program will not affect the populations of winter-run Chinook salmon or CV spring-run Chinook salmon. These populations of salmonids do not occur in the South Delta during the proposed period of herbicide applications and, thus, exposure to individuals is very unlikely. Since no individual fish are exposed, population level effects are absent. Exposure of CCV steelhead is also very unlikely; however, some individual fish may be present during July as indicated by the historical salvage record and, thus, occurrence of fish in CCF during the harvesting and/or herbicide treatments is not impossible. The numbers of CCV steelihead that may be potentially exposed to the harvesting and herbicides is believed to be very small, and therefore demonstrable effects at the population level resulting from exposure are unlikely. The effects to the sDPS green sturgeon population are much more ambiguous due to the lack of information regarding the status of the population in general. Although NMFS estimates that few sDPS green sturgeon will be exposed during the mechanical harvesting and herbicide treatments, the relative percentage ofthe population this represents is unknown. Likewise, the number of sDPS green sturgeon that reside in CCF at any given time and their susceptibility to entrainment is also unknown. This uncertainty complicates the assessment of both population and individual exposure risks. This area of sDPS green sturgeon life history needs further resolution to make an accurate assessment of the impacts to the overall status of the population. 426 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.9 South Delta Agricultural Barrier Operations 2.5.5.9.1 Deconstruct the Action DWR proposes to install and operate three agricultural barriers in the channels of the south Delta each year, and Reclamation requests consultation on the installation and operation of these barriers through 2030. A separate biological opinion has been issued by NMFS for the construction effects of installing these barriers and their operations through 2022 to the U.S. Army Corps of Engineers. Two additional permits, the Incidental Take Permit and the Streambed Alteration Agreement, were issued by CDFW for the construction and operations of the barriers and will expire in 2021. Finally, the section 401 Water Quality Certification from the Regional Water Quality Control Board for the south Delta barriers expires in 2022. DWR plans toreinitiate the permitting process for each of these permits prior to their expiration. DWR constructs the three barriers in the south delta each spring to provide water surface elevation protection for south Delta agricultural diverters [ROC on LTO BA, Appendix A (U.S. Bureau of Reclamation 2019)]. These barriers are constructed on Old River near Tracy, 0.5 miles upstream of the TFCF, on Middle River 0.5 miles upstream of the junction with Victoria Canal, and on Grant Line Canal about 400 feet upstream of the Tracy Boulevard Bridge. The barriers are constructed each spring using large boulders and cobble, and have multiple steel culverts to allow the flow of water through the barrier. The culverts have tidally-operated flap gates which allow the culverts to be completely closed on the ebb tide to trap water behind the barrier, and open on the flood tide to allow water to flow upstream. The center of each barrier is lower than the abutments on each bank and acts as a weir that allows flood tides to overtop it and pass tidal flow upstream. On the ebb tide, water can flow downstream over the weir crest until the upstream water elevation reaches the elevation of the weir crest, at which point the barrier behaves as a low head dam with only minimal river flow passing over it. When the HORB is not installed, construction of the agricultural barriers may begin on May 1 [Table A5-3, Appendix A (U.S. Bureau of Reclamation 2019)]. Closure of the barriers is typically completed by May 15 and the tidal flap gates tied open. From May 15 to May 31, the tidal flap gates may be untied and become fully functional ifDWR clearly demonstrates that water surface elevations in the south Delta are sufficiently low to impact south delta irrigators from diverting water. In addition, the barrier on Grant Line cannot be closed during this period if the Delta smelt incidental take concern limit has been reached. By June I, both Old River and Middle River barriers can become fully functional and the flap gates left untied. The Grant Line barrier may still be left with the flap gates tied open if there are still Delta smelt incidental take issues. Finally, at least one culvert at each barrier will be kept open to allow for fish passage when water temperatures are less than 22°C even if the previous conditions have been met. Starting on September 15, the agricultural barriers at Middle River and Old River at Tracy must be notched to allow for the passage of adult fall-run Chinook salmon. At the Grant Line barrier, the appropriate number of flashboards must be removed to provide for passage of adult fall-run Chinook salmon. By November 15, all barriers must be removed from their respective waterways. Reclamation provided limited information in their BA and supporting documents to assess the impacts of the construction of the three agricultural barriers in the south Delta on listed salmonids and sDPS green sturgeon. Based on previous consultations for the construction of the 427 Biological Opinion for the Long-Term Operation of the CVP and SWP agricultural barriers with the U.S. Army Corps of Engineers, the construction of the barriers will create adverse water quality conditions (turbidity and suspended sediment) as well as create disturbances within the three channels of the south Delta where the barriers are located that will negatively affect listed fish present in the waterways during construction. In contrast, sufficient information regarding the impacts of the operations of the south Delta barriers on listed salmonid migration behavior and increased vulnerability to predation was presented (California Department of Water Resources 2018b) to assess the impacts of the operations of the south Delta barriers under this PA component. Therefore, construction of the barriers will be treated programmatically and additional consultation will occur when DWR seeks to renew their permits with sil:ate and Federal agencies for the south Delta barriers. Operations of the barriers after construction will be covered by this consultation. 2.5.5.9.2 Assess Species Exposure to Proposed South Delta Agricultural Barrier Operations 2.5.5.9.2.1 Winter-run Chinook Salmon Adult winter-run Chinook salmon do not spawn in the San Joaquin River basin and, therefore, are unlikely to be present in the location of the south Delta agricultural barriers during their installation and operations. Juvenile winter-run Chinook salmon have the potential to be in the locations of the south Delta agricultural barriers due to their observed presence in the salvage of the TFCF and the SDFPF from January to April. The Middle River and Old River at Tracy barriers are only 0.5 miles away from waterways known to contain juvenile winter-run Chinook salmon (Old River adjacent to the TFCF, and Victoria Canal at the junction with Middle River). Because the PA does not include installation of the HORB in the spring, construction of the barriers does not start until May I . Therefore, it is unlike ly that any juvenile winter-run Chinook salmon will be present in the waters of the south Delta during the construction and operations of the agricultural barriers. 2.5.5.9.2.2 CV Spring-run Chinook Salmon Both adult and juvenile CV spring-run Chinook salmon are anticipated to be present in the waters surrounding the locations of the south Delta agricultural barriers. Adult CV spring-run Chinook salmon returning to the San Joaquin River basin from the experimental reintroduction population will be entering the waters of the south Delta starting in January and continuing through June with a peak between February and April. These fish will encounter both the construction of the barriers and their operations. Juvenile CV spring-run Chinook salmon from both the San Joaquin River experimental population and the Sacramento River basin populations can be expected to be present in the waters surrounding the south Delta agricultural barriers during construction and operations. Based on historical salvage data, prior to the efforts to reestablish CV spring-run Chinook salmon into the San Joaquin River basin, juvenile CV springrun Chinook salmon were present at the fish salvage facilities from February through June. Since the agricultural barriers on Middle River and on Old River at Tracy are located within close proximity to waterways known to contain CV spring-run Chinook salmon (see winter-run Chinook salmon section above), the presence of juvenile CV spring-run Chinook salmon during construction and operations of the barriers is assumed. Presence of juvenile CV spring-run Chinook salmon from the Sacramento River basin at the Grant Line barrier is also possible given 428 Biological Opinion for the Long-Term Operation of the CVP and SWP the effects of tides in these waterways which can push juvenile salmon upstream to the location of the barrier. For juvenile CV spring-run Chinook salmon emigrating from the San Joaquin River basin, the Old River and Grant Line routes are known migratory routes for juvenile Chinook salmon leaving that basin. The emigration of juvenile CV spring-run Chinook salmon (February through June) will completely overlap with the construction and early operations of the barriers (May and June). 2.5.5.9.2.3 CCV Steelhead Both adult and juvenile CCV steelhead will be present at the locations of the agricultural barriers during construction and operations. Adult CCV steelhead will encounter the barriers during their upstream migrations in fall when the barriers are still in place prior to their removal by midNovember. Adult CCV steelhead migration into the San Joaquin River basin starts in approximately September and continues through early winter (December and January). Juvenile CCV steelhead emigration from the San Joaquin River basin can start in winter but peaks in April and May, which overlaps with the construction and early operations of the barriers. It is also possible to have Sacramento River basin CCV steelhead in the vicinity of the barriers in April and May based on the salvage records from the CVP and SWP fish salvage facilities. 2.5.5.9.2.4 sDPS Green Sturgeon Both juvenile and adult sDPS green sturgeon are assumed to be present in the waters ofthe south Delta adjacent to the location of the agricultural barriers. Based on salvage records from the CVP and SWP fish salvage facilities and sturgeon fishing report cards (see Figure 2.5.5-12 and Figure 2.5.5-13), observations of sDPS green sturgeon have occurred year-round in this region. A summary of the effects of the proposed south Delta agricultural barrier operations is provided in Table 2.5.5-67 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. 2.5.5.9.3 Assess Response of Listed Salmonids DWR issued a report regarding the effects of the south Delta agricultural barriers on the survival of emigrating juvenile salmonids, including both Chinook salmon and steelhead (California Department of Water Resources 20 18b). The report stated that the presence of the south Delta agricultural barriers will considerably reduce juvenile salmonid survival compared to open channels. Survival is lowest when the barriers are installed and the flap gates are closed. Survival improved when the flap gates were tied open. Survival was also reduced during the construction of the barriers. Juvenile salmonids were typically predated upon upstream of the barriers while delayed on their downstream migration. Predator density increased after the construction of the barriers, but most noticeably upstream of the barriers. The barriers increased the time that juvenile salmonids spent in the vicinity of the barriers, which likely increased their vulnerability to predators located upstream of the barriers. Juvenile salmonids encountering the barriers will move downstream through open culverts preferentially, but few fish were detected moving over the weir crest if the culverts were tied open. If the culverts were tidally operated, fish could only go through when the flood tide pushed them open. Under these conditions, more juvenile salmonids went over the weir crest but could only do so when flows overtopped the weir crest on flood tides or on ebb tides before the water elevations declined to the point where water depth was diminished over the crest. By increasing the time that juvenile salmonids spent in the vicinity of the barriers, the fish were also vulnerable to being exposed to elevated water 429 Biological Opinion for the Long-Term Operation of the CVP and SWP temperatures as the season progressed. This could diminish the physiological state of the fish, making them more vulnerable to predation. The barriers are also likely to present a barrier to upstream migration for adult CV spring-run Chinook salmon that will be moving upstream during the spring through the channels occupied by the barriers. The barriers as described in the PA component do not have notches cut in them during the spring to facilitate upstream passage of adult Chinook salmon. Therefore, it is likely that fish will mill around below the barriers either waiting for the weir crest to overtop on the flood tide and providing a passage route, or seeking passage through the tidal flap gates that will open on the flood tide. Adult CCV steelhead migrating into the San Joaquin River watershed should encounter barriers with tlhe notches in place (September 15). However, passage is likely only possible during the flood tides or on the falling ebb tide immediately after slack when there is still adequate water depth to facilitate passage. Under the Proposed Action a portion of the fish from the San Joaquin Basin will route into Old River (HOR) throughout the year at all Vernalis flows. Old River will experience higher velocities towards the export facilities and the San Joaquin River channel will experience lower velocities relative to actual current operations (though these results aren't seen in the modeling results since neither the COS nor PA modeling scenario include spring installation of the HORB). Reach-specific survival (from the Head of Old River to the export facilities) would be expected to improve in the Old River Channel and may decrease in the mainstem San Joaquin River. For purposes of comparing the PA to current operations in terms of the response oflisted salrnonids, NMFS has assessed effects in the south Delta relative to HORB installation and operations. Recent modelling (Buchanan 2019) of the effects of the HORB presence on the estimated CCV steelhead survival from the HOR to Chipps Island indicates that survival is higher when the barrier is installed, compared to when it is not installed. The modelling was conducted using acoustic tag data from the 6-year Steelhead Survival Study (2011-2016). The modelling used a generalized linear multinomial regression model to predict survival to Chipps Island as a function of San Joaquin River inflow at Vernalis, migration route taken by the CCV steelhead (Old River versus the mainstem San Joaquin River), and barrier status (installed versus not installed). The model used fixed year effects for the years with Delta inflow (Vernalis) that was less than 5,000 cfs (years 2012-2016 ofthe 6-year study) and then combined over years in a weighted average using weights equal to the proportion of observations from each year used in the regression model. Buchanan (20 19) found that when the HORB is installed, the probability of total predicted survival from the HOR to Chipps Island was estimated to range from 0.30 (SE = 0.20) for a Vernalis flow of319 cfs to 0.67 (SE=0.20) for a Vernalis flow of5,000 cfs. When the barrier was not installed, the estimated predicted survival ranged from 0.17 (SE = 0.13) for a Vernalis flow of319 cfs, to 0.50 (SE = 0.24) for a Vernalis flow of5,000 cfs. The predicted difference in survival that was attributable to the presence of the barrier was estimated to range from 0.13 (SE = 0.08) for a Vernalis flow of319 cfs to 0.19 (SE = 0.08) for a Vernalis flow of3,889 cfs. Although there is high uncertainty in the predicted survival estimates for both conditions of the barrier's presence, and moderate uncertainty for the predicted effect of the barrier on survival, the predicted survival effect of the barrier (point estimate) was positive for all values of Delta 430 Biological Opinion for the Long-Term Operation of the CVP and SWP inflows at Vernalis. The 95 percent confidence intervals excluded zero at flows above 783 cfs. The difference between survival estimates for the barrier installed and the barrier not installed were always positive for the point estimates. Buchanan (20 19) cautions that this modelling is based on a limited data set (20 11 - 20 16). Additional years of data may change the weighting of years, and the yearly effects, as well as routing probabilities used in the preliminary regression model. In general, the current preliminary modelling results indicate that for flows below 5,000 cfs at Vernalis, survival for CCV steelhead emigrating from the San Joaquin River basin is higher when the HORB is installed than when the HORB is not installed. Based on NMFS's current understanding of survival probabilities based on barrier condition at the Head of Old River, the PA will lead to lower survival of steelhead juveniles emigrating from the San Joaquin River basin by up to 20 percent for flows between 3,800 cfs and 5,000 cfs at Vernalis. This information parallels the information provided by the South Delta Agricultural Barriers Effects Report (California Department of Water Resources 2018b) that indicated reduced survival through the south Delta routes when the agricultural barriers are being constructed and when they are in place. During years in which spring-time Vernalis flows do not exceed 5,000 cfs, Reclamation's P A creates conditions that would reduce steelhead survival to Chipps Island for the Southern Sierra Nevada Diversity Group, further exacerbating the already diminished status of this diversity group. 2.5.5.9.4 Assess Response of sDPS Green Sturgeon There is an absence of information regarding sDPS green sturgeon behavior around the south delta barriers. L ike salmonids, the barriers present a migration blockage for fish moving either upstream or downstream when the barriers are in place. It is unlikely that any sDPS green sturgeon, either an adult or juvenile, will pass over the top of the weir crest, even during flood tides. sDPS green sturgeon may pass through the culverts, but it is unknown whether they will volitionally do this. F ish that are upstream of the barriers after the culverts begin to be tidally operated are likely to be trapped upstream of the barrier. Under these conditions, the only route back to the main Delta waterways may be to swim upstream to the Head of Old River and access the main stem of the San Joaquin River to move back downstream into the Delta. 2.5.5.9.5 Assess Risk to Listed Salmonids Both juvenile CV spring-run Chinook salmon and juvenile CCV steelhead will encounter the barriers when they are present in the channels of Old River, Middle River, and Grant Line Canal. The barriers will present a substantial impediment to downstream migration both as a physical structure, and as a source of mortality to individuals through predation. Delays in migration can also expose fish to elevated water temperatures as the season progresses, making any prolonged delay potentially lethal due to thermal tolerances of the fish. 2.5.5.9.6 Assess Risk to listed sDPS Green Sturgeon Both juvenile and adult sDPS green sturgeon will encounter the barriers when they are present in the channels of Old River, Middle River, and Grant Line Canal. The barriers will present a physical barrier to movements within the Delta for both juveniles and adults. It is unknown whether the barriers will increase predation on juvenile sDPS green sturgeon, or diminish their physiological status. 431 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.10 Conservation Measures 2.5.5.10.1 Fall Delta Smelt Habitat 2.5.5.10.l.1Physical Description of Fall Delta Smelt Habitat Ideal estuarine areas are free of migratory obstructions with water quality, water quantity, and salinity conditions supporting juvenile and adult physiological transitions between fresh and salt water. Current estuarine areas are degraded as a result of the operations of the CVP and SWP. Historically, the Delta provided the transitional habitat for juvenile fish species to undergo the physiological change to salt water. However, as the location of the low salinity zone (X2) was modified to control Delta water quality, and competing species' needs (i.e., Delta smelt), the Delta served more as a migratory corridor for emigrating anadromous fish species. Within the central and southern Delta, net water movement is towards the export facilities, altering the migratory cues for emigrating fish in these regions. Operations of upstream reservoir releases and diversion of water from the south Delta have been manipulated to maintain a "static" salinity profile in the western Delta near Chipps Island. This area of salinity transition, the low salinity zone, is an area of high productivity. Historically, this zone fluctuated in its location in relation to the outflow of water from the Delta and moved westwards with high Delta inflow (i.e., floods and spring runoff) and eastwards with reduced summer and fall flows. This variability in the salinity transition zone has been substantially reduced by the operations of the CVP and SWP. The CVP and SWP's long-tenn water diversions also have contributed to reductions in the phytoplankton and zooplankton populations in the Delta itself as well as alterations in nutrient cycling within the Delta ecosystem. Heavy urbanization and industrial actions have lowered water quality and introduced persistent contaminants to the sediments surrounding points of discharge (i.e., refineries in Suisun and San Pablo bays, creosote factories in Stockton, etc.). The USFWS' 2008 RPA provided a "Fall X2" standard which requires that the location ofthe low-salinity zone (defined as 2 parts per thousand [ppt] isohaline) be located at no greater than 46 and 50 miles (74 and 81 km) from the Golden Gate Bridge in September, October, and November of wet and above normal years, respectively, to improve rearing conditions for Delta Smelt. The low-salinity zone magnitude and dimensions change when river flows into the estuary are high, placing low-salinity water over a larger and more diverse set of nominal habitat types than occurs under low flow conditions. During periods of low outflow, the low-salinity zone contracts and moves upstream. Currently, in addition to D-1641, Reclamation operates to reduce entrainment risk and for Delta Smelt fall habitat in wet and above normal water years through releases of water from storage for Fall X2. The USFWS recommended in its designation of critical habitat for the Delta Smelt that salinity in Suisun Bay should vary according to water year type. For the months of February through June, this element was codified by the SWRCB's "X2 standard" described in D-1641 and the Board's current Water Quality Control Plan. 2.5.5.10.1.2 Deconstruct the Action- Fall Delta Smelt Habitat According to their February 1, 2019 BA, Reclamation proposes to manage for Delta Smelt habitat in the fall of above normal and wet years by releasing additional Delta outflow to move the low salinity zone to beneficial areas to target creation of fall Delta smelt habitat in September 432 Biological Opinion for the Long-Term Operation of the CVP and SWP and October following above normal and wet years. Fall Delta smelt h.abitat would be measured using the physical and biological features of critical habitat; mainly Secchi depth, chlorophyll, water temperature, and salinity. Reclamation would coordinate with USFWS to assess the potential for updating the habitat index to incorporate biotic elements, in particular food (zooplankton prey density), in order to better capture the potential benefits from actions such as operation of the Roaring River Distribution System west-side drain. Achievement ofthese targets would be assessed using current multi-dimensional Delta models, applying the observed outflow and operations, in addition to other necessary inputs to be developed by Reclamation andDWR. Reclamation proposes to operate the SMSCG in September and October of above normal and below normal water year types. Iterative analysis using the DSM2 model would be required to identify associated changes in Delta outflow and reservoir releases required to support changes in outflow. The analysis has not been completed and, therefore, the effects of this operation have not been incorporated in the CalSimii model. The ROC on LTO BA states that the PA would result in X2 being essentially the same as current operations in drier years, but greater (more upstream) than the current operations scenarios in wet and above normal years. Under the current operations scenario, X2 is at 86 km on average in September and 87 krn on average i!n October. Under the PA component, according to the revised Delta Smelt Summer-Fall Habitat Chapter 4 (March 29, 2019 version), Delta outflow could be augmented in above normal or wet years to support a 2 ppt isohaline position of 80 km in September and October. During a May 21, 2019 consultation meeting, Reclamation further clarified that: "As part of the Delta Smelt Habitat Action, Reclamation intends to meet Delta outflow augmentation in the fall primarily through export reductions as they are the operational control with the most flexibility in September and October of above normal and wet years. Storage releases from upstream reservoirs may be used to initiate the action by pushing the salinity out further in August and early September; however, the need for this initial action will depend on the particular hydrologic, tidal, storage, and demand conditions at the time. In addition, storage releases may be made in combination with export reductions during the fall period during high storage scenarios where near-term flood releases to meet flood control limitations are expected. In these scenarios, Reclamation will attempt to make releases in a manner that minimizes redd dewatering where possible. Additionally, Reclamation will consider an implementation strategy that minimizes upstream effects to listed species and is accounted for in the temperature management plans developed in the spring." 2.5.5.lO.L3Assess Species Exposure to Fall Delta Smelt Habitat The Delta waterways function primarily as migratory corridors for winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon, but it also provides holding and rearing habitat for each of these species. Juvenile salmonids may use the area for rearing for several months during the winter and spring before migrating to the marine environment. sDPS green sturgeon use the area for rearing and migration year-round. Generally, as flows increase in the fall and through the winter, adult salmon, steelhead, and green sturgeon migrate upstream through the Sacramento and San Joaquin rivers and juveniles migrate 433 Biological Opinion for the Long-Term Operation of the CVP and SWP downstream in the winter and spring. Adult winter-run Chinook salmon typically migrate through the Delta between November and June with the peak occurring in March. Adult CV spring-run Chinook salmon migrate through the Delta between January and June. Adult CCV steelhead migration jnto the Sacramento River watershed typically begins in August, with a peak in September and October, and extends through the winter to as late as May. Adult sDPS green sturgeon start to migrate upstream to spawning reaches in February and their migrations can extend into July, but they may also be found holding in waters of the Sacramento River basin and Delta year-round. During the proposed Fall Delta Smelt Habitat time period, adult CCV steelhead are typically migrating upstream to spawning grounds in September and October. Juvenile and adult winterrun Chinook salmon and CV spring-run Chinook salmon, as well as juvenile CCV steelhead are unlikely to be present in the Delta at that time. Adult and juvenile sDPS green sturgeon are presumed to be present in the Delta year-round. In contrast to the Delta region, waters below darns in the Central Valley that may be used to augment Delta outflows may contain various life stages oflisted salrnonids and sDPS green sturgeon. For example, the river reaches below Shasta and Keswick reservoirs in September and October may contain incubating winter-run Chinook salmon eggs, newly hatched winter-run alevins, or winter-run Chinook salmon fry. In addition, there is the potential to have either adult spring-run Chinook salmon staging to spawn or already spawning, or adult CCV steelhead holding prior to their spawning activities later in the winter. Furthermore, the upper Sacramento River will also hold both adult and juvenile sDPS green sturgeon during the September and October period when water releases to augment Delta outflow may occur. The species and life stage affected by water releases for fall Delta outflow will depend on which reservoir is utilized to make those releas,es. A summary of the effects of the proposed fall Delta smelt habitat is provided in Table 2.5.5-68 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. 2.5.5.10.l.4Assess Response of Listed Species to the Proposed Fall Delta Smelt Habitat IfReclarnation's PA component would augment Delta outflow with upstream reservoir releases, it could affect plans for water temperatures and flows below the reservoir releasing the water the remainder of the year. Releasing additional water from key reservoirs, such as Shasta Reservoir, to support Delta salinity criteria may deplete the cold water pool faster, and thus impact incubating eggs or larval winter-run Chinook salmon in the tail water reaches below Keswick Darn. A change in Delta Ollltflow or location of the low salinity zone can affect adult CCV steelhead and juvenile and adult sDPS green sturgeon during the fall, as adult CCV steelhead are migrating upstream at this time and sDPS green sturgeon may be migrating or rearing in the Delta. Increased Delta outflow may stimulate adult steelhead to initiate upstream migration earlier as it may resemble a precipitation event in the upper watershed. Changes in Delta outflow and the location of the low salinity mixing zone may influence the location of feeding for juvenile sDPS green sturgeon in the western Delta or influence outmigration of adult green sturgeon following spawning within the Sacramento River rnainstem. 434 Biological Opinion for the Long-Term Operation of the CVP and SWP Since this aspect of the PA component can be implemented in various ways, effects to species or critical habitat are uncertain and will vary year to year and depending on how the outflow augmentation is implemented. Additionally, Reclamation will consider an implementation strategy that minimizes upstream effects to listed species and is accounted for in the temperature management plans developed in the spring. 2.5.5.10.1.5 Risk to Listed Salmonids and sDPS Green Sturgeon Since adult CCV stedhead are typically migrating upstream to spawning grounds in the fall, and adult and sDPS green sturgeon may be present in the action area during the PA component, shifting the low salinity zone upstream for 2 months of the year is not likely to substantially alter food resources of other components that may affect listed salmonids or sDPS green sturgeon as they migrate through or rear in the area. No juvenile salmonids are expected to be present at this time, and adult CCV steelhead are entering from the ocean, traveling from a marine environment to freshwater. Depending on potential changes to exports during the proposed Fall Delta Smelt Habitat action, there may be potential changes to listed fish species migration and survival if outflow is augmented with increased upstream reservoir releases. This could affect plans for water temperatures and flow volumes in both upper river locations and within the Delta. As stated previously, depending on the reservoir making releases to support Delta X2 criteria, different ESUs and DPSs of listed salmonids may be affected. For example, releases made from Shasta Reservoir in September and October may impact eggs and larval winter-run Chinook salmon still in the gravel, and juveniles rearing in the upper Sacramento River below Keswick Dam by depleting the cold water pool necessary for their survival. Since this aspect of the P A component can be implemented in various ways, effects to species or critical habitat are uncertain and will vary year to year and depending on how the outflow augmentation is implemented. Reclamation will attempt to make releases in a manner that minimizes redd dewatering where possible. Additionally, Reclamation will consider an implementation strategy that minimizes upstream effects to listed species and is accounted for in the temperature management plans developed in the spring. 2.5.5.10.2 San Joaquin Basin Steelhead Telemetry Study 2.5.5.10.2.1Physical Description of the San Joaquin Basin Steelhead Telemetry Study Salmonids in the San Joaquin River basin were once abundant and widely distributed, but currently face numerous limiting factors. The NMFS Central Valley Recovery Plan identified that 'Very High' stressors for juvenile CCV steelhead outmigration on the San Joaquin River include habitat availability, changes in hydrology, water temperature, reverse flow conditions, contaminants, habitat degradation, and entrainment (National Marine Fisheries Service 2014b). The impacts of these stressors can be studied using acoustic telemetry, and an updated conceptual model, developed by the South Delta Salmonid Research Collaborative (SDSRC) demonstrates how experimental variables of interest to the 6-Year Study (i.e. Delta water operations, tributary water operations, and habitat) are influential in survival and behavior of emigrating smolts. This conceptual model has guided specific hypotheses and investigations of the 6-Year Study. 435 Biological Opinion for the Long-Term Operation of the CVP and SWP Reclamation conducted a 6-year steelhead telemetry study on the Stanislaus River (20 11-20 16) and is proposing to continue an acoustic tagging study on the San Joaquin River to determine entrainment of San Joaquin River origin CCV steelhead into the Tracy and Jones Pumping Plants. The Stanislaus River Research and Monitoring Program is the most comprehensive and longest running salmon and steelhead monitoring programs in California's San Joaquin Basin, although data are not publicly available. Initiated by FISHBIO personnel in 1993 for the Oakdale and South San Joaquin irrigation dlistricts and Tri-Dam Project, the program's suite of ongoing monitoring activities tracks the abundance, distribution, migration characteristics, and habitat use of salmon and steelhead. 2.5.5.10.2.2Deconstruct the Action- San Joaquin Basin Steelhead Telemetry Study Reclamation proposes to continue the 6-year steelhead telemetry study for the migration and survival of San Joaquin origin CCV steelhead. The PA component incorporates information from the Salmonid Scoping Team and the 6-year steelhead telemetry study to update protections for San Joaquin origin CCV steelhead, continuing the telemetry studies to further refine measures for protecting CCV steelhead. Details of the environmental parameters to be manipulated during the proposed study have not been provided. NMFS assumes that they will be determined during the study development and that the study will be designed to fit within the proposed operations. NMFS assumes that hatchery steelhead would be used for the San Joaquin steelhead telemetry study under the PA, which was not specified in the description for this PA component. Reclamation proposes to insert acoustic tags into juvenile (assumed to be hatchery) steelhead to track them as they move through the south Delta. Acoustic arrays would monitor their presence. This study would help fill a gap in knowledge related to the survival of CCV steelhead originating in the San Joaquin River basin. If Reclamation uses hatchery juvenile steelhead for its acoustic telemetry study and export operations do not differ from the proposed P A, this study will be covered for incidental take under this consultation. However, the details of the acoustic telemetry study were not provided in the PA description. If natural origin CCV steelhead are proposed to be used for the study fish, or if operations of the exports differ from what has been proposed for the PA, then this PA component will be considered as a programmatic consultation. 2.5.5.10.2.3 Assess Species Exposure and Response to the San Joaquin Basin Steelhead Telemetry Study Wild CCV steelhead and fish species may be affected by hatchery releases, as they would compete for food resources and rearing habitat. However, it is expected that the number of tagged fish would be low compared to the number of wild fish present in the system. Furthermore, the overall survival of tagged fish returning from the ocean as adults to spawn is considered to be very low, thus minimizing the effects of hatchery steelhead straying into the system as a result ofthe study implementation. The specifics of the proposed telemetry study, including the number of acoustic tagged fish and release timing were not provided in the ROC on LTOBA. 436 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.10.2.4 Risk to CCV steelhead NMFS assumes that attributes of the proposed 6-year study would be similar to the previous study, including sample size, source of tagged hatchery fish, tagging methods, transport, and release timing. The continuation of the steelhead telemetry study will provide important information about the response of fish migration to flows, exports, and other stressors in the San Joaquin River corridor. NMFS also assumes that the study would continue to assess the relationship of exports to flow, route selection at channel bifurcations in the South Delta and mainstem San Joaquin River, survival in the different channels reaches of the South Delta, and ultimately, survival through the Delta to Chipps Island as a whole. An important aspect of the analysis for CCV steelhead concerns the status of the Southern Sierra Nevada Diversity Group, which is critical to preserving spatial structulre of the CCV steelhead DPS. This diversity group, consisting of extant populations in the Calaveras, Stanislaus, Tuolumne, Merced and upper mainstem San Joaquin rivers, is very unstable due to the poor status of each population. This status is due to both project-related and non-project related stressors. The steelhead telemetry experiment should improve our knowledge base for future consultations. The long-term viability of the Southern Sierra Nevada Diversity Group is expected to depend not only on the continued implementation of the terms and conditions contained within this consultation, but also on actions outside this consultation, most significantly increasing flows in the Tuolumne and Merced rivers. 2.5.5.10.3 Sacramento Deep Water Ship Channel Food Study 2.5.5.10.3.1Physical Description of the Sacramento Deep Water Ship Channel Infrastructure The Sacramento Deep Water Ship Channel (SDWSC) is a 43-mile long artificial channel created in 1963 to allow passage of ocean going vessels from Suisun Bay to the Port of Sacramento in West Sacramento. It begins at RM 0 of the Sacramento River and ends at a navigation lock in West Sacramento between the Sacramento River and the SDWSC. It consists of two sections, Suisun Bay to Cache Slough (lower section), and Cache Slough to West Sacramento (upper section). The upper section consists of the ship channel, a triangular harbor and turning basin called Washington Lake, and a barge canal and navigation lock. The W.G. Stone Lock connects the SDWSC to the Sacramento River via the SDWSC barge channel near Sacramento RM 57 for transfer of barges between waterways. Due to the infrequent usage in the 1980s and 1990s, the lock was de-authorized in 2000, and currently remains in a closed position. However, there is a small amount of water leakage through the lock gate seals. Water exchanges in the SDWSC currently are driven by tidal action. The lack of flow has led to poor water quality conditions, when compared to surrounding areas, conditions in the SDWSC include high salinity and water temperatures, and low DO (Department of Water Resources 2019). Although discontinued use of the lock has likely reduced the attraction of salmonids to the upper SDWSC, a limited, yet unknown number offish, currently enter the channel and arc observed staging below the locks. The survival of salmon and steelhead that migrate into the upper SDWSC is not known. Prior to ceasing lock gate operations, fish could pass through the open 437 Biological Opinion for the Long-Term Operation of the CVP and SWP gates and enter the Sacramento River. Salmon and steelhead that are blocked behind the closed lock gates are thought to be harvested by anglers or die without spawning. Juvenile salmonids are unlikely to enter the SDWSC from the Sacramento River during their emigration due to the limited flow that enters the SDWSC. There is a lack of riparian vegetation and large woody dlcbris along the linear ship channel. Emergent aquatic vegetation, comprised of bulrush cattail and three-square bulrush grows sporadically along the edge of the channel; grasses and forbs grow along the levee slopes. Most of the shoreline is covered with riprap or maintained through vegetation removal and rock applications. 2.5.5.10.3.2Deconstruct the Action- Proposed Operations of Sacramento Deep Water Ship Channel Food Study Reclamation proposes to repair or replace the West Sacramento lock system to hydrologically reconnect the SDWSC with the mainstem of the Sacramento River from mid-spring to late-fall for the purpose of f111.1shing food production into the north Delta to benefit Delta smelt and to provide an alternate migration pathway for fish. Reclamation states that the PA component could result in positive effects on subadult Delta smelt during early fall (U.S. Bureau of Reclamation 2019). The efficacy of the PA component has yet to be tested with pilot studies. In order to re-operate the lock gates, NMFS assumes construction would be required. Since this is a programmatic action, no specific details of construction activity, timing of lock gate operation, or the portion of Sacramento River flow that would be diverted into the SDWSC were provided at this time. Therefore, only a generalized assessment of effects can be assessed based on fish and water moving through the SDWSC during gate operations. 2.5.5.10.3.3Assess Species Exposure to Proposed Sacramento Deep Water Ship Channel Food Study Estimates of the number of salmon, CCV steelhead, and sDPS green sturgeon that enter the SDWSC is unknown. However, Chinook salmon and steelhead are known to have previously migrated through the SDWSC prior to their upstream passage being blocked by the W.G. Stone Locks. Adult Chinook salmon likely migrate into the upper SDWSC and hold below the W.G. Stone Lock, possibly attracted to the small of amount of Sacramento River water leaking through an 8-inch crack in the gates. Known species migration timing indicates that adult Chinook salmon may migrate upstream primarily during spring months and are likely blocked by the lock throughout the summer and fall months, and may be present year-round. Adult winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and the sDPS green sturgeon migrate through the Sacramento-San Joaquin Delta waterways on their way to spawning grounds. The Delta also provides holding and rearing habitats for each of these species as they emigrate as juveniles. Juvenile salmonidls may use the area for rearing for several months during the winter and spring before migrating to the marine environment. sDPS green sturgeon use the area for rearing and migration year-round. All four species are likely to be present in the Delta or Sacramento River during part of all of the mid-spring to late-fall time period, and therefore would be exposed to the P A. Reconnecting the SDWSC to the Sacramento River would allow part of the river to flow through the SDWSC potentially improving some 438 Biological Opinion for the Long-Term Operation of the CVP and SWP water quality parameters. The PA component could also increase the mobilization of accumulated sediment in the channel, which could contain historical pesticides or other contaminants, possibly affecting listed fish species present in the SDWSC or downstream. Assuming that the repair or replacement of the lock system would involve construction activities such as dredging and pile driving, effects from suspended sediment and noise would be expected, and would likely include decreased DO, increased turbidity, and mobilization oftoxic chemicals, according to the Central Valley Regional Water Quality Control Board basin plan (California Regional Water Quality Control Board 2018). Since detailed construction activities were not provided to NMFS, effects to species from construction activities could not be analyzed at this time. A summary of the effects ofthe proposed SCWSC food study is provided in Table 2.5.5-69 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. 2.S.S.10.3.4Assess Response of Species to the Proposed Sacramento Deep Water Ship Channel Food Study Estimates of the number of adult salmon, CCV steelhead, and sDPS green sturgeon that enter the SDWSC and follow it upstream to the lock is unknown. However, existing information indicates that adult Chinook salmon and steelhead migrate into the SDWSC and their upstream passage is blocked by the W.G. Stone Locks. Re-opening the gates may allow adult salmonids and potentially sDPS green sturgeon to migrate between the Sacramento River and SDWSC, which would likely benefit fish that would otherwise be blocked. An increase in flow through the SDWSC may also cause a false attraction for adult salmonids and sDPS green sturgeon, leading to more adults entering the SDWSC rather than migrating up their natural route through the Sacramento River. Allowing flow to enter the SDWSC from the Sacramento River during times of year when juvenile salmonids are outmigrating, may change their route, taking them through the SDWSC rather than through their natural migration route down the Sacramento River. Survival in the SDWSC in unknown, however, it would likely result in decreased survival, due to potential predation and lack of suitable rearing habitat. In-channel large woody debris and shaded riverine aquatic (SRA) habitats are important components for rearing salmonids because they contribute to shade, food production, and cover from predators. The sparse and sporadic distribution of these habitats, in addition to mobilizing potentially contaminated sediment in the SDWSC, limit the value of the channel as rearing habitat for salmon, CCV steelhead, and sDPS green sturgeon. Opening the W.G. Stone Locks would facilitate the upstream passage of adult salmonids and sDPS green sturgeon, but may also divert juvenile salmon and sDPS green sturgeon from the Sacramento River downstream into the SDWSC. Closing or opening the gates may attract increased numbers of adult salmon and sDPS green sturgeon upstream into the SDWSC which may become trapped or delayed behind the gates when they are closed. The primary factors affecting the species' survival within the SDWSC include freshwater flows through the lock, tidal exchange, water temperatures, water quality, riparian habitat, angler harvest, and predation. ESA-listed fish species may be affected by creating false attraction flows, blocking adult salmon and sDPS green sturgeon behind the lock gates, creating unfavorable juvenile outmigration conditions, and reducing the number of individuals that escape to the Pacific Ocean or migrate upriver to spawn. Furthermore, an additional risk for adult sDPS green sturgeon is the 439 Biological Opinion for the Long-Term Operation of the CVP and SWP vulnerability of vessel strikes from large ocean going vessels transiting the SDWSC while traveling to or from the Port of Sacramento. Potential effects from construction activity may include temporary effects from increased turbidity, decreased DO, and pile driving activities. Since detailed activities were not provided, effects to fish are not analyzed at this time. 2.5.5.10.4 North Delta Food Subsidies I Colusa Basin Drain and Suisun Marsh Roaring River Distribution System Food Subsidy Studies 2.5.5.10.4.1Physical Description of the Colusa Basin Drain, and Suisun Marsh Roaring River Distribution System The Colusa Basin drain, located near the town of Dunnigan, California, provides drainage for surface runoff as well as agricultural discharge. The drain also serves as a water source for irrigation users. In the fall, during high irrigation use, water flows from the Colusa Basin drain through Knights Landing outfall gates into the Sacramento River or into Yolo Bypass. Suisun Marsh is a large brackish marsh area that is part of the San Francisco Bay tidal estuary. It is formed primarily by the confluence of the Sacramento and San Joaquin rivers between Martinez and Suisun City, California. The Suisun Marsh facilities are jointly operated by the CVP and SWP, and include the Suisun Marsh Salinity Control Gates (SMSCG), Roaring River Distribution System (RRDS), Morrow Island Distribution System (MIDS), and Goodyear Slough Outfall. The SMSCG are located on Montezuma Slough about 2 miles downstream of the confluence of the Sacramento and San Joaquin rivers, near Collinsville, California. The purpose of gate operation is to decrease the salinity of the water in Montezuma Slough to meet salinity standards set by the SWRCB and Suisun Marsh Preservation Agreement. The SMSCG control salinity by lowering gates during flood tides to prevent flow of higher salinity water from Grizzly Bay into Montezuma Slough and opening gates during ebb tides to retain the lower salinity Sacramento River water that entered the marsh during the previous ebb (outgoing) tide. Currently, SMSCG operation occurs from October to May 0-20 days) where radial gates are lowered during the flood tides and opened during the ebb tides, tlashboards are in place through September, and a boat lock is operated as-needed for passing vessels. Outside of the period, the radial gates remain open, flashboards are removed, and operation of the boat lock is not needed. As of2018, gates are operated during August in "below normal" or "above normal" water years in addition to October to May operation. Roaring River is located north of Honker Bay. The RRDS diverts water from Montezuma Slough through a bank of eight 60-inch-diameter culverts. RRDS is equipped with fish screens into the Roaring River intake pond during high tides, in order to raise the water surface elevation in RRDS above the adjacent managed wetlands. Managed wetlands north and south of the RRDS receive water, as needed, through publicly and privately owned turnouts on the system. 440 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.10.4.2 Deconstruct the Action- Proposed Food Subsidies 2.5.5.10.4.2.1 North Delta Food Subsidies I Colusa Basin Drain Reclamation proposes to increase food entering the north Delta through flushing nutrients from the Colusa Basin into the Yolo Bypass and north Delta. DWR, Reclamation, and water users would work with partners to flush agricultural drainage water from the Colusa Basin Drain through Knights Landing Ridge Cut and the Tule Canal to Cache Slough, to potentially increase aquatic food resources in the north Delta for fish. Reclamation would work with DWR and partners to augment flow in the Yolo Bypass in July and/or September by closing Knights Landing Outfall Gates and routing water from Colusa Basin into Yolo Bypass to promote food production for fish. Under the PA component, approximately 24,000 acre-feet (AF) of agricultural water would be diverted over a 4-week period (during July, August, and/or September) from Colusa Basin into Yolo Bypass rather than out falling into the Sacramento River. This would result in increased flow in Yolo Bypass during late summer. Since this is a programmatic action, the ROC on LTO BA does not provide sufficient detail to conduct an indepth effects assessment for this PA component. Therefore, the assessment of PA effects will be a very high level overview of this PA component and not adequate for a full consultation. Therefore, this PA component will be considered as a programmatic consultation. 2.5.5.10.4.2.2 Suisun Marsh Food Subsidies Reclamation proposes to increase food production for fish in Suisun Marsh through coordinating managed wetland flood and drain operations in Suisun Marsh, RRDS food production, and reoperation of the SMSCG in June through September in above normal and below normal years. As noted in the Delta Smelt Resiliency Strategy, the purpose of this management action is to attract Delta smelt into the high-quality Suisun Marsh habitat, reducing use of the less food-rich Suisun Bay habitat (California National Resources Agency 2016). Infrastructure in the RRDS would be used to help drain food-rich water from the canal into Grizzly Bay to potentially augment Delta smelt food supplies in that area. In addition to the current October through May operation to meet Suisun Marsh water quality standards, Reclamation proposes operating the SMSCG on the tidal cycle in below normal and above normal years in June through September for 60 days, not necessarily consecutive, to improve Delta smelt critical habitat. Under the P A component, Reclamation and DWR would increase tidal operations of the SMSCG to direct more fresh water in Suisun Marsh to reduce salinity, increase food, and improve habitat conditions for Delta smelt. In addition to current operation, SMSCG would operate in June to September in above normal and below normal years. This would be combined with RRDS management for food production and flushing freshwater through the RRDS to increase the low salinity habitat in Grizzly and Honker bays. Reclamation and DWR will continue to meet existing D-1641 salinity requirements in the Delta and Suisun Marsh. Since this is a programmatic action, the ROC on LTO BA does not provide sufficient detail to conduct an in-depth effects assessment for this P A component. Therefore, the assessment ofPA effects will be a very high level overview ofthis PA component and not adequate for a full consultation. Therefore, this PA component will be considered as a programmatic consultation. 441 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.10.4.3Assess Species Exposure to Proposed Food Subsidies Reclamation proposes to route approximately 24,000 AF of agricultural water through the Colusa Basin Drain to the Cache Slough area through the Yolo Bypass during the months of July to September. The timing of observations of listed species in the Delta are determined by Delta Juvenile Fish Monitoring Program (DJFMP) (U.S. Fish and Wildlife Service 2014, 2015b, 20 16a, 20 17)(USFWS 2000-20 16), which conducts annual monitoring of fishes to determine abundance and distribution of juvenile salmonids and other species. According to DJFMP data, juvenile winter-run Chinook salmon are primarily present in the Delta from November to April, juvenile CV spring-run Chinook salmon are present primarily from December through May, and juvenile CCV steelhead were determined to be present in the Delta primarily from December to July. According to DJFMP and salvage data, and sDPS green sturgeon are present year-round. Adult winter-run Chinook salmon are present in the Delta from November to June as they migrate from the ocean up the Sacramento River to their spawning grounds. Adult CV spring-run Chinook salmon are present in the Delta from January through June (California Department of Fish and Wildlife 1998, Yoshiyama et al. 1998, Moyle 2002). Adult CCV steelhead are present in the Delta from August to October on their way to the northern Central Valley tributaries (Moyle 2002), and from March to May on their return to the ocean (Hallock et al. 1961). For San Joaquin River origin fish, adult CCV steelhead peak in November through January (California Department ofFish and Game 2007). There are limited data on the residence time and run timing of adult CCV steelhead of both Sacramento and San Joaquin River origin in the Delta. Adult sDPS green sturgeon may be present in the Delta during all months of the year (Moyle et al. 1995, Heublein et al. 2009). A summary of the effects of the proposed north Delta food subsidies/Colusa Basin Drain is provided in Table 2.5.5-70 in Section 2.5.5.14 Summary Tables ofStressors for each Project Component. 2.5.5.10.4.4Assess Response of Listed Species to the Proposed Food Subsidies The PA component has the potential to increase the exposure of fish to harmful contaminants through diversion of agricultural drainage into the Sacramento River. Chemical forms of water pollution are a major cause of freshwater habitat degradation worldwide. There are many sources of contaminants, and these reflect past and present human activities and land use (Scholz and Mcintyre 2015). Conta minants are typically associated with areas of urban development, agriculture, or other anthropogenic activities. Organic contaminants from agricultural drain water, urban and agricultural runoff from storm events, and high trace element (i.e., heavy metals) concentrations may have deleteriously effects on survival of fish in the Central Valley watersheds. One of the contaminants potentially present is selenium, which was identified as one of the pollutants in San Francisco Bay and the western Delta on the Clean Water Act section 303(d) list (State Water Resources Control Board 2010a). Within the Delta, there are multiple sources of selenium. Presser and Luoma (2013) identify oil refinery wastewaters from processing crude oils at North Bay refineries and irrigation drainage from agricultural lands in the western San Joaquin Valley (mainly via the San Joaquin River) as the two primary sources. Agricultural drainage in the Sacramento Valley west-side creeks in the Yolo Bypass and non-oil industries and wastewater treatment effluents are minor sources of selenium in the Delta. Selenium can elicit a short- and long-term response from aquatic biota depending on the quantity, quality, and 442 Biological Opinion for the Long-Term Operation of the CVP and SWP duration of selenium exposure. The primary exposure pathway for fish and other aquatic organisms to selenium is through their diet (Stewart et al. 2004, Presser and Luoma 2010a, Presser and Luoma 201 Ob, 20 13). Continued exposure of selenium can result in bioaccumulation and/or toxicity to fish in the Delta. Because adult salmon and steel head do not forage extensively while in the Delta before spawning upstream in the rivers (Sasaki 1966), their exposure is likely to be much less than exposure for j uveniles, which spend most of their time in the Delta feeding and foraging for food. Thus, survival and growth of juvenile salmonids may be affected by potential contaminant exposure, due to the timing in which those juveniles occur and feed within the action area. sDPS green sturgeon migrate from major rivers to the Delta and reside within the Delta or in the Pacific Ocean (U.S. Fish and Wildlife Service 2008). Therefore, all life stages of sturgeon have the potential to be exposed to contaminants in the Delta. At Suisun Marsh, the SMSCG would be operated for 60 days in June to September in above normal and below normal years and up to 20 days during October to May. SMSCG would be operated for a total of up to 80 days year-round, primarily during summer months. NMFS assumes the boat lock would remain in the open position during operation, allowing fish passage when gates are closed. Operation of the SMSCG from October through May coincides with the upstream migration of adult Central Valley anadromous salmonids and sDPS green sturgeon. The late winter and spring downstream migration of Central Valley salmon ids also overlaps with the operational period of the SMSCG. During summer operations, juvenile and adult CCV steelhead and sDPS green sturgeon are present in the Delta, and potentially adult winter-run Chinook salmon and CV spring-run Chinook salmon during June. During the majority of the year, the SMSCG will not be operated and no fish passage delays due to the gates are anticipated. However, during the annual 70 to 80 days of periodic operation, individual adult salmonids and sDPS green sturgeon may be delayed in their spawning migration from a few hours to several days. If the destination of a pre-spawning adult salmon or CCV steelhead is among the smaller tributaries of the Central Valley, it may be important for migration to be unimpeded, since access to a spawning area could diminish with receding flows. sDPS green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River, and spring stream flows in the mainstem Sacramento River are generally not limiting their upstream migration. It is also common for sDPS adult green sturgeon to linger for several days in the Delta prior to initiating their active direction migration to the upper Sacramento River (Vogel2008). 2.5.5.1 0.4.5 Assess Risk to Listed Fish Species ESA-Iisted fish species that are most likely to be present during the North Delta Food Subsidies/ Colusa Basin Drain P A component include juvenile and adult sDPS green sturgeon and adult CCV steelhead. Since the PA component includes diversions that would occur during the summer and early fall, most ESA-listed species are unlikely to be present in the Yolo Basin, Tule Canal, Toe Drain, or Cache Slough complex during this period oftime. However, the project description does not provide specific details such as expected changes to water temperature or contaminant load of the diverted agricultural water and therefore, impacts cannot be fully analyzed at this time. Only generalized impacts will be considered in this analysis. This PA component will be considered as a programmatic consultation. The proposed Suisun Marsh Food Subsidies action could affect all four listed species present in the Suisun Marsh, Suisun Bay, Grizzly Bay, and Honker Bay since SMSCG operation would occur year-round, however, operation would only occur up to 80 days of the year. 443 Biological Opinion for the Long-Term Operation of the CVP and SWP Migrating salmonids and sDPS green sturgeon may be affected by the operation of the SMSCG, as it may delay their movement. If the SMSCG are in operation, the gates will open and close twice each day with the tides. On the ebb tide, the gates are open and fish will pass downstream into Montezuma Slough without restriction. On the flood tide, the gates are closed and freshwater flow and the passage of juvenile fish will be restricted. Salmonid smolt predation by striped bass and pikeminnow could be exacerbated by operation of the SMSCG since these predatory fish are known to congregate in areas where prey species can be easily ambushed. However, operation of the SMSCG would be limited to only periods required for compliance with salinity control standards, and this operational frequency is expected to be no more than 80 days per year, mostly during summer months when smolts are unlikely to be present. Therefore, the SMSCG will not provide the stable environment which favors the establishment of a local predatory fish population and the facility is not expected to support conditions for an unusually large population of striped bass and pikeminnow. In addition, most listed Central Valley salmonid smolts reach the Delta as yearlings or older fish. The project description did not include specific details on water quality in the Colusa Basin Drain or whether the SMSCG boat lock would be open during operation or when the flashboards would be installed and removed. In order to fully assess impacts of the PA to ESA-listed fish species for the North Delta and SMSCG Food Studies, more information should be provided. Therefore, this PA component will be considered a programmatic consultation. 2.5.5.10.5 Habitat Restoration in the Bay/Delta 2.5.5.10.5.1 Tidal Habitat Restoration 8,000 acres (U.S. Fish and Wildlife Service 2008) All ESA-listed salmonids and sturgeon must pass through the Delta during their migration to the Pacific Ocean. Although rearing and migration through the Delta represents a short period of these fish's overall life-cycle, a large proportion of juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon are expected to be exposed to 8,000 acres of tidal habitat restoration in the Delta. Tidal habitat restoration is expected to benefit juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and southern DPS green sturgeon in several aspects, including increased food availability and quality, and refuge habitat from predators. These benefits can be manifested by higher growth rates in fish utilizing these habitats and increased survival through the Delta. The in-water construction work window for tidal and channel margin restoration under the PA component is August-October. The following life stages of the listed salmonids and sDPS sturgeon are expected to be present in the Delta during this period and have the potential to be exposed to impacts from in-water construction: immigrating adult CCV steelhead; juvenile sDPS green sturgeon; and some emigrating adult sDPS green sturgeon. Few if any juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, or CCV steelhead are expected to be present during the in-water construction work window. Reclamation lists the following potential effects to listed salmonids and sDPS green sturgeon from construction of restoration projects in the ROC on LTO BA (U.S. Bureau of Reclamation 2019): "temporary loss ofaquatic and riparian habitat leading to increased predation, increased water temperature, and reduced food availability; degraded water quality from contaminant discharge by heavy equipment and soils, and increased discharges of 444 Biological Opinion for the Long-Term Operation of the CVP and SWP suspended solids and turbidity, leading to direct toxicological impacts on fish health/performance, indirect impairment of aquatic ecosystem productivity, loss of aquatic vegetation providing physical shelter, and reducedforaging ability caused by decreased visibility; impediments and delay in migration caused by elevated noise levels from machinery; and direct injury or mortality from in-water equipment strikes or isolation/stranding within dewatered cofferdams. The risk from these potential effects would be minimized through application ofAMMs (Appendix E, A voidance and Minimization Measures)." Reclamation also states in the ROC on LTO BA that "Reclamation and DWR will consult on future tidal habitat restoration with USFWS and NMFS on potential effects to fish from construction-related effects." Due to the lack of specifics project elements and details regarding implementation, and success criteria, this P A component will be considered as a programmatic consultation. 2.5.5.10.5.2 Predator Hot Spot Removal Predator hot spot removal under the PA component (April 30, 2019; Appendix A2) is intended to improve conditions for downstream-migrating juvenile salmonids, including winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead. The PA component may focus removal efforts where predators are likely concentrated along the primary migratory routes of j uvenile Chinook salmon [e.g., hotspots identified by Grossman et al. (2013)]. However, implementation of the PA component could also improve conditions for all life stages of CCV steelhead and potentially juvenile sDPS green sturgeon emigrating downstream. The ultimate effect of predator hotspot removal on juvenile salmonid and sDPS green sturgeon survival is uncertain. Hotspots are limited in scale relative to overall available habitat and previous research has not found a consistent positive effect of predator removal on juvenile salmon survival (Cavallo et al. 2012, Michel et al. 2015, Saba! et al. 2016). In general, there is a lack of detail and specificity in the BA to conduct a thorough effects analysis for this PA component. Analysis of the PA component effects are general in nature and will be considered as a programmatic consultation. 2.5.5.10.5.2.1 Deconstruction of the Predator Hot Spot Removal Reclamation proposes to remove potential predator hot spots that occur in waters of the Delta. These hot spots may include in-water structures such as abandoned docks, outfalls, pump platforms, or pilings, removing overhead lighting at bridges and fish screens that illuminate the water surface at night, or filling in scour holes or other anomalies in the bathymetry that attract predators. The ROC on LTO BA does not identify exact locations or the process that will be undertaken to remove these predator hotspots. 2.5.5.10.5.2.2 Assess Exposure to of Listed Species to Predator Hot Spot Removal In-water construction at predator hot spot removal locations in the lower Sacramento River and Bay/Delta is proposed to occur during the in-water work windows through the summer months, when juvenile listed salmonids are generally still located in the upper river sections of the Sacramento River and San Joaquin River basins. However, the starting and endpoints for the in445 Biological Opinion for the Long-Term Operation of the CVP and SWP water work window were not defmed in the BA. Based on the summer in-water work window, construction actions at hot spot locations is not anticipated to effect juvenile salmonids but could occur when rearing juvenile sDPS green sturgeon are present, due to the year-round use of the Delta by juvenile sDPS green sturgeon for rearing. In addition, locations in the northern Delta could have removal of the hot spots overlap with the presence of adult CCV steelhead, which are migrating through the system in large numbers from Alllgust through November. 2.5.5.10.5.2.3 Assess Response of Listed Salmonids to Predator Hot Spot Removal Since the ROC on LTO BA has not described the methods proposed to remove predator hot spots, it is difficult to assess the response of listed salmonids or sDPS green sturgeon to these actions. NMFS anticipates that heavy construction actions will need to take place to remove structures or pilings in the water, as well as to fill in scour holes or other bathymetry anomalies that attract predators. Typically, heavy construction actions create noise and vibrations in the surrounding aquatic environment that will disturb any fish located in the proximity of the action. Filling in scour holes, typically with some sort of rock substrate, may entail potential crushing or injuries due to the dumping of fill materials into the water column. Normally, any fish present at the onset of such construction activities will leave the location of the disturbance and thus avoid any negative effects. 2.5.5.10.5.2.4 Assess Response of sDPS Green Sturgeon to Predator Hot Spot Removal Although details of the PA components for this action are minimal, NMFS anticipates that responses of sDPS green sturgeon to construction related actions to remove predator hotspots will be similar to listed salmonids. Individuals from the sDPS green sturgeon population may be more susceptible to the construction related actions to remove predator hot spots in the Bay/Delta region due to their year-round presence in the Delta. Elevated construction activity is anticipated to drive sDPS green sturgeon away from areas of the predator hot spot removal as individuals attempt to avoid disturbances in the aquatic environment. As stated previously, the lack of detail in the ROC on LTO BA regarding the predator hot spot action limits the assessment of effects to listed sDPS green sturgeon. 2.5.5.10.5.2.5 Assess Risk to Listed Salmonids from Predator Hot Spot Removal NMFS anticipates that there will be low risk to juvenile listed salmonids associated with the removal of predator hot spots due to the timing of such work. Juvenile listed salmonids are expected to be upriv,e r of the Delta during the summer, and thus will not be exposed to any of the construction actions required to remove identified predator hot spots in the Delta. On the other hand, adult CCV steelhead migrating into the Sacramento River basin may be exposed to the effects of any construction actions required to remove predator hot spots. These fish may be exposed to increased levels of sound, vibrations, or activities along the banks of migratory channels. In most instances, these disturbances will potentially cause migratory delays, or rerouting of fish into migratory pathways with less activity. In the most extreme cases, exposure to the construction activities could cause injury or death. Implementation of the proposed AMMs will reduce the level of risk associated with the construction actions. After removal of in-water structures or other features that create predator hotspots, migratory success ofjuvenile salmonids should be enhanced. However, the improvement may be transitory or less than anticipated due to the beihavior of predators, and the potential that predators would move to adjacent habitat. It 446 Biological Opinion for the Long-Term Operation of the CVP and SWP should be noted that the lack of detail in the description of this PA component limits the level of detail in assessing the risk to listed salmonids. Therefore, this P A component will be considered as a programmatic consultation. 2.5.5.10.5.2.6 Assess Risk to Listed sDPS Green Sturgeon from Predator Hot Spot Removal NMFS anticipates that overall there will be a low to medium risk to juvenile sDPS green sturgeon associated with the removal of predator hot spots in the Delta due to the distribution of individual green sturgeon across the Delta. The greatest risk will come from activities that fill in scour holes or other bathymetric anomalies that attract predators. Such habitat would also tend to attract sDPS green sturgeon due to the increased water depth, thus providing a higher level of overlap between the presence of sDPS green sturgeon and the activities associated with predator hot spot removal. However, the BA does not identify the numbers or locations of such deep water habitat that would be identified as a predator hot spot, thus providing a detailed assessment of the level of risk is not possible. This PA component will be considered as a programmatic consultation. 2.5.5.10.6 Fish Intervention 2.5.5.10.6.1 Reintroduction efforts from Fish Conservation and Culture Laboratory The existing Fish Conservation and Culture Laboratory (FCCL) located adjacent to the SDFPF at the SWP will be used to begin Delta smelt production to supplement the natural Delta smelt population. Information developed through the operations of the FCCL will be used to create a supplementation strategy and inform the construction of the new conservation hatchery. The culture of Delta smelt at the FCCL does not utilize or expose any listed salmonid or sDPS green sturgeon to capture or handling. The facility is located outside of designated critical habitat for CCV steelhead and sDPS green sturgeon on the inlet channel to the Banks Pumping Plant of the SWP. It is not expected that the release of cultured Delta smelt back into the Delta, its historical native habitat, will have any negative impacts on listed salmonids or sDPS green sturgeon present in the Delta. 2.5.5.10.6.2 Delta F ish Species Conservation Hatchery The operation of the Delta Fish Species Conservation Hatchery would not provide benefits to any life stage of winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, or sDPS green sturgeon. Potential negative effects of the Delta Fish Species Conservation Hatchery include inadvertent propagation and spread of invasive or nuisance species, which could affect listed salmonids and sDPS green sturgeon through changes in food web structure. Additional impacts could include reduced water quality resulting from hatchery discharge. Potential negative effects from discharged water are expected to be minimal due to the water sterilization treatments for pathogens and invasive species and the very small size of the discharge compared to flows in the Sacramento River near the hatchery location. Mitigation and minimization measures detailed in the EIR/EIS for the facility (Horizon Water and Environment 2017) indicate that potential impacts are less than significant. Potential exposure of juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon would be restricted to a small spatial area within the primary migration route and rearing habitat where 447 Biological Opinion for the Long-Term Operation of the CVP and SWP effluent from the Delta Fish Species Conservation Hatchery discharges into the Sacramento River. As with the other proposed construction activities in the Bay-Delta, few if any juvenile winterrun Chinook salmon, CV spring-run Chinook salmon, or CCV steelhead would be expected to be exposed to the effects of construction of the Delta Fishes Species Conservation Hatchery based on the timing of in-water construction (August-October) and the typical seasonal occurrence of these fish in the Delta. There may be some exposure of early or late migrating juvenile salmonids to in-water and shoreline construction ofthe hatchery intake and outfall. The year-round occurrence ofjuvenile sDPS green sturgeon in the Delta means that this life stage, as well as adult sDPS green sturgeon occurring in the Delta during May to October, could be exposed to Delta Fish Species Conservation Hatchery construction under the PA component. Individuals occurring near the construction site could be subject to effects similar to those previously described for habitat restoration (e.g., temporary loss of habitat leading to predation, degraded water quality, reduced foraging ability caused by reduced visibility, noise-related delay in migration, and direct effects from contact with construction equipment or isolation/stranding within enclosed areas). The risk from these potential effects would be minimized through application of AMMs [U.S. Bureau of Reclamation (20 19): Appendix E, Avoidance and Minimization Measures]. There is low potential for exposure because of the in-water work window, the application of AMMs, and the small scale of the in-water construction. However due to the lack of specific plans and construction schedule that may require years to complete the facility, a full effects analysis cannot be conducted. Therefore, this PA component will be considered as a programmatic consultation. 2.5.5.11 Supplemental Analysis of June 14, 2019, Final PA During consultation for this opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, BA that was used for the majority of the analysis in this opinion. It was not possible to include these revisions in any modeling due to the White House memorandum that mandated issuance of final biological opinions within 135 days ofthe January 31,2019 (June 17,2019, and subsequently extended to July 1, 2019). The effects description above (Section 2.5.5.1-2.5.5.10) was (unless otherwise noted) based on the modeling associated with the February 5, 2019 PA (Appendix Al, the original PA), and associated modeling that NMFS requested. The following subsection provides a supplemental effects analysis to assess the effects of the June 14, 2019 PA revisions reflected in the final PA (Appendix A3), including a discussion ofwhether and how the PA revisions modifY the effects analyzed above. 2.5.5.11.1 Revisions to OMR Management As a result of discussions, the OMR management section of the PA included sufficient changes and that the final PA (Appendix A3) shows most of the PA component as new text- not changes relative to the February 5, 2019 PA. All details of the revised OMR Management component of the PA are excerpted below; bold, italicized, text is used to highlight key changes assessed in this supplemental analysis. 448 Biological Opinion for the Long-Term Operation of the CVP and SWP Onset of OMR Management: "Reclamation and DWR shall start OMR management when one or more of the following conditions have occurred: • Integrated Early Winter Pulse Protection ("First Flush" Turbidity Event): To minimize project influence on migration (or dispersal) of Delta Smelt, Reclamation and DWR proposes to reduce exports for 14 consecutive days so that the 14-day averaged OMR index for the period shall not be more negative than -2,000 cfs, in response to "First Flush" conditions in the Delta. The population-scale migration of Delta Smelt is believed to occur quickly in response to inflowing freshwater and turbidity (Grimaldo et al. 2009, Sommer et al. 2011). Thereafter, the best available scientific information suggests that fish make local movements, but there is no evidence for further population-scale migration (Polansky et al. 2017)). "First Flush" conditions may be triggered between December 1 and January 31 and include: o o o running 3-day average of the daily flows at Freeport is greater than 25,000 cfs and running 3-day average of the daily turbidity at Freeport is 50 NTU or greater, or real-6me monitoring indicates a high risk of migration and dispersal into areas at high risk of future entrainment. This "First Flush" action may only be initiated once during the December through January period and will not be required if: o o water temperature reaches 12 degrees Celsius based on a three station daily mean at Honker Bay, Antioch, and Rio Vista, and/or ripe or spent Delta Smelt are collected in monitoring surveys. Salmonids Presence: After January 1, if more than 5 percent of any one or more salmonid species (wild young-of-year Winter-Run, wild young-of-year Spring-Run, or wild Central Valley Steelhead) are estimated to be present in the Delta as determined by their appropriate monitoring working group based on available real-time data, historical information, and modeling." Additional Real-Time OMR Restrictions and Performance Objectives: "Reclamation and DWR shall manage to a more positive OMR than -5,000 cfs based on the following conditions: • Turbidity Bridge Avoidance ("South Delta Turbidity"): After the Integrated Early Winter Pulse Protection (above) or February 1, whichever comes first, and prior to April 1, Reclamation and DWR propose to manage exports in order to maintain daily average turbidity in Old River at Bacon Island (OBI) at a level of less than 12 NTU. The purpose of this action is to protect Delta Smelt from damaging levels of entrainment after a First Flush and in years when a First Flush does not occur. This action seeks to avoid the formation of a continuous turbidity bridge from the San Joaquin River shipping channel to the fish facilities, which historically has been associated with elevated salvage of prespawning adult Delta Smelt. If the day daily average turbidity at Bacon Island cannot be maintained less than 12 NTU, Reclamation and DWR will manage exports to achieve an OMR no more negative than -2,000 cfs until the turbidity at Bacon Island drops below 12 NTU. After 5 days, Reclamation and DWR may determine that additional real-time OMR restrictions are not required to avoid damaging levels of entrainment based on the 449 Biological Opinion for the Long-Term Operation of the CVP and SWP • • distribution of Delta Smelt in real-time monitoring and the absence of detections in salvage (i.e. <5% of the population). Larval and Juvenile Delta Smelt: When Q-West is negative and larval or juvenile Delta Smelt are within the entrainment zone of the pumps based on real-time sampling, Reclamation and/or DWR propose to run hydrodynamic models informed by the EDSM, 20 mm or other relevant survey data to estimate the percentage of larval and juvenile Delta Smelt that could be entrained and operate to avoid greater than 10 percent loss of modeled larval and juvenile cohort Delta Smelt (typically this would come into effect beginning the middle of March). Cumulative Loss Threshold: o o o o o Reclamation and DWR propose to avoid exceeding cumulative loss thresholds over the duration ofthe Biological Opinions for wild Winter-Run Chinook Salmon, hatchery Winter-Run Chinook Salmon, wild Central Valley Steelhead from December through March, and wild Central Valley Steelheadfrom April] through June 15th. Wild Central Valley Steelhead are separated into two time periods to protect San Joaquin Origin fish that historically appear in the Moss dale trawls later than Sacramento origin fish. The loss threshold and loss tracking for hatchery Winter-Run Chinook Salmon does not include releases into .Battle Creek. Loss (for development ofthresholds and ongoing tracking) for Chinook salmon are based on length-at-date criteria. The cumulative loss thresholds shall be based on cumulative historical loss from 2010 through 2018. Reclamation's and D WR 's performance objectives will set a trajectory such that this cumulative loss threshold (measured as the 2010-2018 average cumulative loss multiplied by 10 years) will not be exceeded by 2030. If, at any time prior to 2024, , Reclamation and DWR exceed 50% ofthe cumulative loss threshold, Reclamation and D WR will convene an independent panel to review the actions contributing to this loss trajectory and make recommendations on modifications or additional actions to stay within the cumulative loss threshold, if any. In the year 2024, Reclamation and D WR will convene an independent panel to review the first five years ofactions and determine whether continuing these actions are likely to reliably maintain the trajectory associated with this performance objective for the duration ofthe period. If, during real-time operations, Reclamation and DWR exceed the cumulative loss threshold, Reclamation and DWR would immediately seek technical assistance from USFWS and NMFS, as appropriate, on the coordinated operation of the CVP and SWP for the remainder ofthe OMR management period. In addition, Reclamation and D WR shall, prior to the next OMR management season, charter an independent panel to review the OMR Management Action consistent with "Chartering ofIndependent Panels" under the "Governance" section ofthis Proposed Action. The purpose ofthe independent review shall be to evaluate the efficacy of actions to reduce the adverse effects on listed species under OMR management and the non-flow 450 Biological Opinion for the Long-Term Operation of the CVP and SWP measures to improve survival in the south Delta and for San Joaquin origin fish. • Single-Year Loss Threshold: o o o o o o o In each year, Reclamation and DWR propose to avoid exceeding an annual loss threshold equal to 90% ofthe greatest annual loss that occurred in the historical record from 2010 through 2018for each ofwild Winter-Run Chinook Salmon, hatchery Winter-Run Chinook Salmon, wild Central Valley Steelhead from December through March, and wild Central Valley Steelheadfrom April through June 15. Wild Central Valley Steelhead are separated into two time periods to protect San Joaquin Origin fish that historically appear in the Moss dale trawls later than Sacramento origin fish. The loss threshold and loss tracking for hatchery Winter-Run Chinook Salmon does not include releases into Battle Creek. Loss (for development ofthresholds and ongoing tracking) for Chinook salmon are based on length-at-date criteria. During the year, ifReclamation and D WR exceed the average annual loss from 2010 through 2018, Reclamation and DWR will review recent fish distribution information and operations with the fisheries agencies at WOMT and seek technical assistance on future planned operations. Any agency may elevate from WOMT to a Directors discussion, as appropriate. During the year, ifReclamation and DWR exceed 50% ofthe annual loss threshold, Reclamation and DWR will restrict OMR to a 14-day moving average OMR index ofno more negative than -3,500 cfs, unless Reclamatio.n and DWR determine that further OMR restrictions are not required to benefit fish movement because a risk assessment shows that the risk is no longer present based on real-time information. The -3500 OMR operational criteria adjusted and informed by this risk assessment will remain in effect for the rest of the season. Reclamation and D WR will seek NMFS technical assistance on the risk assessment and real-time operations. During the year, if Reclamation and D WR exceed 75% ofthe annual loss threshold, Reclamation and DWR will restrict OMR to a 14-day moving average OMR index ofno more negative than -2,500 cfs, unless Reclamatio.n and DWR determine that further OMR restrictions are not required to benefit fish movement because a risk assessment shows that the risk is no longer present based on real-time information. The -2500 OMR operational criteria adjusted and informed by this risk assessment will remain in effect for the rest of the season. Reclamation and DWR will seek NMFS technical assistance on the risk assessment and real-time operations. Risk assessment: Reclamation and DWR will determine and adjust OMR restrictions under this section by preparing a risk assessment that considers several factors including, but not limited to, real-time monitoring detects few fish in the south Delta and few fish are detected in salvage. Reclamation and D WR will share its technical analysis and supporting documentation with USFWS and NMFS, seek their technical assistance, discuss the risk assessment 451 Biological Opinion for the Long-Term Operation of the CVP and SWP and future operations with WOMT at its next meeting, and elevate to the Directors as appropriate. o If, during real-time operations, Reclamation and DWR exceed the single-year loss threshold, Reclamation and DWR would immediately seek technical assistance from USFWS and NMFS, as appropriate, on the coordinated operation ofthe CVP and SWP for the remainder ofthe OMR management period. In addition, Reclamation and D WR shall, prior to the next OMR management season, charter an independent panel to review the OMR Management Action consistent with ''Chartering ofIndependent Panels" under the "Governance" section ofthis Proposed Action. The purpose ofthe independent review shall be to evaluate the efficacy of actions to reduce the adverse effects on listed species under OMR management and the non-flow measures to improve survival in the south Delta and for San Joaquin origin fish. • Reclamation and DWR shall consider the histo·rical monthly distribution of loss to avoid disproportionately salvaging fish during any single mo.nth. Reclamation and DWR propose to continue monitoring and reporting the salvage at the Tracy Fish Collection Facility and Skinner Delta Fish Protection Facility. Reclamation and DWR propose to continue the release and monitoring of yearling Coleman NFH late-fall run as yearling Spring-Run Chinook Salmon surrogates." Storm-Related OMR Flexibility: "Reclamation and DWR may operate to a more negative OMR up to a maximum (otherwise permitted) export rate at Banks and Jones Pumping Plants of 14,900 cfs (which could result in a range ofOMR values) to capture peak flows during storm-related events. Reclamation and DWR will continue to monitor fish in real-time and will operate in accordance with "Additional Realtime OMR Restrictions," above. Under the following conditions, Reclamation and D WR would not cause OMR to be more negative for capturing peak flows from storm-related events if: • • • • Integrated Early Winter Pulse Protection (above) or Additional real-time OMR restrictions (above) are triggered. Under such conditions, Reclamation and DWR have already determined that more restrictive OMR is required. An evaluation ofenvironmental and biological conditions indicates more negative OMR would likely cause Reclamation and DWR to trigger an Additional real-time OMR restriction (above). Salvage ofyearling Coleman NFH latefall run as yearling Spring-Run Chinook Salmon surrogates exceeds 0.5% within any ofthe release groups. Reclamation:and D WR identify changes in spawning, rearing, foraging, sheltering, or migration behavior beyond those described in the forthcoming biological opinion for this project. Reclamation and DWR will continue to monitor conditions may resume management of OMR to no more negative than -5,000 cfs if conditions indicate the above offramps are necessary to avoid additional adverse effects. If storm-related flexibility causes the conditions in "Additional RealTime OMR Restrictions", Reclamation and DWR will implement additional real-time OMR restrictions." 452 Biological Opinion for the Long-Term Operation of the CVP and SWP End of OMR Management: "OMR criteria may control operations until June 30 (for Delta Smelt and Chinook salmon), until June 15 (for steelhead/rainbow trout), or when the following species-specific off ramps have occurred, whichever is earlier: • • Delta Smelt: when the daily mean water temperature at CCF reaches 25°C for 3 consecutive days; Salmonids: o o when more than 95 percent of salmonids have migrated past Chipps Island, as determined by their monitoring working group, or after daily average water temperatures at Mossdale exceed 72°F for 7 days during June (the 7 days do not have to be consecutive)." Real-Time Decision Making and Salvage Thresholds "Reclamation and DWR may confer with the Directors ofNMFS, USFWS, and CDFW if they desire to operate to a more negative OMR than what is specified in "Additional Real-Time OMR Restrictions." Upon mutual agreement, the Directors of NMFS and USFWS may authorize Reclamation to operate to a more negative OMR. than the "Additional Real-Time OMR Restrictions", but no more negative than -5000 cfs. The Director ofCDFW may authorize DWR to operate to a more negative OMR. than the "Additional Real-Time OMR Restrictions", but no more negative than -5000 cfs." The key changes in the OMR management component ofthe June 14, 2019 final PAin comparison to the February 5, 2019, PA are summarized in Table 2.5.5-71. The specific cumulative and single-year loss thresholds are described in detail in Appendix J and summary figures are provided showing historical loss and associated loss thresholds for wild winter-run Chinook salmon (Figure 2.5.5-34), hatchery winter-run Chinook salmon ( 453 Biological Opinion for the Long-Term Operation of the CVP and SWP Combined CVP/SWP hatchery winter-run Chinook loss as percent of hatchery JPE by Water Year 0.200 Ql VI VI u 0 0.. 0 .... - s 0.150 0 .!: VI .S::. Q:-u > u "0 Ql c: ::J .... 0.100 I .... c: ·c: ..0 · - E :: 0 0.050 u 0.000 2010 - 2011 • 2012 - 2013 Annual loss 2014 - 2015 - 2016 2017 2018 Average --- 90% of max=annualloss limit --- SO% of 90% of max --- 75% of 90% of max Figure 2.5.5-35) and wild steelhead (Figure 2.5.5-36 and Figure 2.5.5-37). 2.5.5.11.1.1 Assess Effects to Species of Revisions to OMR Management 2.5.5.11.1.1.1 Assess Exposure to Species from Revised OMR Management The revised OMR management component in the final P A (and any associated changes in exports) will not affect overall seasonal presence of listed salmonids and sDPS green sturgeon in the Delta. To the extent that changes in OMR management under the fmal PA may change distribution of fish within the south Delta, fish may be more (if OMR more negative) or less (if OMR more positive) vulnerable to entrainment into and loss at the south Delta export facilities. There is interannual variability in loss rates observed for wild and hatchery winter-nun Chinook salmon, and wild CCV steelhead (see Figure 2.5.5-34 through Figure 2.5.5-37). Some of this variability is likely due to interannual variability in population size, but note that variability is observed even for wild winter-run Chinook salmon after scaling to estimated population size (Figure 2.5.5-34). Other sources of variability that may influence loss rates include juvenile survival to the Delta, the fraction of juveniles that route into the south Delta where fish are vulnerable to entrainment, hydrologic conditions, and operations. The mix of single-year and long-term cumulative thresholds is designed to accommodate this interannual variability while controlling for long-term loss. 454 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.11.1.1.2 Assess Response to Species from Revised OMR Management NMFS's approach to linking hydrodynamics with species responses is described earlier in the Delta effects section . So, to understand the species responses, NMFS first assesses the likely difference in hydrodynamic conditions under the final PA compared to the original P A It is uncertain how exactly exports and OMR flows under the final PA will change in a given month and year type compared to the original PA, but NMFS makes the following assumptions for this supplemental analysis. • • • • • • The changes to the turbidity-related OMR triggers likely have little to no effect on our analysis, since the OMR limits in the final PA are consistent with the modeling assumptions used for the modeling provided with the original BA. The removal of the 10 steelhead/TAF loss trigger may reduce the frequency of short-term "pulse protection" at a -2,500 cfs OMR limit for steelhead, but in our original analysis (in the previous sections), NMFS expressed concern that this protective action would rarely be triggered, so the loss of a rarely-triggered protective action does not substantively change our analysis. Based on discussion among the Federal directors, NMFS understands that the average historical loss threshold is a "yellow light" to discuss and manage future operations; the other interim loss thresholds (50 percent and 75 percent ofthe annual loss limit of90 percent of maximum historical loss) are also ''yellow lights" that are associated with even more formal risk assessment and discussion. The cumulative and single-year loss thresholds are lower in the final PA, and thus the interim thresholds at 50 percent and 75 percent of the annual loss threshold are more likely to be reached and a potential OMR action response considered. When 50 percent or 75 percent of a loss threshold is reached, operations under the final PA are less certain to result in a more positive OMR than under the original PA. While the action response in the final PAis contingent on the conclusion ofReclamation's and DWR's risk assessment, the action response will occur "unless Reclamation and DWR determine that further OMR restrictions are not required to benefit fish movement because a risk assessment shows that the risk is no longer present based on real-time information." Additionally, the risk assessment will undergo inter-agency review, since "Reclamation and DWR will share its technical analysis and supporting documentation with USFWS and NMFS, seek their technical assistance, discuss the risk assessment and future operations with WOMT at its next meeting, and elevate to the Directors as appropriate." So, while it is not certain whether OMR limits more positive than -5,000 cfs are more or J,e ss likely under the final P A, the multiple process steps in the final PA provide some assurance that species risks will be conservatively managed. Change in the date-based offramp criterion for steelhead from June 30 to June 15 means that, if OMR management is not in effect for another species, OMR management might end up to two weeks sooner for steelhead, potentially exposing steelhead migrating through the Delta in late June to hydrodynamic conditions less suited for successful outmigration. 455 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.11.1.1.3 Assess Risk to Species from Revised OMR Management The cumulative and single-year loss thresholds were developed to limit loss for key (and reliably measurable) populations to loss rates observed under implementation of the NMFS 2009 Opinion. The intent of these PA revisions was to limit direct loss at the south Delta export facilities as a way to limit some of the higher-magnitude effects under the original P Aspecifically, effects associated with DCC operations, OMR Storm Flexibility, and increased exports in April and May. The concept was that, rather than use the hydrodynamic metric of OMR to manage species risks, we could use a metric of historical loss rates to keep risks comparable to risks under the NMFS 2009 Opinion. NMFS concludes that this approach is a reasonable way to limit risks associated with the near-field effects (entrainment into and loss at) the export facilities. While there are some uncertainties in how this new approach will be implemented, the final PA includes triggers for review and technical assistance anytime observed loss exceeds average annual historical loss, which provide some assurance that species risks will be conservatively managed. While loss is still expected to occur under the final PA, NMFS notes that the loss thresholds are expected to limit loss to levels less than estimated using the Salvage Density Model results described in Section 2.5.5.8.3.1 , and to levels comparable to loss observed under the COS. The Salvage Density Model showed the greatest differences in the PA vs. the COS during April and May, and NMFS expects that the benefits of the revised loss thresholds (relative to the original PA) will be greatest during this April-May period during outmigration of CCV steelhead (particularly from the San Joaquin basin) and young-of-year CV spring-run Chinook salmon. It is less certain whether this approach will fully limit risks associated with the far-field effects (potential disruptions to migration rate or route) of the export faci lities. Because NMFS assumes that far-field effects are correlated with exports (both footprint and magnitude of hydrodynamic effect greater at higher exports), limiting near-field effects to historical rates could be assumed to limit far-field effects to historic rates. However, it is likely that OMR (and associated Delta hydrodynamics) may still be more negative under the final PA than observed under the COS, especially in April and May. Under the COS, the OMR exceedance plots show that OMR is positive for approximately 50% of years, yet under the final PA, the most-restrictive OMR limit (which is not guaranteed to be implemented) is -2,500 cfs. NMFS does acknowledge that, especially in drier years, other factors may control OMR and lead to OMR flows more positive than the OMR limits associated with the loss thresholds of the final PA. For example, the modeling even for the original BA showed that April and May OMR flows under the original PA during critical years were about -1 ,500 cfs. 2.5.5.11.2 Assess effects to species of additional conservation measures 2.5.5.11.2.1 Address scour hole at Head of Old River 2.5.5.11.2.1.1 Deconstruct the Action for the scour hole at the Head of Old River The final PA describes this action as follows: • "Reclamation and DWR would form a project team to address the scour hole in the San Joaquin River at the Head of Old River. The project team would plan and implement 456 Biological Opinion for the Long-Term Operation of the CVP and SWP measures to reduce the predation intensity at that site through modifications to the channel geometry and associated habitats." 2.5.5.11.2.1.2 Assess species exposure, response, and risk Reducing predation at the scour hole in the San Joaquin River at the Head of Old River is a specific example of the conservation measure in the original PA to "remove predator hot spots in the Bay-Delta", described in Section 2.5.5.10.5.2. The effects are expected to be as described there, with benefits most likely accruing to CCV steelhead and CV spring-run Chinook salmon entering the Delta from the San Joaquin River. As for the overall measure to address predator hot spots, this PA component will be considered as a programmatic consultation. 2.5.5.11.2.2 Delta Cross Channel operations 2.5.5.11.2.2.1 Deconstruct the Action for the DCC operations The PA revisions associated with DCC operations clarified that December through January DCC openings would be limited to occasions when drought conditions are observed (defined as 90 percent exceedance hydrology) and gate opening will help to address water quality concerns-for a joint probability of less than 10 percent. The final PA also includes a new commitment to reduce combined CVP/SWP exports to health and safety levels (NMFS assumes that this is I ,500 cfs) during any DCC gate opening in December or January. 2.5.5.11.2.2.2 Assess species exposure, response, and risk During December and January, a substantial proportion of the juvenile winter-run Chinook salmon cohort may be at risk of entrainment into the DCC, but that additional risk, rdative to under COS conditions, is expected to be realized in less than 10 percent of years. Because these DCC revisions to the PA were provided to NMFS earlier than other revisions, the effects are already analyzed in the primary effects section. 2.5.5.11.2.3 Steelhead Lifecycle Monitoring Program and San Joaquin Basin Steelhead Collaborative 2.5.5.11.2.3.1 Deconstruct the Action for the Steelhead Lifecycle Monitoring Program and San Joaquin Basin Steelhead Collaborative The final PA included the following items: • Steelhead Lifecycle Monitoring Program: Develop infrastructure that will support a functioning life cycle monitoring program in the Stanislaus River and a Sacramento basin CVP tributary (e.g. Clear Creek, Upper Sacramento, American River) to evaluate how actions related to stream flow enhancement, habitat restoration, and/or water export restrictions affect biological outcomes including population abundance, age structure, growth and smoltification rates, and anadromy and adaptive potential in these populations. The goal of this monitoring program will be to improve understanding of steelhead demographics and, when combined with other steelhead-focused parts of the PA (San Joaquin and Delta steelhead telemetry study), inform actions that will increase steelhead abundance and improve steelhead survival through the Delta. 457 Biological Opinion for the Long-Term Operation of the CVP and SWP • San Joaquin Basin Steelhead Collaborative: Within 1 year, Reclamation will coordinate with CSAMP to sponsor a workshop for developing a plan to monitor steelhead populations within the San Joaquin Basin and/or the San Joaquin River downstream of the confluence of the Stanislaus River, including steelhead and rainbow trout on nonproject San Joaquin tributaries. The plan would be delivered to the IEP for prioritization and implementation, where feasible, for actions within the responsibility of tihe CVP and SWP and other members of the IEP. If the IEP is not able to implement the plan, the plan may be raised at the Director Level Collaborative Planning Meeting described under the "Governance" section of this PA for resolution. 2.5.5.11.2.3.2 Assess species exposure, response, and risk NMFS supports both of these efforts to get better information about CCV steelhead which may inform development of beneficial actions to increase steelhead abundance or survival. NMFS considers both items to be programmatic consultations. 458 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.12 Delta Effect Section Figures Societal lcontro!lablel Drivsrs Flood PoiHtlf rt>gui.>lion control light I I • Stressors Phnical Drh·ers W.1l£'r quJhty I • 1 I • l I • ct Air 0t(>l r.: upe dltu..: V•ti.ttiur PreCtpitatton J 1 Scduneut Cortl•um dtrb lnp.1t I Physical Process Effect Biologic.-..! Effect lnterllction Effects Outcomes Individual Endpoints Populiltion Endpoints Figure 2.5.5-1. Conceptual model from the South Delta Salmonid Research Collaborative Effort describing factors affecting survival of juvenile salmonids in the South Delta. Green highlights indicate model components included within the narrower scope of the SST report. Blue highlights indicate model components also potentially relevant to export effects and recommended by the SST for inclusion in an expanded research program. [Source: Figure 2-1 of{Salmonid Scoping Team 2017a)] 459 Biological Opinion for the Long-Term Operation of the CVP and SWP . . . Hydrodynamics Driver Drivers Export Rate (Primary Driver) San Joaquin River Flow Rate DCC Gate Operations HORB CCFR Gat e Operations .. 1 Linkage: Central/Sou th Delt a Chann el Hydrodynam ics . Outcom e Channel Velocity Flow Di rection . Sal m onid M igration Behavior Linkage .. Drivers Channel Velocity Flow Direction "' Linkage: Behavioral Response to Hydrodynamic Migrat ion Cues .Outcome M igration Rate . M igration Route .. Drivers M igration Rate M igration Route Su rvival Outcome Linkage: Expo sure Duration (Time) Linkage: Habitat Exposure (Geographic) . Outcome Predat ion M ortal ity Entrainment M ortality Survival to Chipps Island .. Figure 2.5.5-2. Gener al framework linking hydrodynamic effects of CVP and SWP project operations to migration behavior and survival. 460 Biological Opinion for the Long-Term Operation of the CVP and SWP Increasing Delta inflow 12,000 cfs 21,000 cfs 38,000 cfs April & May exports: -tj 0 COS: 1 500-3 500 cfs 0 o_ N en t 0 a. >< Q) Ol c "(ij ro Q) PA: 2 300-7 800 cfs en ....... 0 0 0 o_ . ·;:;; c Above Normal Q) a o.6 1922 -2 Wet 0.752 1942 -1 0 0.764 Scenario 0.4 cos PA 0.2 0.0 -2 -1 0 1 -2 0 1 Velocity (ft/s) -1 Figure 2.5.5-5. Proportion overlap of velocity distributions in the South Delta (Old River at Highway 4; downstream of the export facilities) for the P A and COS scenarios in March through May. [Source: Supplem ental modeling provided in support of ROC L TO BA] 463 1 Biological Opinion for the Long-Term Operation of the CVP and SWP 1979 (WY type = BN) - cosl - PA ____ \._._ __! iii \_ 0 ci 8_ en 8 l Oct Nov Dec Jan Ma r Feb Apr May Jun DCC Ope DCC Clos Jul Figure 2.5.5-6. Mean daily survival through the Delta simulated for the Proposed Action (PA) and the Current Operating Scenario (COS) (middle panel) and difference in the mean daily survival between the PA and COS (bottom panel). The top panel shows the flows at Freeport on a logarithmic scale for the two scenarios, as weD as the operations of the DCC gates (open or closed). 464 Biological Opinion for the Long-Term Operation of the CVP and SWP 1979 (WY type =BN) - cosl - PA \. r .f Ol c c d Cll 0 :c N ci e D.. N $ 0 0 u I '"" - 0 /'\. f / [ .E Oct Nov Dec Jan Mar Feb Apr May Jun Jul Figure 2.5.5-7. Mean daily probability of entering the interior Delta simulated for the Proposed Action (PA) and the Current Operating Scenario (COS) (middle panel) and difference in the mean daily probability of routing into the interior Delta between the PA and COS (bottom panel). The top panel shows the flows at Freeport on a logarithmic scale for the two scenarios, as well as the operations of the DCC gates (open or closed).. 465 Biological Opinion for the Long-Term Operation of the CVP and SWP 1979 (WY type= BN ) - cosl --. "' ...-.. 5 E a. - PA § ci .., 0 :1! 8 u: ro ci (/) I a 0 \ r ).. ""'\. - _f -:; l [lJl 80 o6 DCC Open DCC Closed .., m il 0 .r: 01 :;, e = E Q) .., j co g U> c: lll .., :0 Q) :2 N en 0 .., (.) I g_ N Q) § j 0 .!: ..,. g Q) :1 Ci - '-"""" .., I Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-8. Median daily travel time through the Delta in days simulated for the Proposed Action (PA) and the Current Operating Scenario (COS) (middle panel) and difference in the median travel time through the Delta between the PA and COS (bottom panel). The top panel shows the flows at Freeport on a logarithmic scale for the two scenarios, as well as the operations ofthe DCC gates (open or closed). 466 Biological Opinion for the Long-Term Operation of the CVP and SWP C! 0 v U) co 0 <0 0 ci a.. ._, 0 a.. N (.) ... -.:: 0 0 ci Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-9. Boxplots showing the distribution of the probability that through-Delta survival for the P A scenario is less than survival for COS. Each box plot represents the distribution among years for a given date ofthe probability that the difference between PA and COS is less than zero. The point in each box represents the median, the box hinges represent the 25'h and 751h percentile, and the whiskers display the minimum and maximum. ..- - co 0 0 1\ U) <0 0 ci a.. a.. ci (.) 'lit N 0 C! 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-10. Boxplots showing the distribution of the probability that the difference in med!ian travel time through the Delta between the COS and PA scenario is greater than zero. Each box plot represents the distribution among years for a given date of the probability that the difference between PA and COS is greater than zero. The point in each box represents the median, the box hinges represent the 25'h and 75'h percentile, and the whiskers display the minimum and maximum. 467 Biological Opinion for the Long-Term Operation of the CVP and SWP C! - co 0 0 ci a.. ._, 0 a.. N 0 1\ U) <0 (.) ... -.:: 0 0 ci Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-11. Boxplots showing the distribution of the probability that the difference in routing into the Interior Delta between the COS and PA scenario is greater than zero. Each box plot represents the distribution among years for a given date of the probability that the difference between PA and COS is greater than zero. The point in each box represents the median, the box hinges represent the 25th and 75th percentile, and the whiskers display the minimum and maximum. U) 0 (.) • a.. I!) 0 0 (ij > '2: ::J II) .s 0 'I""" 0I c !!! 0;1 :e 6 1.0 N 0 I Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-12. Boxplots of daily med.ian differences in through-Delta survival between the PA and COS scenario. Each box plot represents the distribution of median survival differences among years for a given date. The point in each box represents the median, the box hinges represent the 251h and 751h percentile, and the whiskers display the minimum and maximum. 468 Biological Opinion for the Long-Term Operation of the CVP and SWP ...... C/) 0 (.) "¢ I <( Q. Cl) § ,S Cl) 0 c: ('I') N ...0 ...I NI 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 2.5.5-13. Daily boxplots of median differences in median travel time between the PA and COS scenario. Each box plot represents the distribution of median travel time differences among years for a given date. The point in each box represents the median, the box hinges represent the 251h and 751h percentile, and the whiskers display the minimum and maximum. - C/) 0 --o .g (.) Q) • C:<( Q. 1.0 ·; 0 - cC» o.S c:Q) ;:, 0 -- (i 0 =Ql Cl 1.0 0 0 I Oct Nov Dec Jan Feb Mar Apr May J un Jul Figure 2.5.5-14. Daily boxplots of median differences in routing to the Interior Delta betwen the P A and COS scenario. Each box plot represents the distribution of median routing differences among years for a given date. The point in each box represents the median, the box hinges represent the 251b and 751b percentile, and the whiskers display the minimum and maximum. 469 Biological Opinion for the Long-Term Operation of the CVP and SWP Wet 0 0 0 <;> N 9 - Above normal 0 0 0 Cii 9 0 (..) ........ (ij > :::::l rll £ Ill 0 0 0 0 "? .... <;> c: Ill tt: 0 ;; Dry 0 0 q N 9 0 0 9 N "? Od Mny Jnn Jun Jul Figure 2.5.5-15. Daily boxplots of median differences in median through-Delta survival between the PA and COS scenario by water year type. Each box plot represents the distribution of median survival differences among years for a given date. The point in each box represents the median, the box hinges represent the 251h and 75th percentile, and the whiskers display the minimum and maximum. 470 Biological Opinion for the Long-Term Operation of the CVP and SWP .. ::!c:: ... N Cll :t: 0 0 -;- "' "' ,."' 0 '7 "l' Mny Jnn Jun Jul Figure 2.5.5-16. Daily boxplots of median differences in median travel time between the PA and COS scenario by water year type. Each box plot represents the distribution of median travel time differences among years for a given date. The point in each box represents the median, the box hinges represent the 251h and 75th percentile, and the whiskers display the minimum and maximum. 471 Biological Opinion for the Long-Term Operation of the CVP and SWP Figure 2.5.5-17. Daily boxplots of median differences in interior Delta routing !between the PA and COS scenario by water year type. Each box plot represents the distribution of median routing differences among years for a given date. The point in each box represents the median, the box hinges represent the 251b and 751h percentile, and the whiskers display the minimum and maximum. 472 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994- 2017 juvenile Winter Chinook Sacramento Trawls (Sherwood Harbor) (Raw Catch), 711 - 6/30 BY2017 I BY2016 BY2015 BY2014 1 BY2013 g----g ! I BY2012 BY2011 BY2010 BY2009 BY2008 BY2007 BY2006 BY2005 BY2004 BY2003 BY2002 BY2001 BYZOOO BY1999 BY1998 BY1997 BY1996 BY1995 BY1994 1011 11/1 1211 1/1 2/1 3/1 4/1 0 If) - First -Last 5-95% - 10-90% 25-75% - 50% • • Today 0 0 rl If) rl 0 0 0 0 If) N N It Passage Based on Raw Catch. Preliminary dat a from USFWS Lodi: subje ct to revision. www.cbr.washington. edutsacramento/ 11 Mar 201 9 11:55:27 PDT Figure 2.5.5-18. Juvenile winter-run C hinook salmon migration timing past the Shenvood HarborSacramento T r awl location for Brood Years 1994-2017. 473 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994 - 2017 juvenile Winter Chinook Chipps Island Trawls (Raw Catch), 7/1 - 6/30 BY2017 BY2016 BY2015 .. BY2014 BY2013 BY2012 BY2011 BY2010 BY2009 BY2008 BY2007 BY2006 BY2005 BY2004 BY2003 BY2002 BY2001 BYZOOO BY1999 BY1998 BY1997 BY1 996 BY1 995 BY1 994 12/1 - 1/1 First -Last 5-95% 2/1 1 0-90% 25-75% 3/1 4/1 5/1 000000000 LllOollOLI'lOollO rl......-t NN(Y)(Y) q- - 50% • • Today It Passage Based on Raw Cat ch. Preliminary dat a from USFWS Lodi: subject t o revision. www.cbr.washington. edutsacramento/ 11 Mar 201 9 1 2:00:15 PDT Figure 2.5.5-19. Juvenile winter-run C hinook salmon migration timing past the Chipps Island Trawl location for Brood Years 1994-2017. 474 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994 - 2017 juvenile Spring Chinook Sacramento Traw ls (Sherwood Harbor) (Raw Catch), 10/ 1 - 9/ 30 BY2017 BY2016 BY2015 BY2014 BY2013 BY2012 BY2011 BY2010 BY2009 BY2008 BY2007 BY2006 BY2005 BY2004 BY2003 BY2002 BY2001 BYZOOO BY1 999 BY1998 BY1 997 BY1 996 BY1995 BY1 994 12/1 1/ 1 2/1 - First -Last 10-90% - 5-95% 25-75% 3/1 4/1 511 - 50% • • Today 6/1 00000000 0000000 If) 0 If) 0 If) 0 If) rl r l N N M M # Passage Based on Raw Catch. Preliminary dat a from USFWS Lodi: subject to revision. www.cbr.washington. edutsacramento/ 11 Mar 201 9 15:48:13 PDT Figure 2.5.5-20. Juvenile CV spring-run Chinook salmon migration timing past the Sherwood Harbor Sacramento Trawl location for Brood Years 1994-2017. 475 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994- 2017 juvenile Spring Chinook Chipps Island Trawls (Raw Catch), 10/ 1 -9/30 BY2017 BY2016 BY2015 '§!:=' BY2014 BY2013 BY2012 lo 2 ,, ' I ,,, •' t:t=' 2 I BY2011 BY2010 BY2009 BY2008 II $1 I I !! tt=t-1 I I 2 l 1 BY2007 BY2006 BY2005 BY2004 BY2003 BY2002 BY2001 BYZOOO BY1999 BY1998 I t=j:l I A I BY1997 BY1996 BY1995 BY1994 111 - First -Last 5-95% 2/1 3/1 10-90% 25-75% 4/1 5/1 6/1 7/1 8/1 - 50% , , Today 9/1 1CM1 o o o o o o o 0000000 0000000 r-!NMo;tlll!DI' # Passage Based on Raw Catch. Preliminary dat a from USFWS Lodi: subject to revision, www.cbr.washington. edutsacramento/ 11 Mar 201 9 15:53:46 PDT Figure 2.5.5-21. Juvenile CV spring-run Chinook salmon migration timing past the C hipps Island Trawl location for Brood Years 1994-2017. 476 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994 - 2018 juvenile NA Steel head Sacramento Trawls (Sherwood Harbor) (Raw Catch), 1/'1 -12131 BY2018 BY2017 BY2016 BY2015 BY2014 ....l:!' 1 • BY2013 BY2012 BY2007 BY2006 BY2005 BY2003 BY2002 BY2001 BY2000 BY1 999 BY1998 BY1997 BY1996 BY1 995 BY1994 1/ 1 211 3/1 - First -Last - 5-95% 4/1 - 5/1 1 0-90% 25-75% 6/1 711 8/1 9/1 1011 11/1 1211 0000000000 lflOif)OiflOiflOifl .......-t r---t NN("t')(Y)q- q- - 50% • • Today It Passage Based on Raw Catch. Preliminary dat a from USFWS Lodi: subject to revision. www.cbr.washington. edutsacramento/ 11 Mar 201 9 1 6:01 :40 PDT Figure 2.5.5-22. Juvenile unclipped CCV steelhead migration timing past the Sherwood Harbor Sacramento Trawl location for Brood Years 1994-2017. 477 Biological Opinion for the Long-Term Operation of the CVP and SWP Migration Timing, Brood Years 1994 -2018 juvenile NA Steel head Chipps Island Trawls (Raw Catch), 1/ 1 -1 2131 BY2018 BY2017 BY2016 BY2015 BY2014 tt' ' BY2013 BY2012 BY2011 BY2010 BY2009 BY2008 BY2007 BY2006 BY2005 BY2004 BY2003 It I tt1 _ __..,. BY2002 BY2001 BY2000 BY1998 BY1997 BY1996 BY1995 BY1994 1/1 211 3/ 1 4/1 5/1 - First -Last - 10-90% - 5-95% - 25-75% 6/1 7/1 8/1 9/1 10/1 11/1 - 50% • • Today 1211 1/<1> 0 0 0 0 0 0 0 0 0 0 U'lOU'lOU'lOU'lOU'lO It Passage Based on Raw Catch. Preliminary dat a from USFWS Lodi: subject to revision. www.cbr.washington. edutsacramento/ 11 Mar 201 9 16:08:14 PDT Figure 2.5.5-23. Juvenile unclipped CCV steelhead migration timing past the C hipps Island Trawl location for Brood Years 1994-2017. 478 Biological Opinion for the Long-Term Operation of the CVP and SWP CDFW Adult Green Sturgeon Report Card Catch so ..c 40 uro 30 u ...... a::: 20 • 10 Figure 2.5.5-24. CDFW adult raw catch data for sDPS green sturgeon in the Delta fr om 2007-2014. The monthly median is marked by a horizontal line splitting each box. The upper and lower whiskers show the maximum and minimum values for each month over all years. 1981-2012 CVP SWP Juvenile Green Sturgeon Salvage Data 400 ..c 300 .....u ro u 200 ro a: 100 0 '\'b .J:.. I l • I "" "" <} '!>..q; - .+. 'l:' oe Figure 2.5.5-25. Monthly raw salvage data for juvenile green sturgeon by month at the SWP and CVP fish salvage facilities (1981-2012). The monthly median is marked by a horizontal line splitting each box. The upper and lower whiskers. show the maximum and minimum valuel! for each month over all years. 479 Biological Opinion for the Long-Term Operation of the CVP and SWP Flow at 400 m 3 s· 1 ••••• Catch spike 1999 2000 2001 wet year above normal yea r dry year - 0 i, "'E. 8 1061 -.""".. 0 1131 .. .. ... ... , .... 01<1 RJYer downslroomof ... .. ... ...... ( C - 89) eo- 0 881 1112$ "'Y 0911 111$9- -091 .... 0102 - - r -·-.. .... ,__ O51 Wot 0001 \815 0769 .. •• ·• -- ,_ 1 ·-- ·• v-.cy(!\1>1 OOQI ""' .. " •• SJR "'"'' Jcr-.oy PolniiChon""l 49) C.Oico "'Y 0.952 IUU ... ...... ... 0(00 • VdotJ!tyCfWI .-.. . f•o .. .. u 1&51 AboYo NormM Wot 0.1&.5 1M2 •• A M -. ..000 ............... ., .... " Figure 2.5.5-29. Velocity Density Plots for different locations in the South Delta: Dec - Feb Plots 483 ·--.. Old Rivt< near woooward lllaod 0104 SJR ne01 HOR (Chonnelll) • 1981 ., ·-- Biological Opinion for the Long-Term Operation of the CVP and SWP ·I .u- 11m 0911 111:12 o.04s tGI> o.m Dry Cribcal em.otNoi'INII Dry Crillcll Old River downstream of lacllities (ChEtnnel89) IMtddle River near WOOIJw&d lsl&rKI (Channel 143) Middle River near Vldona Cenal (Qlarll"'ef 133) ... 1991 0921i 1926 1022 19-42 Below Normal Ollli7 197S 0839 015 , ,..., Wot AIQO 1971 .,. Woo 0.824 ... •(U IU 0!> HI ·10 O lbull 00 •• ,, hloowNor'"ll Dry 19e1 0.111 r -. ..cos .... .. " •• "" .,. .. lit . . 19:22 0744 ..., 4 - ·,,,. .. . VMlcirytWa) 1!10 V-(ft!J) Old Rive< @ Q- 4 (Channel 90) Otd R.var noat WOOdward ISland Old RM>r ,.,.., HOR (01annol55) 18:24 "'""'' 0 002 18e7 .,.. .. ,.,, Illy Cdbl ,.....,Norfi'W Illy 0.128 1023 Oty Q$) a.iow Ncnlal 0.693 0700 00 Old River upstream of radlitles (Channel 78) . "", Cr- Illy 8elowNQrmol SJR HOR & R nHr JttMy PoirC (Chl:innol49) • teltl o.aoe 1987 ., 01127 ·': ·.--,..:.·.-. . z..O.OO "" .......'",. Figure 2.5.5-30. Density Plots for different locations in the South Delta: Mar - May Plots 484 Biological Opinion for the Long-Term Operation of the CVP and SWP Middle Rtvor ncar Vk:lor1a Canal (Chanool 133) CnlicaJ Ul76 " " t" " " Wei 0.975 1052 .l .. .. -- ..... 0.981 1939 -- 11193 ,," Dry O.SIOB 01126 00 1916 "' Ct1tlcol ... 0966 1988 0- - .... -r Woo 0.948 1986 Ot 1951 •• • coo ., 0946 1979 A-- -•..= 1952 • ' V-(111>) ... VIIOoly tftlt) ..,. " r w.. ' --. cos I 0 Old Rrver upsuoam of !oai... (Channel 78) Crilf o.J03 1... li78 .04 .01 10 01 O"<<• -- 0.1 07 1919 - 0 Wt . _l -... • .0 te 0.801 D7 t• V-1""1 SJR near Mokelumne (ChanneJ 45) Ct- .. ._____... ._ ......... ., • ' V-l)'(ltlt ) Figure 2.5.5-31. Velocity Density Plots for different locations in the South Delta: Jon - Aug Plots 485 -• ..co• O.!MA 4 .oa " .. u woo ·• 0.945 1986 •• c.- 0927 0 ·- -. cos SJR: noor Jorscy Point (Channel •9) Below Nomnl Dry Cntical .. "' Above Normal 1951 '"' ,,. 9-- 0 818 1959 " I SJR near HOR (Charnel 9) " . oos Dry .. Wot ! "'""""" •• Of -... .. 09111 Old River @ Hwy 4 (Channel 90) Dry ...,,. Below Normal 0.811 1959 0,&8 0.773 1964 1976 - - - - - · rooo Wel OliOS 0.8 1976 .,, 1951 " o.oos - - 0851 "' 000 .. •• ,_, ... " Ot:lcol , Dry 193U ,,.. 010 Rlver near Woodwaro ISland (C·n annet 95) " Ol>cal f.: ... ........ -. ..coo Old River downstream of facilities (Chamel89) MiOCI •-..= Biological Opinion for the Long-Term Operation of the CVP and SWP Natural Processes Ab iotic Factors PrecrprtatiOO Tides Basin Runoff Evaporation undcover Other Drivers Pollution Resource Use Habitat Change Preyavailabflity Predation Food W2bllynamu:< Consumpuv9usa Geometry Flood control t.and use/Restorar Biotic Factors Management Decisions Figure 2.5.5-32. Detailed Conceptual Diagram of the Linkages Between Flows and Fishes in the Delta. (Source: Appendix B from Delta Independent Science Board 2015) ....... ..__ l lmi:!DI -I I NOEC .J. .. (low) R.airoowtroul (bw) 1Coho .."- t Lese LOEC LCSO, NOEC. LOEC ..t t l lnjandarl...otado Ralf\bcw.ohut 1l n>nnow Bluog.ll(hogh) LCSC. NOEC, LOEC Roonbow ..._1LCSO. NOEC. LOEC EC25 F1thNd mlrmow loec Chinook Ulmon 1&53·''·'·111 l t Fa1nudtiWinow NOEC 1 Fillhead I LOEC l tt LCSO LOEC EC25 NOEC, LOEC EC25 B«d Bird (low) (high) l m:ra•Cti I•I+!ICIDIII·IIIII 1 1 10 < 1 ppb • nonct.lect 100 1,000 10.000 iJ911 (ppb)- Log,. sure 100,000 l 10,000,00< 1,000,.000 I• Study....,_ by 06W Figure 2.5.5-33. Exposure concentrations for surrogate and fish species endpoint effects for endothaU (Jlg/L or ppb, CDBW 2017) 486 I Biological Opinion for the Long-Term Operation of the CVP and SWP Combined CVP/SWP unclipped winter-run-sized Chinook JPEscaled loss by Water Year (stacked by time period) -- DecemberMarch "0 C1l VI VI 100.00 c.. 0 c..- 90.00 0 80.00 o..:E 70.00 :.:: u c: 0 c: :J Vl-o "0:-:!J " u "0 Ql c: ::J .... 0.100 I .... c: ·c: ..0 · - E :: 0 0.050 u 0.000 2010 - 2011 • 2012 - 2013 Annual loss 2014 - 2015 - 2016 2017 2018 Average --- 90% of max=annualloss limit --- SO% of 90% of max --- 75% of 90% of max Figure 2.5.5-35. Combined CVP/SWP hatchery winter-run Chinook loss for WY 2010 through WY 2018, as a percent of the number released into the Sacramento River. Bars represent cumulative loss observed withiin the water year of release. Horizontal reference lines indicate the loss thresholds relevant for OMR management. 488 Biological Opinion for the Long-Term Operation of the CVP and SWP Combined CVP/SWP unclipped steelhead loss by Water Year (stacked by month)-- December-March Ill Ill 0 -c 2000 ro Q) ti "'0 1800 1600 1400 Q) --------------------------------------------- 1200 u 1000 c: ::::::J 800 a.. s Vl a::> u "C ------------------------- 600 400 200 Q) c: 0 .0 2010 E 0 u - 2011 2012 2013 December February Average SO% of 90% of max 2014 - 2015 I 2016 2017 2018 Janua ry March --- 90% of max=annualloss limit --- 75% of 90% of max Figure 2.5.5-36. Combined CVP/SWP wild steelhead loss for WY 2010 through WY 2018. Bars represent cumulative loss from December through March, stacked by month. Horizontal reference lines indicate the loss thresholds relevant for OMR management. 489 Biological Opinion for the Long-Term Operation of the CVP and SWP Combined CVP/SWP unclipped steelhead loss by Water Year (stacked by month) -- April-June 15 Vl Vl 0 '"0 "' .s= Q) Q) Q) 2000 1800 tn 1600 0. 0. 1400 u 1200 :J 1000 s 800 c a.. V') c:> u 600 '"0 400 c .c 200 Q) E 0 u 0 2010 2011 I 2012 2013 April June --- 90% of max=annualloss limit --- 2014 - 2015 2016 • 2017 2018 May Average 50% of 90% of max Figure 2.5.5-37. Combined CVP/SWP wild steelhead loss for WY 2010 through WY 2018. Bars represent indicate cumulative loss from April through June 15, stacked by month. Horizontal reference the loss thresholds relevant for OMR management. 490 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.13 Delta Effects Section Tables Table 2.5.5-2. Driver-linkage-outcomes analyzed in SST 2017 related to Hydrodynamics. [Source: Table 2-1 ofSST2017a) . • • • • . Drivers Ex-pon s River inflow (Sacramento and San Joaquin) Tide Channel morphology . • • • Linkages Proximity to ex-pon s Channel configuration/barrier deployment Clifton Court Forebay (CCF) ope ration radial gate operations (e.g.. opening to fill CCF and then closing to isolate the pwnping plant operations from the Delta) • • • • • • • • Outcomes Instantaneous velocities or flows Net daily flow Sub-daily velocity Percent posia"ve Dow J,Vater temperature Salinicy Residence time Source/origin of water Note: Red italicized te:t7. indicates DLOs chat were not included i n che analysis. Table 2.5.5-3. Driver-linkage-outcomes analyzed in SST 2017 related to Behaviior. [Source: Table 2-2 of SST 2017a) • • • • • • Drivers Instantaneous flow/velocity (c hannels) Instantaneous flow/velocity (junctions) Water quah"ty (e.g., temperature, dissolved oxygen, salinicy, rurbidicy. contaminants Hydraulic residence time Spatial/temporal heterogeneity of h ydrodynamic/w ater quality drivers SmaD-scale hydrodynamics as a/J"ected by stroctuies/bathymerry • Linkages Physiological and behavioral responses to hydrodynamic or water quality conditions. gradients, or variability, such as: - Rearing - Active swimming - Lateral distribution in the channel - PassiYe displacement - Diel movements - Energy e.\pendicure - Selecth·e a"dal saeam aansport • • Note: Red italicized text indicates DLOs chat were not included in the analysis. 491 Outcomes Individual outcomes: - M.igration rare - Migr ation route - Migration timing - Timing ofDelta entry - Delta residence time - Rearing location Population outcomes: - Population -scale outcomes depend on the spatial/temporal he terogeneity of individual outcomes Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-4. Driver-linkage-outcomes analyzed in SST 2017 related to salmonid survival. [Source: Table 23 of SST 2017a) . Drivers • • Outcomes Linkages Migration route selection Nligration rate • • E:-.-posure to variables (e.g., habitat and predators) that affect differential sun;val between routes or between years for the same route Duration of e:-..-posure to route-specific conditions that affect survival • Mortalitr Table 2.5.5-5. Temporal occurrence of winter-run Chinook salmon in the Delta with darker shades indicating months of high presence and lighter shades indicating montihs of low presence. Adult WR 1 Juvenile WR 2 Salvaged WR 3 HIGH - MED - LOW NONE 1 Adults enter the Bay November to June (Hallock and Fisher 1985) and are in spawning ground at a peak time of June to July (Vogel and Marine 1991.). 2 Juvenile presence in the Delta was determined using DJFMP data. 3 Months in which salvage of wild juveniEe winter-run at State and Federal pumping plants occurred (NMFS 20 16) Table 2.5.5-6. Temporal occurrence of CV spring-run Chinook salmon in the Delta with darker shades indicating months of high presence and lighter shades indicating months of low presence. - HIGH MED LOW 1 NONE Adults enter the Bay late January to early February (CDFW 1998) and enter the Sacramento River in March (Yoshiyama et al. 1998). Adults travel to tributaries as late as July (Lindley et al. 2004). Spawning occurs September to October (Moyle 2002). 2 JuveniJe presence in the Delta based on DJFMP data. 3Juvenile presence in the Delta based on salvage data (NMFS 2016). 492 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-7. Temporal occurrence of CCV steelhead in the Delta with darker shades indicating months of high presence and lighter shades indicating months of low presence. Jun Feb Jul Adult SH 1 Juvenile SH 2 Salvaged SH 3 - 1 HIGH - MEO - LOW NONE Adult presence was detennined using information in Moyle (2002), Hallock eta!. ( 1961 ), and (California Department offish and Wildlife 2015b). 2 Juvenile presence in the Delta was determined using DJFMP data. 3Months in which salvage of wild juvenile steelhead at State and Federal pumping plants occurred; values in cells are salvage data reported by the facilities (He and Stuart 2016). Table 2.5.5-8. Temporal occurrence of sDPS green sturgeon in the Delta with darker shades indicating months of high presence and lighter shades indicating months of low presence. Jan Feb I Mar I Apr May I Jun I Jul Aug I Sep I Oct Nov I Dec 1 MED MED MED MED MED MED MED MED MED MED MED MED *Juvenile GS MED MED MED MED MED MED MED MED MED MED MED MED Salvaged GS3 LOW LOW LOW I LOW LOW1NONEIMED ..IGH 1LOW LOW LOW I LOW *AdultGS 2 !LOW MED I LOW INONEl NONE 1 Adult presence was detennined to be year round according to information in CDFW 2008-2014, Lindley eta!. (2004), and Moyle (2002). 2 Juvenile presence in the Delta was determined to be year round by using information in (USFWS DJFMP data), Moyle et a!. (1995), and Radtke (1966). Table 2.5.5-9. Delta Cross Channel October 1-November 30 Proposed Action Component Date Action Triggers Action Responses October 1November 30 Water quality criteria per D-1641 are met and either the Knights Landing Catch Index or Sacramento Catch Index is greater than five fish per day Within 48 hours, close the DCC gates and keep closed until the catch index is less than three fish per day at both the Knights Landing and Sacramento monitoring sites October 1November 30 Water quality criteria per D-1641 are met, either Knights Landing Catch Index or the Sacramento Catch Index are greater than three fish per day but less than or equal to five fish per day Within 48 hours of trigger, DCC gates are closed. Gates will remain closed for 3 days October 1November 30 Water quality criteria per D-1641 are met, real-time hydrodynamic and salinity modeling shows water quality concern level targets are not exceeded during Within 48 hours of start of Lower Mokelumne River attraction flow release, close the DCC gates for up 493 Biological Opinion for the Long-Term Operation of the CVP and SWP Date October 1November 30 October 1November 30 Action Triggers Action Responses 28-day period following DCC closure and there is no observed deterioration of interior Delta water quality to 5 days (dependent upon continuity of favorable water quality conditions) Water quality criteria per D-1641 are met, real time hydrodynamic and salinity modeling shows water quality concern level targets are exceeded during 14day period following DCC closure No closure of DCC gates 'fhe KLCI or SCI triggers are met but water quality criteria are not met per D-1641 criteria Monitoring groups review monitoring data and provide to Reclamation. Reclamation and DWR determine what to do with a risk assessment Ta ble 2.5.5-10. Water Quality Concern Level Targets (Water Quality Model simula ted 14-day average Electrical Conductivity) Proposed for the Opening of the DCC Gates to AUeviate Water Quality Concerns in the Delta Interior. Location Electrical Conductivity Jersey Point 1800 umbos/em Bethel Island 1000 umbos/em Holland Cut 800 umhos/cm Bacon Island 700 umhos/cm Table 2.5.5-11. T iming of juvenile winter-run C hinook salmon passage past Sherwood Harbor (Sacramento Trawl) for Brood Years 1994 - 2017 (Source: SacPas. Available at: http://www.cbr.washington.edu/sacramento/tmp/hrt 1552451186 673.html). Br ood Year Average (1 994-17) M edia n (1994-17) 20t7 First Pa ssage Date 5-Dec 5% P assage Date 17-Dec 10% Passage Date 24 -Dec 25% Passage Da te 9-Jan SO% Passa ge Date 1-Feb 75% Passage Da t.e 20-Fcb 90% Passage Date 12-M ar 95% Passage Date 17-Mar Last Passage Date 31-Mar 25-Nov 11-Dec IS-Dec 29-Dec 13-Feb 4-M ar 19-Mar 25-Mar 9-Apr 1/13/ 18 1/ 13/ 18 1115/ 18 2/ 11118 3/ 15/ 18 3/ 18118 3/24118 3/24/ 18 3/25/ 18 20t6 3/3117 3/ 13/ 17 3116/17 3/22/ 17 3/30/ 17 4/4117 4/8117 4/ t0/ 17 4/2 1117 2015 11/6115 1116115 12/24115 1212411 5 3/ 16/1 6 3/25116 411116 4122/ 16 4122116 2014 11/5114 11/5114 11/28114 12/8114 1218114 12/22114 3120115 4/6/ 15 4/ 17115 20l3 219114 2/ 12114 21 12/ 14 2/ 13114 2115114 315114 3110114 3114/ 14 4/4/ 14 2012 11123/ 12 11/23112 11/23112 11/26/ 12 11/26/12 12/3112 12/3/ 12 12/ 3/ 12 1217/12 20tl 1125112 1127112 2/ 1/ 12 3/ 16112 3/ 19112 3/30112 3/30112 3/30112 4/ 13112 2010 10/29/ 10 10129/ 10 10129110 12113/ 10 2122111 3118/11 4113/ 11 4/ 13/ 11 4/ 15111 2009 10/23/09 10123/09 10/23/09 11/6/09 2/5/10 2117110 2/26110 2/26110 2/26110 2008 12122108 12122108 1128/09 2/ 17109 2118109 2118/09 2127109 2127/09 2127109 2007 117/08 117/08 l n/08 1/9/08 1/28/08 216108 2/27/08 2/27/08 3/3/08 494 Biological Opinion for the Long-Term Operation of the CVP and SWP Brood Year First Passage Date S% 10% 2S% SO% 7S% 90% 95% Passage Date Passage Date Passage Date Passage Date Passage Da te Passage Date Passage Date Last Passage Date 2006 11120/06 12/11106 12/ 15/06 12118/06 2/ 12/07 2112/07 2/ 16/07 2/28/07 2128/07 2005 1112/05 11/ 14/05 11/ 14/05 12/5/05 12/23/05 3/8/06 3/20/06 3/29/06 4/24/06 2004 11/ 1/04 11/10/04 12/ 10/04 12/13/04 1/3/05 2/22/05 2/25/05 3/4/05 4/4/05 2003 12/6/03 12/10/03 12/ 10/03 12/10/03 12/ 10/03 1/5/04 2/ 18/04 3/ 12/04 3/22/04 2002 1118/02 12/16/02 12/ 16/02 12/16/02 1/ 15/03 3/3/03 3/ 19/03 3/26/03 4/28/03 200 1 9110/01 11119/01 11/23/01 11/26/01 11/30/01 12/21 /01 2/23/02 2/23/02 4/5/02 2000 1115/01 1/26/01 1/31/01 2116/01 2/23/01 2/23/01 3/ 12/01 3/ 19/01 4113/01 1999 1/18/00 1/ 18/00 1120/00 1/31 /00 2/11 /00 3/22/00 3/22/00 3/27/00 3129100 1998 I 0/ 19/98 11/23/98 11123/98 11/24/98 11/27/98 12/7/98 3/ 18/99 3/ 19/99 4/ 15/99 1997 11124/97 11126/97 11/29/97 2123/98 3117/98 3/ 19/98 3123/98 4/3/98 4/ 17/98 1996 11/25/96 12/11/96 12/ 12/96 2/ 18/97 2/27/97 3/ 18/97 3/26/97 3/27/97 4/22/97 1995 12115/95 12/16/95 12/ 16/95 1/2/96 3/ 1/96 3/ 19/96 3/26/96 3/27/96 4/2/96 1994 12/27/94 2/2 1/95 2/24/95 2/27/95 3/7/95 417195 4/ 13/95 4/14/95 4127195 Table 2.5.5-12. Timing of juvenile CV spring-run Chinook salmon passage past Sherwood Harbor (Sacramento Trawl) for Brood Years 1994- 2017 (Source: SacPas. Available at: http://www.cbr.washin2ton.edu/sacramento/tmp/hrt 1552495104 288.html). Brood Year S% 10% 2S% SO% 7S% 90% 9S% Passage Date Passage Date Passage Date Passage Date Passage Date Passage Date Pa.ssage Date Last Passage Date 29-Dec 10-Feb 25-Feb 19-Mar 1 1-Apr 19-Apr 25-Apr 27-Apr IS-May Median 13-Dec 18-Feb 9-Mar 28-Mar 11-Apr 19-Apr 25-Apr 27-Apr 11-May ( 1994 2017) 20 17 2/ 15118 3/3118 3/ 15/ 18 3/24/ 18 4111 / 18 4/ 16118 4/20/ 18 4/27118 5/ 11/18 2016 11/23/ 16 3/28/ 17 4/ 1/ 17 4/5/ 17 4/ 12/ 17 511117 515117 5/7/17 6/21117 2015 l / 11fl6 3/21fl6 3/28/ 16 4/ 1/ 16 4fll / 16 4/ 15fl6 4fl5/ 16 4/l8fl6 5/6/ 16 2014 12/5114 12/8/14 12/ 15fl4 12/24/ 14 4/ 10/ 15 4/ 17fl5 4/27/ 15 4/29115 4/29fl5 2013 2/ 11/ 14 2115/ 14 2/22/ 14 317/14 4/7/14 4/ 11/ 14 4/14/ 14 4/ 18/ 14 5/ 13114 2012 12/3/ 12 4/ 1113 4/ 1/ 13 4/ 10/ 13 4/ 17113 4/ 19/ 13 4/ 19/ 13 4/22/ 13 517/13 2011 1/25/ 12 3116/ 12 3/ 19/ 12 3/30112 3/30112 4/ 18/ 12 4/25/ 12 4/25/ 12 5/3/ 12 2010 12/8/ 10 12/20/10 1/3/ 11 4/ 13/ 11 4/20/ 11 4/22111 4/27/ 11 4/27/ 11 5/ 10/ 11 2009 2/3/ 10 3/ 1110 4/9/10 4/ 16/10 4/ 16/ 10 4123/ 10 4/30/ 10 4/30110 5/ 11110 Average First Passage Date (19942017) 2008 2/23/09 4/2/09 4/ 10/09 4/ 15/09 4116/09 4/24/09 5/2/09 5/7/09 517109 2007 ln/08 1/7/08 1111108 2/27/08 4/ 14/08 4/25/08 5/2/08 5/ 2/08 5/2/08 2006 2nt07 2/14/07 2/14/07 4/9/07 4/ 17/07 4/ 17/07 4/30/07 511/07 5/ 14/07 2005 12/5/05 1/6/06 1/20/06 2/8/06 417/06 4/28/06 511106 5/ 3/06 5/ 12/06 2004 12/10/04 2/22/05 3/4/05 4/ 1105 4/20/05 4/22/05 4/22/05 4/27/05 5/ 19/05 2003 12/10/03 12117/03 12/26/03 2/ 17/04 4 /21 /04 4/23/04 4/23/04 4/28/04 5/ 13/04 2002 12/16/02 116/03 2/ 19/03 3/ 19/03 4/ 11/03 4123/03 4/25/03 4/25/03 5/ 15/03 2001 11/26/01 12/ 17/01 1/ 10/02 317/02 4/5/02 4/22/02 4/26/02 4/26/02 5/2/02 2000 2/ 16/0 1 2/ 16/01 2/ 16/0 1 2/ 16/01 4/9/01 4/ 18/01 4/23/0 1 4/25/01 5/4/01 1999 1/ 18/00 2/11100 3/ 13/00 3127/00 4/3/00 4/ 14/00 4119/00 4/ 19/00 5/31 /00 495 Biological Opinion for the Long-Term Operation of the CVP and SWP Brood Year 1998 First Passage Date 11/30/ 1998 5% Passage Date 1/22/1999 10% Passage Da te 3/23/ 1999 25% Passage Date 4/3/ 1999 50% P assage Date 4110/ 1999 75% Passage Date 4/20/99 90% Passage Date 4/24/99 95% Pa.ssage Date 4/27/99 Last Passage Date 5/5199 1997 11/25/97 3/9/98 3/ 18/98 3/25/98 4/3/98 4/ 15/98 4/22/98 4/27/98 6/5/98 1996 11/27/96 2/21/97 3/20/97 4/8/97 4/ 17/97 4/22/97 4/24/97 4/25/97 6/9/97 1995 12/15/95 3/5/96 3/22/96 3/27/96 4/2/96 417/96 4/26/96 4/29/96 611 196 1994 12/5/94 2/24/95 2/28/95 3/ 16/95 4/ 10/95 4/ 18/95 4/27/95 4/29/95 5/ 19/95 Table 2.5.5-13. Timing of juvenile CCV steelhead passage past Sherwood Harbor (Sacramento Trawl) for Brood Years 1998- 2017 (Source: SacPas. Available at : http://www.cbr.washington.edu/sacramento/tmp/hrt_1552496507_849.html Brood Year Average (1998 - 2017) Media n (1998 . 2017) 2017 First Passage Date 16·Jan 5% Passage Date 24·Jan 10% Passage Date 28··Jan 25% Passage Date 7·Feb 50% Passage Da te 18·Fcb 75% Passage Da te 3·Mar 90% Passage Date 31·Mar 95% Passage Date 18·Apr L ast P assage Date I·Jul 15·Jan 22·Jan 2S..Jan 5·Feb 16·Fcb 2·Mar 20·Mar 3·Apr 2·Jun 1/ 12/18 1/1 6/18 1/22/18 1/26/1 8 2/24/18 3/3/18 3117/18 3/2 1/ 18 5/14/ 18 2016 1130/ 17 2/2/ 17 2/4/17 2/24!17 3/4/ 17 3/ 14/17 4/2/17 5/25/ 17 6/2/17 2015 1/ 11/ 16 1/ 11/ 16 1/29/ 16 2/5116 2/8/ 16 2/8/ 16 2/ 18/ 16 3/ 18/ 16 4/4/ 16 2014 1/23115 1123115 219115 2/9/15 2/11115 2/ 18115 411115 4/20/ 15 4/20/ 15 2013 1/31!14 217/14 2/8/ 14 2/ 11!14 2/ 12/14 2/ 15/14 2/ 16!14 3/5/ 14 4/ 18/ 14 2012 1!18!13 1/1 8113 1/30113 1/30/ 13 2/8/13 4/ 12/13 4/30113 5/3 1113 5/31/ 13 201 1 1/ 17/ 12 1/23112 1123/ 12 1/30/ 12 2/ 13/ 12 2/24/12 3/9/12 3/30112 5/ 1112 2010 1/ 12/ 11 1/ 1911 1 2/4/ 11 2/ 16/ 11 2/ 18/ 11 3/2/11 317/11 4/25/ 11 6/21 / 11 2009 1/27/ 10 2/ 1/ 10 2/3110 2/ 10!10 2/ 17/ 1() 2/24110 4/16/ 10 4/ 19/ 10 6110/ 10 2008 1/28/09 1/28109 1/28/09 2/6/09 2/17/09 2/ 17/09 2/23/09 3/30/09 517109 2007 1/ 11/08 1/ 16/08 1/ 18/08 2/8/08 2/11/08 2/ 15/08 2/ 15/08 2/ 19/08 3/3/08 2006 1117/07 2/5/07 219/07 2/ 12/07 2/ 16/07 2/28/07 4117/07 5/ 15/07 6/12/07 2005 1/20/06 1/27/06 2/J /06 2/ 13/06 2/ 17/06 3/3/06 3/13/06 3/27/06 6!14106 2004 1/ 12/05 1/ 19/05 1/ 19/05 2/2/05 2/22/05 3/2/05 4/ 15/05 5/ 10/05 5/24/05 2003 1/2/04 1/2/04 1116/04 1/30/04 2/4/04 2/20/04 3/8/04 3/ 15/04 12/6/04 2002 1/ 15/03 1/22/03 1/22/03 1/24/03 2/5/03 2/ 19/03 4/ 14/03 4/28/03 4/28/03 2001 1/ 15/02 1/22/02 1/24/02 1/26/02 2/23/02 3/9/02 12/16/02 12/ 16!02 12/ 16/02 2000 1113/0 1 1/ 15/01 1/ 15/01 1/31/01 2/2/01 2/ 12/01 2/ 16/01 3/ 14/0 1 9/ 19/01 1999 1/3/00 1/ 17/00 1/ 17/00 1/20/00 1/27/00 2/ 11/00 3/ 13/00 3/22/00 4/21 /00 1998 1/ 12/99 1/2 1/99 1/21 /99 1/25/99 2111/99 3/5/99 3/23/99 4/23/99 12/ 13/99 496 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-14. Monthly diverted volumes in acre feet (at) from the Barker Slough Pumping Plant for the water years 2008-2018. Year Jan Feb Mar Apr May Jun Ju1 Aug Sep Oct Nov Dec 2008 2491 1395 937 4 142 5739 7023 7068 7039 6355 5776 4797 2915 2009 3235 1909 95 1390 5504 5560 5264 5140 4368 3914 4305 1611 2010 921 1172 539 1467 4369 5856 6555 6434 6104 5131 4204 1382 201 1 323 742 239 580 3426 4674 6151 6029 6255 4532 4315 3064 2012 2430 306 332 412 2033 5311 5792 5592 6490 5225 4607 1501 2013 952 1137 659 2314 6275 6573 6322 6452 5588 5932 3871 3468 2014 3728 1165 1133 3579 6615 4789 3928 4095 2568 3006 1218 833 2015 1121 1544 1629 3358 3561 3377 3313 4447 4 186 4 196 3285 1167 20 16 977 948 19 519 3083 4735 5385 4753 4 180 3670 2847 2050 2017 1014 944 222 411 2944 3265 3357 5895 5789 5513 4695 4 182 2018 2735 3502 1562 325 4665 60 13 5971 5975 5589 SOli 5312 3431 I Table 2.5.5-15. Average monthly diverted flows in cubic feet per second (cfs) from the Barker Slough Pumping Plant for the water years 2008-2018. Oct Nov Dec 106.8 93.9 80.6 47.4 7 3.4 63.7 72.3 26.2 104.6 102.6 83.4 70.7 22.5 100.0 98.1 105.1 73.7 72.5 49.8 94.2 90.9 109.1 85.0 77.4 24.4 I 10.5 102.8 104.9 9 3.9 96.5 65. 1 56.4 107.6 80.5 63.9 66.6 43.2 48.9 20.5 13.6 56.4 57.9 56.8 53.9 72.3 70.3 68.2 55.2 19.0 8.7 50.1 79.6 87.6 77.3 70.2 59.7 47.8 33.3 3.6 6.9 47.9 54.9 54.6 95.9 9 7.3 89.7 78.9 68.0 63.1 25.4 5.5 75.9 101.1 97.1 97.2 9 3.9 81.5 89.3 55.8 Year Jan Feb Mar Apr May Jun Jul Aug Sep 2008 40.5 25. 1 15.2 69.6 93.3 118.0 114.9 114.5 2009 52.6 34.4 1.5 23.4 89.5 93.4 85.6 83.6 2010 15.0 2 1.1 8.8 24.7 71.1 98.4 106.6 201 1 5.3 13.4 3.9 9.8 55.7 78.5 2012 39.5 5.5 5.4 6.9 33.1 89.3 2013 15.5 20.5 10.7 38.9 102.1 2014 60.6 21.0 18.4 60.1 2015 18.2 27.8 26.5 2016 15.9 17.1 0.3 2017 16.5 17.0 2018 44.5 Mean 29.5 24.2 10.9 28.3 71.3 87.4 87.4 91.4 87.8 76.7 66.4 37.9 Median 18.2 21.0 8.8 23.4 71.1 89.3 94.2 95.9 9 3.9 81.5 72.3 33.3 Minimum 5.3 5.5 0.3 5.5 33.1 54.9 53.9 66.6 43.2 48.9 20.5 13.6 Maximum 60.6 63. 1 26.5 69.6 107.6 118.0 114.9 114.5 109.1 96.5 89.3 68.0 497 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-16. Catches of Chinook salmon in the North Bay Aqueduct Larval Fish Survey (1994-2004) Date 2/27/2004 2/28/2001 3/8/2001 2/15/2000 3/ 1811 999 3/7/1998 2/23/1997 Species Number Caught Site Location Chinook salmon I 724 Chinook salmon 2 724, 726 Chinook salmon 1 724 Chinook salmon 5 723(1), 724 (3), 726 (I ) Chinook salmon 1 7 18 1 721 Chinook salmon salmon Chinook 1 726 Table 2.5.5-17. Timing of unclipped juvenile winter-run Chinook salmon salvage (length at date) at the CVP and SWP fish salvage facilities. for Brood Years 1994-2017. Start Year Avera ge (19942017) Median (19942017) 2017 First Salvage Date 5% Salvage Date 10% Salvage Date 25% Salvage Date 50% Salvage Date 75% Salvage Date 90% Salvage Date 95% Salvage Date Last Salvage Date Number Salvaged 26-Dec 9-Jan 22-Jan 4-Feb 24-Feb 11-Mar 24-Mar 29-Mar 22-Apr 1210 18-Dec 4-Jan 25-Jan 14-Feb 2-Mar 14-Mar 24-Mar 31 -Mar 2 1-Apr 811 2/5118 3/1/18 3/6/18 3/22118 3/25/18 3/29/ 18 4/3118 4/5118 5115/18 237 2016 12/20116 12120116 12/20/16 12/27116 2114117 3/29117 4/5117 4124117 4/24117 40 2015 12/28115 12128/ 15 115116 1114116 1/28116 2/22116 3/22116 3122/ 16 3/22116 36 2014 12/24/14 12124/14 12/24/14 12/26114 114115 1121/ 15 1121115 213115 3/31/15 53 2013 3/3114 3/5/14 3/6114 3/9114 3/ 15114 3/20114 4/4/ 14 4110114 4114114 192 2012 12/4/ 12 12115/12 12116/12 12/19112 3/9113 3/21113 3/25113 3128113 4/6/ 13 271 2011 1125/12 2116112 2127/J2 317/12 3/17/12 3123112 3/31112 411112 5/29112 841 2010 12/3110 1217/10 12/29/10 1129111 311111 3114111 3/20/ 11 3/2311 1 4113/ 11 1703 2009 12/8/09 1/30110 2/6110 2124/10 3/5110 3118110 3/22110 3/26110 4/20/10 1064 2008 12/30/08 119/09 2/26/09 3/3/09 3/8109 3113/09 3/16/09 3118/09 4/17/09 582 2007 1111108 1118/08 1128108 2117/08 311/08 3113/08 3/22/08 3126/08 4/29/08 660 2006 12/ 18106 1122/07 2/8/07 2125/07 3/2/07 3/9/07 3/24/07 4/3/07 4/22/07 2764 12123/05 1124/06 2121106 311/06 3114/06 3/26/06 411/06 5/3/06 1008 4/20/05 469 5119/04 2728 2005 12/12105 2004 112/05 116105 1/11/05 2/5/05 311/05 3116/05 3/26/05 4/4/05 2003 12115/03 116/04 1127/04 2124/04 311/04 3110/04 3/16/04 3119/04 2002 12/ 18102 12124/02 12/26/02 117/03 2/24/03 3/5/03 3/ 19/03 3126/03 517/03 2265 2001 12/5/01 12113/01 12118/01 12/31101 3/5/02 3/25/02 3/31102 4/6/02 4/27/02 1442 2000 12/ 12100 212101 2/14/0 1 2123/01 3/6/01 3/ 13/01 3119/01 3/23/01 4/23/01 5932 1999 112/00 1/26/00 1128/00 2112/00 2/19/00 3117/00 3/30/00 4/3/00 4114/00 1924 1998 1124/99 2/23/99 3/5/99 3113/99 3/21/99 411/99 4/8/99 4111199 4/26/99 1510 1997 12/4/97 12/6/97 1218197 1211 1197 114/98 3/9/98 3/21/98 3123/98 3/27/98 726 1996 12/10/96 12112/96 3/8/97 3/20/97 3/26/97 3/27/97 3/30/97 3/3 1/97 4/6/97 388 1995 12118/95 1/2196 117/96 1116/96 1/25/96 217/96 3/ 16/96 4/2196 4/ 18/96 781 1994 12116/94 12124/94 12/28/94 1113/95 1120195 1/29/95 4/21195 4/26/95 516195 1416 498 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-18. Timing of unclipped juvenile CV spring-run sized Chinook salmon salvage (length at date) at the CVP and SWP fish salvage facilities for Brood Years 1994 - 2017. Start Year Average (1994-2017) Media n (1994- 2017) F irst Salvage Date 5% Salvage Date 10% Salv.age Date 25% Salvage Date SO% Salvage Date 75% Sal vage Date 90% Salva.ge Date 95% Salvage Date Last Salvage Date Start Year 12-Feb 26-Mar 31 -Mar 7-Apr 19-Apr 28-Apr 8-May 14-May 4-Jun 14762 19-Feb 27-Mar 30-Mar 6-Apr 18-Apr 27-Apr 7-May 13-May 4-Jun 8832 2017 3/14118 3/27/ 18 3/28/ 18 3/30/ 18 4/7/18 4/ 16/ 18 5/2118 5/9/ 18 5/23/ 18 9487 2016 2/ 16/ 17 4/ 10/ 17 4/ 18117 4/27/ 17 517117 5/ 14/ 17 5/22/ 17 6/ 1117 6129117 26713 2015 2/ 11116 2/ 12/16 2/28/ 16 3118/16 4/ 17/16 5/2/16 5/13116 5/14/ 16 5/ 19/ 16 158 2014 3/30/ 15 3/30/ 15 3/30/ 15 4/5/ 15 4/22/ 15 4/24/ 15 514115 5/18/ 15 5/ 18/15 50 2013 3/ 13/ 14 3/19/ 14 3/21 / 14 4/5/ 14 4/9/ 14 4/ 19/ 14 4/23/ 14 4/29/ 14 5/ 10/ 14 484 2012 3117/ 13 3/24/13 3/27/ 13 4/8113 4/24113 5/2/13 5/8/13 5113/ 13 5/25/13 909 201 1 3/ 10/ 12 3/25/12 3/28/ 12 4/2/ 12 4/ 15/ 12 4/21112 5/2/12 5/7/12 6/8112 1063 2010 1/3/ 11 4/ 13/ 11 4/22/ 11 4/30/ 11 5/7/11 5/ 16/ 11 5/29/ 11 6/3/ 11 6124/11 17654 2009 3/9/10 3/3 1/10 4/6/10 4/ 16/ 10 5/2/ 10 5116110 5/26/ 10 5/29/ 10 6/5110 4068 2008 3/ 15/09 3/30/09 4/2/09 4/ 11/09 4/23/09 511109 5/10/09 5/13/09 6115109 4730 2007 3/11108 4/3/08 417/08 4/ 18/08 4/27/08 5/4/08 5/10/08 5/14/08 6/5/08 5100 2006 3/2/07 411/07 4/4/07 4/ 10/07 4115/07 4/18/07 4/21 /07 4/24/07 5130107 3378 2005 2/9/06 3/23/06 4/4/06 4/ 12/06 5/2/06 5125106 5/29/06 615106 6/ 19/06 5822 2004 2/25/05 3125105 3/27/05 414105 4/21 /05 4/29/05 5/ 12/()5 5/22/05 6111105 14694 2003 1/ 18/04 3/9/04 3/ 14/04 3/21 /04 4/4/04 4/ 13/04 4/27/04 5/4/04 5/26/04 4534 2002 117/03 3121/03 3/25/03 3129/03 4/6/03 4/ 14/03 4/26/03 4/30/03 5/29/03 15706 2001 1/ 1/02 3128102 3/30102 4/3/02 4/8/02 4/ 14102 4/21102 4/30/02 6/3/02 8177 2000 9/26/00 3/25/01 3/30/01 4/3/01 4112/01 4/18/01 4/28/01 5/2/01 5/ 14/01 17940 1999 2/ 13/00 3129/00 4/2/00 4/6/00 4/10/00 4/ 14/00 4/24/00 4/28/00 6/ 1100 42468 1998 2/2/99 3/28/99 4/4/99 4/ 10/99 4/ 18/99 4/26/99 517199 5/ 13/99 6/4/99 46655 1997 2/22/98 3125/98 3/26/98 4/ 1/98 4/29/98 5/9/98 5/ 18/98 5/22/98 6/25/98 30589 1996 2/8/97 3/24/97 3/25/97 3/28/97 4/3/97 4/9/97 4/ 17/97 4/24/97 6/5/97 42906 1995 217/96 4/5/96 417/96 4/ 10/96 4/ 13/96 5/2/96 5/23/96 5/27/96 6/ 12/96 26785 1994 2/22/95 4/ 13/95 4/ 19/95 4/29/95 5/ 11/95 5/26/95 6/8/95 611 I /95 6/30/95 24224 499 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-19. Timing of juvenile unclipped CCV steelhead salvage at the CVP and SWP fish salvage facilities for Brood Years 1998-2017. Start Year Average (1998-2017) Median (1998- 2017) F irst Salvage Date 5% 10% 25% 50% 75% 90% 95% Salvage Date Salvage Date Salvage Date Salvage Date Salvage Date Salvage Date Salvage Date L ast Salvage Date Nu mber Salvaged 4-Dec 23-Jan 8-Feb 24-Feb 19-Mar 10-Apr 1-May 13-May 17-Jun 1395 19-Dec 26-Jan 10-Feb 24-Feb 20-Mar 6-Apr 25-Apr 9-May 22-Jun 1074 2017 2/ 1118 3/ 14/ 18 3/ 17/18 3/24/ 18 413/ 18 4/ 15/ 18 5/ 15118 5123/ 18 6/ 11/18 1119 2016 11127/16 11/27/ 16 12/3 1/ 16 1125/17 5/8/ 17 5/24/ 17 6/6/ 17 6/ 16117 6116117 65 2015 1/20116 2/ 1116 212/ 16 2/ 16/16 3/ 15/16 3/25/16 4/3/16 512/ 16 5123116 119 2014 11/ 16/ 14 11/ 16/ 14 2/16/ 15 2/17/ 1s 2127/1 s 4117/ 15 4/28/1s S/8/ 1S S/8/ [ S 43 2013 1123fl4 2/ 19/ 14 2/20/14 3/7/14 3/25/ 14 4nt14 4/ !0fl4 4123/ 14 5/6/[ 4 185 2012 11123112 I /22/ 13 2/12/13 3122/13 3/31113 4/26/ 13 5/ 13/13 5127113 7/2113 797 2011 9/ 12111 1/S/ 12 3/9/ 12 3/24/ 12 3/30/ 12 4/4/ 12 4/ 18/12 4/21112 6/3/ [2 342 2010 10128/ 10 2/ 12/ 11 2/17/11 3/2111 4/13/ 11 5/28/ 11 6/ 12111 6120/ 11 6127!1 1 738 2009 12120/09 2/3/ 10 2/6/1 0 2/10/ 10 2123/10 4/2/ 10 5/3 1/ 10 6/ 19110 6/21110 1030 2008 1125/09 2/ 1 1/09 2/20/09 3/2109 3/ 16/09 3/30/09 4/28/09 5/ 11/09 7/7/09 372 2007 1/ 18/08 1/30/08 2/2/08 2/ 12/08 2/23/08 3/ 14/08 4/22/08 5/4/08 7/6/08 984 2006 12/3 1/06 2/ 12/07 2/15/07 3/5/07 3/ 24/07 4/9/07 4/ 17/07 4/20/07 6nt07 2774 2005 1/4/06 2110/06 2/24/06 3/4/06 3/30/06 5/31106 6/ 14/06 6/24/06 715106 1601 2004 11/3/04 1/1 1/05 1128/05 2/25/05 3/25/05 4/ 14/05 S/21/05 6/3/05 7/3/05 1351 2003 12/ 18/03 1/ 12/04 1/28/04 2/ 15/04 311 /04 3112/04 3130/04 4/5/04 5127!04 1785 2002 12120/02 1/8/03 1/ 12/03 1/21/03 313/03 3/22/03 4/ 14/03 5/ 11/03 6/24!03 2189 2001 12/20/0 1 I / 18/02 1/25/02 2/22/02 3112/02 3/29/02 4/ 14/02 4/29/02 7/4/02 1632 2000 10/3 1/00 1/22/0 1 2/9/0 1 2/23/01 3110/0 1 3/25/0 1 4/5/0 1 4/13/0 1 611101 4610 1999 8125/99 1/22/00 1/30/00 2/ 10/00 2/20/00 3/7/00 4/5/00 4/ 17/00 7129!00 3866 1998 10123/98 216199 2/11/99 3115/99 4/8/99 4/ 19/99 5/ 18/99 5126199 7/2/99 2292 500 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-20. Total n umber of listed salmonids and sDPS green sturgeon collected at the Rock Slough Intake for years 1999-2011, prior to the operation of the Rock Slough Fish Screen. Species Total Number Collected 1999-2011 Number Collected by Year -- -- Headworks 1999-2011 Winter-run Chinook salmon Spring-run Chinook salmon 0 All years- 0 15 juveniles 2004-3 2005-4 2006-3 2008- 1 2000-3 2004-5 2005 - 10 2006- 1 2008-2 2005 -4 2006-2 2007- 1 2008- 8 All years- 0 Fall-run Chinook salmon 23 juveniles Central Valley steelhead 15 juveniles Green sturgeon 0 Pumping Plant # 1 2004-2011 All years- 0 2004-3 2006- 1 2004-2 All years- 0 All years- 0 Note: No momtormg was conducted at the Headworks m 2010 and 2011 due to the construction of the Rock Slough Fish Screen. Monitoring continued at Pumping Plant # 1 until the Rock Slough Fish Screen became operational in October 2011. 501 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-21. Proposed Action Component minus Current Operations Scenar io for Old and Middle River (OMR) flows, monthly averages. Proposed Aotion 011 519 minus &urrenl Opera1lions 0113191 oa St:ris!ic Nl)lj' llort!h!! Flow !CFS] lbr A,pr Jm J:Jn Jul Prc»:aflilq of EX<:u dbn..e HJ'Iio 21J% 723 721 -110 483 676 72 31J'Iio 5 64 e.1s 2441 40% 521 :522 50% -158 -75 ·S:2D 60% -1,257 1()'1. -2.012 BIJ'I. -2.0G7 90% -2.050 -1,241> 171 91 -2. 031> 1,403 -14JB 466 -1,000 7 13 27 1 ED -4413 -111 -1101> 236 ·21 :5 -445 21 -2.."7 -1 ,1>9 s. -325 -3,338 li>B1 -au -1,011> -3,325 -1.000 51io1 -315 -4$9 -2,808 -1.000 -4,1S7 241 &lio1 -1 517 36 9 -2,23& -2 ,721 -183 &2 657 -22G 111'6 716 -2 ,230 -2AS2 -12 -,111 1 2..516 -22G -2,110 -2,5G4 -1 82 3.5 $90 -GS -22G -250 0 0 0 0 -2, 102 -2 .1:05 0 68 -114 394 383 461 -427 192 468 -3.48 -598 -:!59 -2,701; -2.7G7 -1058 232 -151J 2 15 -1,47& -1,05& 297 Long Term Ful Simul:lli.e AbD¥e f1i'A) lj;t loY (1J%) -1 ,455 Ory (2'%1 e. iiese.foo bAs dri'md ii:'6e lel.f5 d' JU e aooe 314 -255 1.,WJ -725 493 4,053 256 -3,8SS 34 78 238 28 -4JGS 56 -1,01& 387 756 7J6 5oo --652 -1 ,001 -55:> -2 ,603 -2 ,002 1.034 15.5 -133 -1.271 -1. 124 - 1,482 ·1..SG3 -1.487 1.C 67 -270 244 641 :593 167 -120 -1,587 -1.-'12 -'S8 -755 · 1.07:t 443 129 195 lma lf.Jm 'te' 1, 1!199). a; Miih 2!125 br 225 338 smkllicn peftod. Ire Seaoemelb -3,550 o!teipi:.am = !M.--.ge em! 1Smuee Je.oe rise. b ... 502 -71 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-22. Proposed Action Component minus Current Operations Scenario for total Delta Exports, monthly delivery. Proeosed Action 0115119 minus Current Oeerations 011319 Monthly Delivery (CFS) Statistic Probability of Exceedance Nov Ocl 10% 20% 30% 40% 50% 60% 70% Jan Feb Mlar Jun Aer J ul A!!II See 3,461 32 -35 -126 -1 40 -449 4,529 4,571 -521 11 0 0 3,638 3,215 1,945 2 ,081 -758 -1,670 46 533 -78 15 -565 -359 4,815 4,497 4,974 4,235 -90 -364 0 144 0 -20 0 0 2,330 1,299 361 1,575 1,172 491 -773 -700 -696 312 398 308 213 402 373 53 211 318 4,438 3,838 3,062 4 ,086 3,693 2,836 -324 747 1,296 -93 -506 -415 0 543 926 130 1,019 747 182 27 -170 -231 -700 -47 380 680 729 1,703 1 ,145 1 ,225 1,707 1,304 2,211 1,734 -783 -1 ,462 120 151 -136 -173 -174 -21 -118 1,381 2,951 2,198 954 877 1,401 2,304 1,441 -665 32 -105 1,397 726 -548 393 742 404 2,971 2,977 660 -272 149 215 2,688 2,341 -474 312 -31 -502 4,476 4,244 -232 -24 -79 304 2,645 99 445 24 258 52 -281 -1,579 -615 -157 -163 899 737 148 110 149 1,071 1,371 -225 548 1,234 4,433 2,737 1,549 3,966 2,865 2,069 -1 52 1,656 1,544 400 226 -1,161 1,709 1 ,535 713 781 1,089 -512 -58 1,099 252 -176 144 518 69 64 80% 90% Long Term Full Simulation Period" Dec Water Year Types"·e Wet (31'/o) Above Normal (16%) Below Normal (13%) Dry (24%) Critical 34 a Based on IN 82-year ,;n..Ja5on period. Valley40-J0.30 lnclexVia:e. Y""' Hycf:ologic Oas.mca:ion {SWRC!l 1909). c The-se teS\11\s are cli>j>laye 8 fishff AF 5 5 #> IOfish/TAF Difference %change 3 2 2 3 60% 5 3 - 40% -· Average % Change - 2 40% - 0 I - - - - - - 18 13 5 28% 0 0 0 0 0% 0 0 0 0% 0 8 3 5 63% - 0 0 0% - - - 0 0 0% - - 26% reduction in the number of trigger exceedances (all water years 2010-2018) 46% reduction of trigger exceedances in water years with any exceedances Table 2.5.5-24. Average annual adipose fin-clipped winter-r un-sized Chinook salmon juvenile salvage and loss from brood year 1999-2017. Because the number of juveniles released are known genetic winterrun Chinook salmon, but some winter-run-sized fm-clipped Chinook salmon are not genetic winter run, this table overestimates the loss as a percent of release. Brood Year Total Fish Salvage Total Fish Loss #Juvenile Released Loss/Release 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 20 12 20 13 20 14 20 15 20 16 20 17 987 965 2,259 7,751 6,094 1,103 477 1,353 2,919 179 1,230 463 460 187 6 62 213 368 48 1,428 477 2,101 1,013 2,482 3,295 6,734 22,748 19,319 3,964 1,251 2,034 5,618 435 2,356 1,449 1,210 595 12 2 14 628 1,010 183 3,976 1,449 6,311 3,042 153,908 30,840 166,206 252,684 233,613 218,617 168,261 173,344 196,288 71 ,883 146,211 198,582 123,859 194264 181857 193155 420006 141388 431,793 194,566 181,857 96,720 46,618 1.61% 10.68% 4.05% 9.00% 8.27% 1.81% 0.74% 1.17% 2.86% 0.61% 1.61% 0.73% 0.98% 0.31% 0.01% 0. 11% 0. 15% 0.71% 0.04% 2.39% 0.98% 3.27% 1.58% Mean Median so 95%CI 504 Biological Opinion for the Long-Term Oper ation of t he CVP and SWP Table 2.5.5-25. Unclipp ed (wild) annual winter-run Chinook salmon juvenile salvage and loss from brood year 1999-2017. Brood Year Total Fish Salvage Total Fish Loss J PE Loss/JPE 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 Mean Median SD 95% CI 1,053 1,337 1,416 781 397 726 1,514 1,936 5,932 1,442 2,277 2,728 469 1,008 2,764 660 582 1,064 1,703 841 271 192 53 36 46 114 1,205 925 1,247 504 4,003 2,769 4,582 2,376 630 1,525 3,715 5,828 20,062 3,331 6,816 7,779 1,373 2,601 3,297 1,292 1,515 1,656 4,360 2,079 732 322 106 56 Ill 301 3,201 2,228 4,027 1,626 246, 157 90,546 74,491 338,107 165,069 138,316 454,792 289,724 370,221 1,864,802 2,136,747 1,896,649 881,719 3,831,286 3,739,069 589,911 617,783 1,179,633 332,012 162,051 532,809 1,196,387 124,521 101,716 166, 189 201,409 835,466 354,164 1,051 ,836 424,846 1.6% 3.06% 6.15% 0.70% 0.38% 1.10% 0.82% 2.01% 5.42% 0.18% 0.32% 0.41% 0.16% 0.07% 0.09% 0.22% 0.25% 0.14% 1.31% 1.28% 0.14% 0.03% 0.09% 0.06% 0.07% 0.15% 1.01% 0.28% 1.59% 0.64% 505 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-26. Estimated annual loss of winter-run Chinook salmon (based on the salvage-density method) for the February 5, 2019, PA a.nd COS scenarios at the SWP/CVP export facilities - by water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. There is a specific loss threshold for winter-run Chinook salmon from December through March. Water Yeartype Predicted loss under COS I 12,417 6,369 5,830 4,106 1,230 Wet Above Normal Below Normal Dry Critical Predicted loss uoderPA 13,788 6,805 6,812 5,070 1,702 PA-COS % change 1,371 437 982 965 472 11 7 17 23 38 Table 2.5.5-27. Estimated monthly loss of winter-run Chinook salmon (based on the salvage-density method) for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities, aU water year types combined. Revised loss thresholds in the June 14,2019 PA are expected to limit loss to be more comparable to the COS scenario. I l\looth October November December January February April June July August September " 'inter-run Chinook salmon Predicted Predicted % loss under loss ond er PA-COS cha nge cos PA -0 0 0 0 518 2,807 903 7,141 1,046 2 0 0 0 0 0 459 2,987 922 6,703 2,713 4 0 0 0 0 506 0 -59 180 19 -438 1,667 2 0 0 0 0 --11 6 2 -6 159 135 --- --- Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-28. Estimated entrainment index (number offish lost, based on normalized historical loss data and the salvage-density method) of juvenile winter-run Chinook salmon for the Febr uary 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - by water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scen ario. - Water Year Type - State Water Project - - Central Valley Project cos PA PAvCO S (%change) 1,456 756 1,024 959 394 1,553 895 1,095 1,1 33 572 97 (6.7%) 139 (18.4%) 71 (7.0%) 173 (18.1%) 178 (45.3%) -- cos PA PA -COS (%change) Wet Above Normal Below Normal Dry Critical 10,961 5,613 4,807 3, 146 837 12,235 5,911 5,717 3,938 1,130 1,275 (11.6%) 298 (5.3%) 910 (I 8.9%) 791 (25.1%) 294 (35.1%) Table 2.5.5-29. Estimated entrainment index (number offish lost, based on normalized historical loss data and the salvage-density method) of juvenile winter-run Chinook salmon for the February 5, 2019, PA and COS scena rios at the SWP/CVP export facilities- Wet water year type. Revised loss thresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. Month - - -- cos PA October November December January February March April May June July August September Annual Average State Water Project PA -COS (%change) - - cos PA 0 0 0 0 0 0 0 412 2,641 701 6,295 910 2 0 0 0 0 10,961 0 361 2,821 734 5,877 2,439 0 -51 (-12.4%) 180 (6.8%) 33 (4.7%) -418 (-6.6%) 1,529(168%) 2 (135%) 0 0 0 0 I ,275 (I 1.6%) 0 106 166 202 846 136 0 0 0 0 0 1,456 4 0 0 0 0 12,235 98 166 188 826 274 0 0 0 0 0 1,553 Central Valley Project PA vCOS (%change) 0 0 -7(-7.0%) 0 (0.1%) -14 (-7.1%) -20 (-2.4% 139 (102.3%) 0 0 0 0 0 97 (6.7%) Table 2.5.5-30. Estimated entrainment index (number offish lost, based on normalized historical loss data and the salvage-density method) of juvenile winter-run Chinook salmon for the Februa ry 5, 2019, PA and COS scena rios at the SWP/CVP export facilities - Above Normal water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA - COS (%change) cos PA PAvCOS (%change) October November December January 0 0 359 682 0 0 359 816 0 0 0 (0.1%) 134 (19.7%) 507 0 0 20 66 0 0 20 71 0 0 0 6 (8.5%) Biological Opinion for the Long-Term Operation of the CVP and SWP Month February March April May June July August September Annual Average - - 2,558 1,940 75 0 0 0 0 0 5,613 2,633 1,850 253 0 0 0 0 0 5,911 - - State Water Project 76 (3.0%) -91 (-4.7%) 178 (238.2%) 0 0 0 0 0 298 (5.3%) 239 355 70 4 241 352 196 13 I I 0 0 0 756 0 0 0 895 Central Valley Project 2 (0.9%) -3 (-0.8%) 125 ( 178.1 %) 9 (228.7%) 0 0 0 0 139 (18.4%) Table 2.5.5-31. Estimated entrainment index (number offish lost, based on normalized historical loss data and the method) of juvenile winter-run Chinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities- Below Normal water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA - COS (%change) cos PA PA vCOS (%change) October November December January February March April May June July August SeQtember Annual Average 0 0 110 328 1,677 2,630 21 41 0 0 0 0 4,807 0 0 100 383 2,020 3,042 54 118 0 0 0 0 5,717 0 0 - 10 (-9.0%) 55(16.7%) 343 (20.5%) 412 (15.7%) 33 (155.8%) 77 (188.7%) 0 0 0 0 910 (18.9%) 0 0 46 101 410 467 0 0 0 0 0 0 1,024 0 0 42 109 466 478 0 0 0 0 0 0 1,095 I 0 0 -4 (-7.8%) 8 (8.3%) 55 (13.5%) I I (2.4%) 0 0 0 0 0 0 71 (7.0%) Table 2.5.5-32. Estimated entrainment index (number offish lost, based on normalized historical loss data and the method) of juvenile winter-run Chinook salmon for the Febr uary 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Dry water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA - COS (%change) cos PA PAvCOS (%change) October November December January February March April 0 0 227 125 726 1,974 95 0 0 228 130 867 2,539 174 0 0 I (0.5%) 5 (4.1%) 141 (19.4%) 565 (28.6%) 79 (83.2%) 508 0 0 37 78 286 514 44 0 0 34 79 364 595 61 0 0 -3 (-9.0%) 1 (1.0%) 78 (27.4%) 80 (15.6%) 17 (39.8%) Biological Opinion for the Long-Term Operation of the CVP and SWP Month May June July August September Annual Average - - 0 0 0 0 0 3, 146 0 0 0 0 0 3,938 - State Water Project 0 0 0 0 0 791 (25.1%) - 0 0 0 0 0 959 0 0 0 0 0 1,133 Central Valley_Project 0 0 0 0 0 173 ( 18.1%) Table 2.5.5-33. Estimated entrainment index (number offish lost, based on normalized historical loss data and the salvage-density method) of juvenile winter-run Chinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Critical water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. Month -October November December January February March April May June July August September Annual Average - cos 0 0 0 145 222 447 22 0 0 0 0 0 837 - State Water Project - - Central Valley Project PA PA -COS (%change) cos PA PAvCOS (%change) 0 0 0 147 300 641 42 0 0 0 0 0 1,130 0 0 0 2(1.6%) 78 (35.0%) 194 (43.4%) 19 (86.1%) 0 0 0 0 0 294 (35.1%) 0 0 0 45 115 229 4 0 0 0 0 0 394 0 0 0 46 164 357 5 0 0 0 0 0 572 0 0 0 1 (2.0%) 48 (4 1.8%) 12&(56. 1%) n (17.2%) 0 0 0 0 0 178 (45.3%) Table 2.5.5-34. Average a nnual adipose fin-clipped CV spring-run Chinook salmon juvenile salvage and loss from brood year 1999-2017. Brood Year Total Fish Salvage Total Fish Loss # Juvenile Released Loss/Release 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 20 11 2 226.00 270.00 2,754.00 864.00 205.00 2,488.00 601.00 3 l.OO 107.00 15.00 42.00 276.00 142.00 8 657.00 726.00 4,373.00 2,520.00 586.00 3,633.00 632.00 44.00 25l.OO 11.00 73.00 793.00 289.00 171 340.00 No Data 254,591.00 128,200.00 No Data 561,920.00 No Data 5,219,080.00 214,159.00 108,085.00 51 ,762.00 3,258,949.00 2,314,266.00 5.0525% No Data 1.7177% 1.9657% No Data 0.6465% No Data 0.0008% 0.1172% 0.0 102% 0.1410% 0.0243% 0.0125% 509 Biological Opinion for the Long-Term Operation of the CVP and SWP Brood Year Total Fish Salvage Total Fish Loss 2012 2013 2014 2015 2016 2017 7.00 12.00 8.00 650.00 962.70 1,010.00 667 270 881 425 15.00 8.00 7.00 560.00 1,787.00 1,745.27 1,406 586 2,169 1,045 Mean Median SD 95%CI # Juvenile Released 92,396.00 2,997,011.00 2,090,391.00 2, 127,482.00 1,788,310.00 663,434 .00 1,377,586 612,677 1,524,528 734,799 Loss/Release 0.0162% 0.0003% 0.0003% 0.0263% 0.0999% 0.2631 % 0.6309% 0.0631 % 1.3293% 0.6407% Table 2.5.5-35. Unclipped (wild) annual CV spring-run Chinook salmon juven:ile salvage and loss from brood year 1999-2017. Brood Year· Total Fish Salvage Total Fish Loss 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 7,721 3,555 24,200 26,785 42,908 30,597 46,655 42,513 17,940 8,177 15,706 4,534 14,694 5,822 3,378 5,100 4,730 4,068 17,654 1,063 909 484 50 158 26,713 9,487 14,062 7,949 14,276 13,265 3,785 29,905 36,85 1 54,855 24,943 105,615 90,118 40,696 10,206 40,383 10,985 27,319 13,002 5,213 11,771 8,840 6,082 52,505 2,394 2,496 349 70 298 72,013 18,314 26,241 13,134 28,597 Mean Median SD 510 Biological Opinion for the Long-Term Operation of the CVP and SWP Brood Year Total Fish Salvage Total Fish Loss 95%CI 5,766 11,550 Table 2.5.5-36. Estimated annual adjusted loss of CV spring-run Chinook salmon (based on the salvagedensity method) for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities by water year type. Revised loss thresholds in the June 14, 2019 PA may limit loss to be more comparable to the COS scenario, though there is not a specific loss threshold for spring-run Chinook salmon. I Water Yeartype Predicted loss under COS Predicted loss underPA Wet Above Normal 851 461 116 278 153 1,732 1,193 234 482 249 Below Konnal Dry I Critical PA-COS % change 881 732 117 205 104 159 101 74 64 97 Table 2.5.5-37. Estimated monthly adjusted loss of CV spring- run Chinook salmon (based on the salvagedensity method) for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities, all water year types combined. Revised loss thresholds in the June 14,2019 PA may limit loss to be more comparable to the COS scenario, though there is not a specific loss threshold for spring-run Chinook salmon. I CY spring-run Chinook salmon (adjusted loss) I :Month October November December January February l April l I May June July August September Predicted Predicted % loss under loss under PA-COS change cos PA 0 0 0 0 0 0 0 0 5 5 191 437 207 11 0 0 0 181 1,062 473 10 0 0 0 511 0 0 0 0 0 -9 625 266 0 0 0 0 48 --- -3 -5 143 128 -2 --- -- Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-38. Table showing estimation procedure for estimate juvenile production estimate (JPE) for CV spring-run C hinook salmon. Winter-run and spring-run Chinook salmon escapement from May 9, 2019 GrandTab. Winter-run JPE from NMFS JPE letters. ....---- " rater Year Brood 2010 2011 2012 2013 2014 2015 2016 2017 2018 2009 2010 2011 2012 2013 2014 2015 2016 2017 WR escapemeat \\'RJPE Year 4,537 1,596 827 2,671 6,084 3,015 3,440 1,547 977 Estimated SR JPE JPE multiplier SR (SR Tributary (WR JPEm'R. Tn"butary escapemeat x JPE escapemeat) escap emeat multiplier) 1,179,633 332,012 162,051 532,809 1,196.387 124,521 101,716 166,189 201,409 260 208 196 199 197 41 30 107 206 3,457 2,962 5,805 18,688 19,516 7,125 1,195 6,453 1,059 898,830 616,178 1, 137,492 3,727,868 3,837,720 294,266 35,334 693,224 218,313 Table 2.5.5-39. Estimated entrainment index (number of fish lost, based on historical loss data and the salvage-density method) of juvenile CV spring-run Chinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - by water year type. Revised loss thresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. Water Year Type - - State Water Project - - Central Valley Proj ect -- cos PA PA-COS (%change) cos PA PAvCOS (%change) 26,589 16,286 4,632 10.659 5,131 58,046 43,560 9,819 19,692 9,272 31,457 (ll8%) 27,273 (167.5%) 5,187 (112.0%) 9,034 (84.8%) 4,141 (80.7%) 15,943 6,770 1,183 3,226 2,497 28,560 16,100 1,860 4,426 3,201 12,617 (79.1 %) 9,329 (137.8%) 677 (57.3%) 1,200 (37.2%) 705 (28.2%) Wet Above Normal Below Normal Dry Critical Table 2.5.5-40. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile C V spring-run C hinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Wet water year type. Revised loss thresholds in t he June 14, 2019 PA are expected. to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA-COS (%change) cos PA PAvCOS (%change) 512 Biological Opinion for the Long-Term Operation of the CVP and SWP Month October November December January February March April May June July August September Annual Average - - 7 0 0 0 198 5,76I I3,5I5 6,755 354 0 0 0 26 589 10 0 0 0 208 5,378 36,2I8 15,874 357 0 0 0 58,046 State Water Project 3 (48.5%) 0 0 0 9 (4.7%) -382 (-6.6%) 22,703 (168.0%) 9,120 (I 35.0%) 4 (1.0%) 0 0 0 31 457 (118.3%) - - 0 0 0 0 29 3,766 8,353 3,620 175 0 0 0 15 943 0 0 0 0 27 3,676 I6,897 7,797 163 0 0 0 28,560 Central Valley Project 0 0 0 0 -2(-7.1%) -90 (-2.4%) 8,544 (102.3%) 4,177 (115.4%) -12 (-6.7%) 0 0 0 12,617 (79.1%) Table 2.5.5-41. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CV spring-run Chinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Above Normal water year type. Revised loss thresholds in the June 14,2019 PA are expected to limit loss to be more comparable to the COS scenario. Month - . -- cos PA October November December January February March April May June July August September Annual Average 0 0 0 4 56 4,610 9,774 1,778 55 0 0 9 16,286 0 0 0 5 57 4,395 33,057 5,974 62 0 0 9 43,560 State Water Project PA - COS (%change) . cos . Central Valley Project PA PAvCOS (%change) 0 0 0 I (19.7%) 2 (3.0%) -215 (-4.7%) 23,283 (238.2%) 4,196 (236.0%) 7 (13.0%) 0 0 0 27,273 (167.5%) 0 0 0 6 18 1,663 4,442 627 14 0 0 0 6,770 0 0 0 7 I8 1,649 12,353 2,061 I3 0 0 0 16,100 0 0 0 I (8.5%) 0 (0.9%) -14 (-0.8%) 7,9ll (178. 1%) 1,434 (228.7%) -2 (-10.8%) 0 0 0 9,329 (137.8%) 513 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-42. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CV spring-run C hinook salmon for the February S, 2019, PA and COS scenarios at the SWP/CVP export facilities - Below Normal water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Proj ect - - Central Valley Project cos PA PAvCOS (%change) 0 0 0 0 0 577 480 126 0 0 0 0 1,183 0 0 0 0 0 591 933 336 0 0 0 0 1,860 0 0 0 0 0 14 (2.4%) 453 (94.4%) 210 (167.0%) 0 0 0 0 677 (57.3%) --- cos PA PA-COS (%change) October November December January February March April May June July August September Annual Average 0 0 0 0 11 27 1,806 6,219 1,756 0 0 0 0 9,819 0 0 0 2 (16.7%) 5 (20.5%) 245 (15.7%) 3,788 (155.8%) 1,148 (188.7%) 0 0 0 0 5,187 (112.0%) 0 0 9 22 1,561 2,431 608 0 0 0 0 4,632 Table 2.5.5-43. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CV spring-run Chinook salmon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - D ry water year type. Revised loss thresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project cos PA PAvCOS (%change) 0 0 0 6 2 591 2,510 1 12 4 0 0 0 3,226 0 0 0 6 3 683 3,509 218 6 0 0 0 4,426 0 0 0 0 I (27.4%) 92 (15.6%) 999 (39.8%) 106 (94.5%) 2 (39.8%) 0 0 0 1,200 (37.2%) -- cos PA PA-COS (%change) October November December January February March April May June July August SeiPtember Annual Average 0 0 0 0 0 1,084 6,600 2,975 0 0 0 0 10,659 0 0 0 0 0 1,394 12,089 6,210 0 0 0 0 19,692 0 0 0 0 0 310 (28.6%) 5,489 (83.2%) 3,235 (108.7%) 0 0 0 0 9,034 (84.8%) 514 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-44. Estimated entra inment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CV spring-run C hinook salmon for the February S, 2019, PA and COS scenarios at the SWP/CVP export facilities -Critical water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the C OS scenario. Month - - State Water Project - - Central Valley Project cos PA PAvCOS (%change) 0 0 0 0 0 95 1,345 1,054 3 0 0 0 2,497 0 0 0 0 0 148 1,577 1,471 6 0 0 0 3,201 0 0 0 0 0 53 (56.1%) 232 (17.2%) 418 (39.6%) 2 (67.8%) 0 0 0 705 (28.2%) -- cos PA PA - COS (%change) October November December January Fe bruary March April May June July August September Annual Average 0 0 0 0 0 138 2,736 2,240 0 0 0 0 0 198 5,092 3,909 73 0 0 0 9,272 0 0 0 0 0 60 (43.4%) 2,356 (86.1%) 1,669 (74.5%) 56 (319.6%) 0 0 0 4,141 (80.7%) n 0 0 0 5,131 Ta ble 2.5.5-45. Ann ual clipped juvenile CCV steelhead salvage and loss from Brood Yea rs 1999 to 2017. Brood Year T otal Fish Sa lvage Total Fish Loss 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 20 12 20 13 20 14 2015 2016 20 17 Mean Median 181 5432 8191 1885 10388 7976 2046 2169 2853 2836 994 3576 721 593 701 523 1322 43 732 2,798 1,885 367 7950 15723 3345 28222 20917 4148 8110 10052 7548 2489 11272 1214 1829 1588 1841 3567 164 2463 6,990 3,567 515 # Juvenile Released 1476342 1398412 1633825 1496220 1523646 1434217 19639 11 1644777 1915192 2085566 1391770 1470438 1234235 1556276 1583302 1869101 -* -* -* 1,604,827 1,539,961 Loss/Release 0.02% 0.57% 0.96% 0.22% 1.85% 1.46% 0.21% 0.49% 0.52% 0.36% 0.18% 0.77% 0.10% 0. 12% 0.10% 0.04% -* -* -* 0.50% 0.29% Biological Opinion for the Long-Term Operation of the CVP and SWP Brood Year Total Fish Salvage Total Fish Loss Loss/Release so # Juvenile Released 3,034 1,463 7,569 3,648 236,485 113,982 0.53% 0.26% 95%CI *Data were not available, therefore, the percent loss could not be calculated. Table 2.5.5-46. Unclipped(wild) annuamjuvenile CCV steelhead salvage and loss from Brood Years 1998-2017. Brood Year Total Fish Salvage Total F ish Loss 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2211 3728 4458 1576 2146 1761 1215 1201 2756 970 360 941 557 324 744 185 43 119 65 1119 1324 1045 1226 574 6353 8299 8655 4414 4716 4087 2460 2313 8395 1716 932 2783 800 517 1600 660 157 293 193.85 2852 3110 2387 2854 1336 Mean Median so 95%CJ 516 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-47. Estimated annual loss of CCV steelhead (based on the salvage-density method) for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - by water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. There are specific loss thresholds for CCV steelhead from December through March and April through June 15. Water Yeartype Predicted loss under COS 6,560 12,558 10,188 9,743 5,158 Wet I Above Normal Below Normal Dry Critical Predicted loss uoderPA 7,988 14,489 12,056 12,478 7,107 PA-COS % change 1,428 1,932 1,867 2,735 1,949 22 15 18 28 38 Table 2.5.5-48. Estimated monthly loss of CCV steelhead (based on the salvage-density method) for the February 5, 2019, .PA and COS scenarios at the SWP/CVP export facilities, all water year types combined. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scenario. There are specific loss thresholds for CCV steelhead from December through March and! April through June 15. CCV steelhead I Predicted loss under cos I O ctober November D ecember January February April June July August September .P redicted % loss under PA-COS. change PA 40 14 43 1,447 1,756 1,995 604 354 269 31 3 4 60 16 38 1,533 1,809 1,880 1,528 822 267 29 3 4 517 20 2 -5 86 54 -116 923 467 -1 -1 0 0 48 16 -12 6 3 -6 153 132 0 -4 -1 2 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-49. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelhead for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - by water year type.. Revised loss thresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. - Water Year Type - State Water Project - - Central Valley Project cos PA PAvCO S (%change) 1,120 2,349 3,092 2, 170 1,056 1,296 2,676 3,503 2,656 1,413 177 (15.8%) 327 (13.9%) 4 12 (13.3%) 486 (22.4%) 357 (33.8%) -- cos PA PA - COS (%change) Wet Above Normal Below Normal Dry Critical 5,440 10,208 7,097 7,573 4,102 6,692 11,813 8,552 9,822 5,694 1252 (23.0%) 1605 (15.7%) 1456 (20.5%) 2249 (29.7%) 1592 (38.8%) Table 2.5.5-50. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelhead for the February 5, 2019, PA and COS scenarios at the SWP/CVPexport facilities - Wet water year type. Revised loss t hresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. Month -October November December January February March April May June July August September Annual Average cos PA 40 1I 38 1,253 1,507 1,600 465 297 217 4 3 4 60 13 33 1,338 1,578 1,494 1,246 699 219 4 3 4 PA -COS (%change) 20 (48.5%) 2 (16.7%) -5 (-12.4%) 85 (6.8%) 71 (4.7%) -106 (-6.6%) 781 (I 68.0%) 401 (135.0%) 2 (1.0%) 0(2.3%) 0 (- 1.4%) 0 (1.7%) 5,440 6,692 1,252 (23.0%) State Water Project 518 cos PA 0 3 5 194 249 395 139 57 52 26 0 0 0 3 5 194 23 1 386 282 123 48 25 0 0 PAvCOS (%change) 0 0 (12.2%) 0 (-7.0%) 0 (0.1%) -18 (-7.1%) -9 -2.4%) 143 (102.3%) 66 (115.4%) -3 (-6.7%) -1 (-5.0%) 0 0 1,120 1,296 177 (15.8%) Central Valley Project Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-51. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelbead for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Above Normal water year type. Revised loss thresholds in t he June 14,2019 P A are expected to limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA-COS (%change) cos PA PA vCOS (%change) October November December January February March April May June July August September Annual Average 4 29 303 2,796 4,618 1,978 289 130 53 8 0 0 10,208 5 35 304 3,345 4,755 1,886 979 437 60 8 0 0 11,813 l (32.5%) 6 (20.3%) 0 (0.1 %) 550 (19.7%) 137 (3.0.%) -92 (-4.7%) 690 (238.2%) 307 (236.0%) 7 (13.0%) 0 (6.1%) 0 0 1,605 (15.7%) 0 7 31 1,014 768 400 80 42 7 2 0 0 2,349 0 6 31 1,101 775 397 223 137 6 2 0 0 2,676 0 - 1 (-12.6%) 0 -0.5%) 87 (8.5%) 7 (0.9%) -3 (-0.8%) 143 (178.1%) 95 (228>7%) -1 (-10.8%) 0 (-3.4%) 0 0 327 (13.9%) Table 2.5.5-52. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelhead for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Below Normal water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comp·arable to the COS scenario. Month - - State Water Project - - Central Valley Project -- cos PA PA -COS (%change) cos PA PAvCOS (%change) October November December January February March April May June July August SeiPtember Annual Average 0 0 0 0 0 0 0 113 0 103 0 -10 (-9.0% 0 8 0 7 0 -1 (-7.6%) 33 1 386 5,208 55 (16.7%) 4,324 885 (20.5.%) 63 2,164 68 2,456 292 ( 13.5%) 2,227 2,577 349 (15.7%) 782 801 19 (2.4%) 47 122 74 (155.8%) 42 81 40 (94.4%) :54 157 103 (188.7%) 34 90 57 (167%) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7,097 0 8,552 0 I ,456 (20.5%) 0 3,092 0 3,503 0 412 ( 13.3%) 519 5 (8.3%) Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-53. Estimated entrainment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelbead for the February 5, 2019, PA a nd C OS scenarios at the SWP/CVP export facilities - Dry water year type. Revised loss thresholds in the June 14, 2019 P A are expected to limit loss to be more comparable to the COS scenario. Month - - -- cos PA October November December January February March April May June July August Se!Ptember Annual Average 2 43 93 621 2,437 3,539 634 177 14 12 3 52 94 647 2,911 4,552 1,162 370 22 10 0 0 9,822 0 0 7,573 State Water Project PA - COS (%change) - - cos PA I (32.4%) 9 (21.0%) 0 (0.5%) 25 (4.1%) 474 (19.4%) 1,012 28.6%) 527 (83.2%) 193 (108.7%) 8 (59.8%) -2 (-13.1%) 0 0 2,249 (29.7%) 0 2 3 73 702 1,121 243 20 7 0 0 0 2,170 0 2 2 74 894 1,296 339 39 10 0 0 0 2,656 Central Valley Project PAvCOS (%change) 0 0 (-7.7%) 0 (-9.0%) 1 (1.0%) 192 (27.4%) 175 (15.6%) 97 (39.8%) 19 (94.5%) 3 (39.8%) 0 0 0 486 (22.4%) Table 2.5.5-54. Estimated entr a inment index (number offish lost, based on historical loss data and the salvage-density method) of juvenile CCV steelbead for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Critical water year type. Revised loss thresholds in the June 14, 2019 PA are expected to limit loss to be more comparable to the COS scena rio. Month - - State Water Project cos PA PAvCOS (%change) 0 0 0 234 624 141 46 10 0 0 0 0 1,056 0 0 0 239 885 221 54 14 0 0 0 0 1,413 0 0 0 5 (2.0%) 261 (41.8%) 79 (56.1%) 8 ( 17.2%) 4 (39.6%) 0 0 0 0 357 (33.8%) -- cos PA PA-COS (%change) October November December January February March April May June July August September Annual Average 0 0 0 196 2,944 644 187 111 10 9 0 0 4,102 0 0 0 200 3,975 924 348 194 43 10 0 0 5,694 0 0 0 3 (1.6%) 1,031 (35.0%) 280 (43.4%) 161 (86.1%) 83 (74.5%) 33 319.6%) 1 (9.7%) 0 0 1,592 (38.8%) 520 Central Valley Project Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-55. Estimated entrainment index (number offish salvaged, based on salvage data a nd the salvage-density method) of juvenile sDPS green sturgeon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Wet water year type. Revised loss thresholds in the June 14,2019 PA m.ay limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project PA - COS (%change) cos PA PAvCOS (%change) 2 (48.5%) 1 (16.7%) 0 0 2 (4.7%) 0 0 0 0 0 0 0 5 (4.4%) 8 4 10 0 0 0 2 5 7 20 5 12 73 8 4 9 0 0 0 3 -- cos PA October November December January February March April May June July August September Annual Average 3 6 0 2 42 4 0 0 2 l 30 18 107 5 7 0 2 44 3 0 0 2 I 30 18 112 11 7 19 5 13 80 0 0 -l -7.0%) 0 0 0 2 (102.3%) 6 (115.4%) 0 (-6.7%) - 1 (-5.0%) 0 (0.4%) 0 (3.7%) 7 (9.3%) Table 2.5.5-56. Estimated entrainment index (number of fish salvaged, based on salvage data and the salvage-density method) of juvenile sDPS green sturgeon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Above Normal water year type. Revised loss thresholds in the June 14, 2019 PA may limit loss to be more comparable to the COS scenario. Month - - -- cos PA October November December January February March April May June July August September Annual Average 0 0 0 2 6 0 0 0 0 0 0 0 3 6 0 0 0 0 4 0 0 12 4 0 0 12 Central Valley Project State Water Project PA - COS (%change) cos PA 0 0 0 1 (19.7%) 0 (3.0%) 0 0 0 0 0 0 0 l (7.1 %) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 521 0 0 PAvCOS (%change) 0 0 0 0 0 0 0 0 0 0 0 0 0 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-57. Estimated entrainment index (number offish salvaged, based on salvage data and the salvage-density method) of juvenile sDPS green sturgeon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Below Normal water year type. Revised loss thresholds in the June 14, 2019 PA may limit loss to be more comparable to the COS scenario. Month - - State Water Project - - Central Valley Project cos PA PA vCOS (%change) -- cos PA PA - COS (%change) October November December January February March April May June July August September Annual Average 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Table 2.5.5-58. Estimated entrainment index (number offish salvaged, based on salvage data and the salvage-density method) of juvenile sDPS green sturgeon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Dry water year type. Reviised loss thresholds in the June 14,2019 PA may limit loss to be more comparable to the COS scenario. Month - - -- cos PA October November December January February March April May June July August September Annual Average 0 1 16 0 0 4 0 0 0 0 0 0 21 0 1 16 0 0 5 0 0 0 0 0 0 22 State Water Project PA-COS (%change) - - Central Valley Project cos PA PA vCOS (%change) 0 0 (21.0%) 0 (0.5%) 0 0 1 (28.6%) 0 0 0 0 0 0 l (6.6%) 19 25 8 3 0 0 0 0 0 0 0 0 55 21 23 7 4 0 0 0 0 0 0 0 0 55 2 (8.7%) -2 (-7.7%) -1 (-9.0%) 0 (1.0%) 0 0 0 0 0 0 0 0 -1 (-1.6%) 522 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-59. Estimated entrainment index (number offish sa lvaged, based on salvage data and the salvage-density method) of juvenile sDPS green sturgeon for the February 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - Critical water year type. Revised loss thresholds in the June 14, 2019 P A may limit loss to be more comparable to the COS scenario. - Month - State Water Project - - Central Valley Project cos PA PA vCOS (%change) 0 0 0 4 0 0 3 0 0 0 0 0 8 0 0 0 4 0 0 4 0 0 0 0 0 9 0 0 0 0 (2.0%) 0 0 1 (17.2%) 0 0 0 0 0 l (8.7%) -- cos PA PA - COS (%change) October November December January February March April May June July August September Annual Average 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Table 2.5.5-60. Estimated entrainment index (number offish salvaged, based on historical salvage dat and the salvage-density methoda) of juvenile sDPS green sturgeon for the Februa ry 5, 2019, PA and COS scenarios at the SWP/CVP export facilities - by water year type. Revised loss thresholds in the June 14, 2019 PA may limit loss to be more comparable to the COS scenario. WaterYear Type - - -- cos PA Wet Above Normal Below Normal 107 12 0 21 0 112 12 Dry Critical 0 22 0 State Water Project PA - COS (%change) 5 (4.4%) 1(7.1%) 0 (0.0%) l (6.6%) 0 (0.0%) 523 - - Central Valley Project cos PA PAvCOS (%change) 73 0 0 80 0 0 55 55 8 9 7 (9.3%) 0 (0.0%) 0 (0.0%) -1 (-1.6%) 1 (8.7%) Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.14 Summary Tables of Stressors for each Project Component Table 2.5.5-61. Summary of Life Stage, Timing, Stressor, Response and F requency table for species and lifestages affected by the Delta Cross Channel Gate Operations. Species WRCS Life-stage present Adult migration or holding: Timing of presence Jan- June cv Jan - June SRCS CCVSH Jul- May sDPS GS All Year Winterrun Chinook salmon Juveniles, migration/ rearmg Oct-April Stressor Response Open DCC gates; Routing into alternative migratory paths Increased straying into the Mokelumne River system due to open gates, delay behind closed gates Springrun Chinook salmon Juveniles, migration/ rearmg Dec May Annual, gates normally open Oct - Nov, Gates operated infrequently between Dec and Jan Pr obable Fitness Change Delayed migration ' Open DCC gates: • Routing into Delta interior • Increased transit times to western Delta • Altered downstream hydrodynamics Higher vulnerability to entrainment at SWPandCVP fish collection facilities Open DCC gates: Routing into Delta interior increased transit times to western Delta Altered downstream hydrodynamics Increased mortality, low survival Annual, gates normally open Oct - Nov. Gates operated infrequently between Dec and Jan, closed Feb I May20, 50% ofjuvenile population migrates into Delta by end! of January Reduced survival Increased mortality, low survival Annual, gates normally open Oct - Nov. Gates operated infrequently between Dec and Jan, closed Feb I May20. 5%of Reduced survival • cv Frequency/ Exposure • • • 524 Biological Opinion for the Long-Term Operation of the CVP and SWP Species Life-stage present Timing of presence Stressor • Response Higher vulnerability to entrainment at SWPandCVP fish collection facilities CCV Steelhead Juveniles, migration/ rearing NovJune Open DCC gates: • Routing into Delta interior • increased transit times to western Delta Altered • downstream hydrodynamics • Higher vulnerability to entrainment at SWP andCVP fish collection facilities Increased mortality, low survival sDPS Green Sturgeon Juveniles, migration/ rearing Year round Open DCC gates: • Routing into Delta interior • increased transit times to western Delta • Altered downstream hydrodynamics • Higher vulnerability to entrainment at SWPandCVP fish collection facilities Movement into and through the interior Delta Abbreviations: WRCS CVSRCS CCVSH sDPSGS Frequency/ Exposure YOYSR migrate into Delta by endl of January, higher percentage of yearlings Annual, gates normally open Oct -Nov. Gates operated infrequently between Dec and Jan, closed Feb 1 May20. 2550% of juvenile steelhead migrate into Delta by endl of January, Annual,Gates open midJune through the end of Nov. operated infrequently between Dec and Jan, closed Feb I May20 = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment ofNorth American Green Sturgeon 525 Probable Fitness Change Reduced survival Uncertain impacts to fitness due to extended rearing behavior in the Delta Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-62. Summa r y of Life Stage, Timing, Stressor, R esponse and F requency t able for sp ecies and lifestages affected by the North Bay Aqueduct Operations . Species WRCS Timing of presence Juveniles, migration/ rearing OctApril Routing, delayed migration Increased mortality, lower survival Year round pumping/ low exposure risk due to location DecMay NovJune Oct April Entrainment/impingement on fish screens Injury and mortality Year round pumping/ low exposure risk due to location Minimal change in fitness Impingement/ capture during weed removal Injury and mortality Infrequent cleaning/ seasonal Minimal change in fitness Entrainment during sediment cleaning Injury and mortality Infrequent cleaning/ seasonal Minimal change in fitness Routing Delayed migration to western Delta Year round pumping/ low exposure risk due to location Minimal Reduction in survival cv SRCS CCVSH WRCS Juveniles, mjgrationl rearing cv sDPS GS Juveniles, migration/ rearmg cv sDPS GS cv Juveniles, migration/ rearing Oct April DecMay NovJune All Year SRCS CCVSH sDPS GS sDPS Green Sturgeon Oct April DecMay Nov June All Year SRCS CCVSH WRCS Response DecMay Nov June AU Year SRCS CCVSH WRCS Stressor F requency/ Exposure Probable Fitness C hange Minimal Reduction in survival Life-stage present Juveniles, Delta rearing Abbreviations: WRCS Year round presence = Sacramento River winter-run Chinook salmon 526 Biological Opinion for the Long-Term Operation of the CVP and SWP CV SRCS CCVSH sDPSGS = Central Valley spring-run Chinook salmon = California Central Valley Steelhead =southern Distinct Population Segment of North American Green Sturgeon Table 2.5.5-63. Summa ry of Life Stage, Timing, St ressor, Response a nd F requency table for sp ecies a nd lifestages affected by the Contr a Costa Water District - Rock Slough Operations. Species WRCS Life-stage present Timing of presence Juveniles, migration! rearing OctApril CV SRCS Dec- May CCVSH Nov June sDPS Green. Sturgeon AbbreviatiOns: WRCS CVSRCS CCVSH sDPSGS Juveniles, Delta reanng Year round presence Response Stressor Frequency/ Exposure Probable Fitness Change Routing, delayed migration Increased mortality, lower survival Year round pumping/ low exposure risk due to location Minimal Reduction in survival Routing Delayed migration to western Delta Year round pumping/low exposure risk due to loca tion Minimal Reduction in survival = Sacramento Rjver winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon 527 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-64. Summary of Life Stage, Timing, Stressor, Response and F requency table for sp ecies and lifestages affected by the Extension of the Water Transfer Window. Species Life-stage present Timing of presence Stressor Response Winter-run Chino,ok salmon Juveniles, migration/ rearing October through April Transit times Reduced transit times in riverine sections of the mainstems CV Springrun Chinook salmon Juveniles, migration/ rearing December through May Transit times Reduced transit times in riverine sections of the mainstems CCV Steelhead Adult, upstream migration July through May Low Autumn flows Increased flows may stimulate upstream migration and reduce straying CCV Steelhead Juveniles, migration/ rearing Nov- June Transit times Reduced transit times in riverine sections of the mainsterns sDPS Green Sturgeon Adult migration/ holding Year round Low Autumn Flows Stimulate fall downstream migration 528 Frequency/ Exposure Perhaps annually during October and November, uncertain volumes and duration Perhaps annually during October and November, uncertain volumes and duration and fish presence in November (yearlings) Perhaps annually during October and November, uncertain volumes and duration of transfer flows Perhaps annually during October and November, uncertain volumes and duration Perhaps annually during October and November, uncertain volumes and duration Probable Fitn ess Change Minimal benefit to fitness and survival Minimal benefit to fitness and survival Increased fitness Minimal Increased fitness Uncertain benefits Biological Opinion for the Long-Term Operation of the CVP and SWP *Export effects will be addressed in the South Delta Export Operations. Abbreviations: WRCS CV SRCS CCVSH sDPSGS = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon Table 2.5.5-65. Summary of Life Stage, Timing, Stressor, Response and Frequency table for species and lifestages affected by the Suisun Marsh Salinity Control G ate Operations/ Roaring River Food Distribution Studies. Species Life-stage present Timing of presence Stressor • Changes in flow • Predation • Physical barrier Jan-June • Changes in flow CV SRCS Jan - June • Physical barrier CCVSH July- May WRCS Juvenile migration/ rearing Oct- April CV SRCS Dec- May CCVSH Nov- June sDPS GS WRCS sDPS GS Abbreviations: WRCS CVSRCS CCVSH sDPSGS Response Frequency/ Exposure Temporary delays by closed radial gates; boat lock open 70-80 days of operation, mostly summer Probable Fitness Change Minimal change in fitness Lower survival due to predation at gates All Year Adult migration/ holding Temporary delays in migration, boat lock open 70-80 days of operation, mostly summer All Year = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon 529 Minimal change in fitness Biological Opinion for the Long-Term Oper ation of t he CVP and SWP Table 2.5.5-66. Sum ma r y of Life Stage, Timing, Stressor, R esp onse a nd F requency table for sp ecies a nd lifestages affected by the CVP/SWP South Delta Export O perations. Species WRCS cv Lifestage present Juveniles, migration/ rearing Timing of pr esence OctApril Dec- May SRCS Stressor South Delta Exports: • Entrainment and loss CCV SH Nov - Jun • Altered hydrodynamics sDPS GS WRCS ALI Year • Predation Juveniles, migration/ rearing cv SRCS CCV SH sDPS GS WRCS OctApril Nov- Jun Juveniles, migration/ rearing OctApril Dec - May CCV SH Nov- Jun sDPS GS ALI Year Juveniles, migration/ rearing OctApril Dec- May SRCS • Annual, year round operations Reduced survival and fitness Injury or death from contact with sampling gear January through June- Minimal reduced survival multi-year study, infrequent sampling and fitness Fish narcosis due to hypercapnia/ potential death of small fish Late fallearly summer when listed salmonids present More fish entrained at CVP, reduced predation impact from CCF Annual when listed fish present and CVP capacity available Increased facility efficiency resulting in increased survival of entrained fish, some reduced fitness/ survival due to C02 exposure Increased survival Predation C(h Injector Use • Hypercapnia • Reduced predator population Shift in Operations from SWP to CVP - • • CCV SH Reduced survival due to export operations ALI Year SRCS cv F requency/ Exposure Dec- May cv WRCS Predator Studies: • Capture in sampling gear Pr obable Fitness R esponse Exports/ entrainment Predation Nov- Jun 530 Biological Opinion for the Long-Term Operation of the CVP and SWP Species sDPS GS sOPS GS L ifestage present Timing of presence R esponse Frequency/ Exposure Reduced physiological fitness, potential death Potentially annually during summer Stressor Probable Fit ness C hange ALI Year Juveniles, migration/ rearing Adults All year Abbreviations: WRCS CV SRCS CCVSH sDPSGS Aquatic weed control CCF in summer • Herbicide exposure • Water quality Reduced fitness = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook sallmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon Table 2.5.5-67. Summary of Life Stage, Timing, Stressor, Response and Frequency table for species and lifestages affected b y the South Delta Agricultural Barrier s Operations. Species Life-stag e present Timing of presence Stressor Dec - May • CCVSH Nov - Jun • • sOPS GS All Year CV SRCS Adult/ migratory • • Oct - April • CV SRCS Dec - May • CCVSH Nov- Jun • sDPS GS All Year • • WRCS Abbreviations: WRCS CV SRCS CCVSH sDPSGS Juveniles, migration/ rearing Increased transit time Physical barriers to movement Reduced water quality Altered hydrodynamics Increased transit time Physical barriers to movement Reduced water quality Response Frequency/ Exposure Migratory delays and physiological decline Annually from May to Nov Reduced survival and increased transit through time Annually juveniles exposed during the May the south Delta waterways through early June period Predation Altered Hydrodynamics = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon 531 Probable Fitness Change Reduced fitness and potentially spawning fitness Reduced fitness and potentially spawning fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Ta ble 2.5.5-68. Summary of Life Stage, Timing, Stressor, Response and Frequency t able for species and lifestages affected by the Fall Delta Smelt Habita t Operations. Species WRCS Life-stage present Juveniles, migration/ rearing cv T iming of presence Oct- April Dec- May SRCS CCVSH Nov- Jun sDPS GS All Year CCVSH Adult migration Jul- May Stressor Adult migration All Year • • Flow conditions • Water Temperature • Water Quality • Exports • • sDPS GS R esponse Flow Conditions Exports Changes in upstream water quality conditions below reservmrs Changes in • migratory behavior • Changes in D elta Hydrodynamics related to outflow and exports Upstream releases stimulate upstream migration Frequency/ Exposure Above normal and Wet years m September and October Above normal and Wet years m Flow conditions Upstream releases stimulate downstream migration Probable Fitness Cha nge Variable responses depending on implementation. September and October Above normal and Wet years m Variable response depending on implementation. Variable response depending on implementation. September and October Abbreviations: WRCS CV SRCS CCVSH sDPSGS = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead =southern Distinct Population Segment of North American Green Sturgeon 532 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.5-69. Summa ry of Life Stage, Timing, Stressor, R esponse and F requency t able for sp ecies and lifestages affected by the Sacramento Deep Water Ship Channel Food Study. Species Life-sta ge pr esent Timing of presence Stressor • R esponse Frequency/ Exposur e Fish movements blocked by closed boat locks. Angler bycatch Unknown how frequently boat locks would be opened for food studies Probable Fitness Change Uncertain due to lack of clarity on timing and duration of lock operations resulting in variable responses. Oct- April • Passage impediment Barrier CV SRCS Dec - May • Angling pressure • Water temperatures • CCVSH Nov- Jun • Water quality • Flow conditions • Entrainment • Predation • A ltered flows and operations of locks may decrease water quality sDPS GS All Year • High predator population of non-native fish present in ship channel WRCS Juveniles, migration/ rearing Jan- June • Passage impediment Barrier • Angling pressure • Fish movements blocked by closed boat locks. Unknown how frequently boat locks would be Uncertain due to lack of clarity on timing and duration of CV SRCS Jan- June • Water temperatures • Flow conditions • Anglers/ hooking mortality opened for food studies lock operations resulting in variable responses. CCVSH Jul- May • • Altered flows and operations of locks may decrease water quality sDPS GS AI Year • Entrainment • Ship traffic WRCS Adult migration and holding Water quality 533 • Ship strikes to gsDPS green Sturgeon Biological Opinion for the Long-Term Operation of the CVP and SWP Abbreviations: WRCS CV SRCS CCVSH sDPSGS = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead =southern Distinct Population Segment of North American Green Sturgeon Table 2.5.5-70. Summa r y of Life Stage, Timing, Stressor, R esponse and F requency t able for sp ecies and lifestages affected by the North Delta F ood Subsidies/ C olusa Dra in Studies. Species Life-stage present Timing of presence St ressor Response Exposure to contaminants, low D O, increased water temperatures and high nutrient loads may decrease physiological status. In extreme exposures possibly morbidity or death Reduced physiological status and growth sDPS GS Juvenile migration/ rearing All Year • Contaminants pesticides, heavy metals • Low Dissolved Oxygen • Increased Water temperature • Nutrients CCVSH Adult migration/ holding July - May • Contaminants pesticides, heavy metals • Low Dissolved Oxygen • Increased Water temperature • Nutrients sDPS GS Abbrev1at10ns: WRCS CVSRCS CCVSH sDPSGS All Year Frequency/ Exposure July through Minimal September change in for multiple fitness study years. If successfuM perhaps annually. July through September for multiple study years. If successful perhaps annually = Sacramento River winter-run Chinook salmon = Central Valley spring-run Chinook salmon = California Central Valley Steelhead = southern Distinct Population Segment of North American Green Sturgeon 534 Probable Fitness Change Minimal change in fitness Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.5.15 Revisions to OMR Management Table 2.5.5-71. Summary of key changes in the OMR management component of the June 14,2019 final PA in comparison to the February 5, 2019, P A Element February 5, 2019 (original) PA June 14, 2019 (final) PA Onset of OMR Management OMR limit associated with "First Flush" Turbidity event -3,500 cfs (PA text) -2,000 cfs (PA Modeling in Appendix D ofBA) -2,000 (PA text) No new modeling. Additional Real-Time OMR Restrictions OMR limit associated with Turbidity Bridge A voidance -5,000 cfs (PA text) -2,000 cfs (PA text) -2,000 cfs (PA Modeling in Appendix D ofBA) No new modeling. OMR limit of -2,500 cfs for 5 days whenever more than 5 percent of steelhead are present in the Delta and daily loss of natural origin steelhead exceeds 10 steelhead per TAF. No daily loss trigger; replaced with revised steelhead loss threshold. Loss threshold (cumulative): for specified populations None identified Cumulative historical loss from 20 10-20 18 (measured as the 2010-2018 average cumulative loss multiplied by 10 years) will not be exceeded by 2030. Salvage or Loss Thresholds (annual): Wild winter-run Chinook salmon (loss) 1 percent of the JPE (genetically confirmed or 2 percent based on length at date) 90% of the greatest annual loss that occurred in the historical record from 2010 through 2018 (DecemberMarch): 1.17% of the JPE Wild Central Valley Steelhead Protection 535 Biological Opinion for the Long-Term Operation of the CVP and SWP Element Salvage or Loss Thresholds (annual): spring-run Chinook salmon (loss) February 5, 2019 (original) PA June 14, 2019 (final) PA 1 percent ofthe JPE (or 0.5 percent of spring-run surrogates for yearlings) None identified None identified 90% of the greatest annual loss that occurred in the historical record from 20 I 0 through 201 8: O.H6% ofthe hatchery JPE Salvage or Loss Thresholds (annual): wild steelhead (salvage in original PA; loss in fmal PA) 3,000 (salvage) 90% of the greatest annual loss that occurred in the historical record from 20 10 through 20 18 for two separate periods: December-March (loss of 1,414 steelhead) and April-June 15 (loss of 1,552 steelhead) Salvage or Loss Thresholds (annual): Green sturgeon (salvage) 100 None identified Salvage or Loss Thresholds (annual): OMR action response when observed loss exceeds average historic loss None identified Reclamation and DWR will review information and seek technical assistance from NMFS Salvage or Loss Thresholds (annual): OMR action response when observed loss -3,500 cfs OMR limit until the species-specific offramp 16 is met. -3,500 cfs OMR limit until the species-specific offramp is met, unless Reclamation Salvage or Loss Thresholds (annual): Hatchery winterrun Chinook salmon (loss) 16 In the PA and throughout this table, "species-specific offramp" refers to the conditions that would end OMR management for a particular species. Specifically, the June 14, 2019 PA defines the end ofOMR management as follows: "OMR criteria may control operations until June 30 (for Delta Smelt and Chinook salmon), until June 15 (for steelhead/rainbow trout), or when the following species-specific off ramps have occurred, whichever is earlier: • Delta Smelt: when the daily mean water temperature at CCF reaches 25°C for 3 consecutive days; • Salmonids: o when more than 95 percent of salmonids have migrated past Chipps Island, as determined by their monitoring working group, or o after daily average water temperatures at Mossdale exceed 72°F for 7 days during June (the 7 days do not have to be consecutive)." 536 Biological Opinion for the Long-Term Operation of the CVP and SWP Element February 5, 2019 (original) PA exceeds 50% of the loss threshold Salvage or Loss Thresholds (annual): OMR action response when observed loss exceeds 75% of the loss threshold June 14, 2019 (final) PA and DWR determine that further OMR restrictions are not required based on risk assessment. Reclamation and DWR will seek technical assistance from NMFS. -2,500 cfs OMR limit until the species-specific offramp is met. -2,500 cfs OMR limit until the species-specific offi·amp is met, unless Reclamation and DWR determine that further OMR restrictions are not required based on risk assessment. Reclamation and DWR will seek technical assistance from NMFS. Storm Related OMR Flexibility Conditions when storm flex would not occur Additional real-time OMR restrictions in effect Additional real-time OMR restrictions in effect, plus some additional limits End of OMR Management Date-based offramp for Chinook salmon and steelhead June 30 for Chinook salmon and steelhead June 30 for Chinook salmon, June 15 for steelhead 2.5.6 Stanislaus River (East Side Division) Operational effects of dams on rivers and the species that live in them are multi-faceted and compl ex. This analysis focuses on key elements ofReclamation's operation ofNew Melones Dam, and related dams of the East Side Division (see area map in Figure 2.5.6-1 and deconstructed action in So, for example, if, after conducting a risk assessment, Reclamation and DWR implemented a -3,500 cfs OMR limit action on June 3 after exceeding 50% of the April-June 15 steelhead loss threshold, that OMR action would not extend past June 15 due to the date-based offramp for OMR management for steelhead. Note that the -5,000 cfs OMR limit will be in effect until offramps for all species are met. 537 Biological Opinion for the Long-Term Operation of the CVP and SWP Core Operations Proposed Action Scheduling Collaborative Planning Not Consulted On Seasonal Operations & Stanislaus Stepped Release Plan Stanislaus River pulse flows I Stanislaus River (East Side Division) Alteration of Stanislaus DO Requirement San Joaquin River r--- Conservation Measures ___J,._ Spaw ning and Rearing Habitat Restoration I San Joaquin Restorat ion Program I PA Conditions Conservation Measures --:::J...._ Temperature Management Study Lower SJR Habitat Figure 2.5.6-2), that may affect life history stages of CCV steel bead and any CV spring-run Chinook salmon when they are in the Stanislaus River. 538 Biological Opinion for the Long-Term Operation of the CVP and SWP Stanislaus River Legend N • Dams/ Pumping Plants • Temperature or D1ssolved O xygen Compliance - - Hydrology Ao 5 10 Miles Figure 2.5.6-1. Area map of key locations in the CVP East Side Division (modified from Figure 1-7 of ROC on LTOBA). 539 Biological Opinion for the Long-Term Operation of the CVP and SWP Core Operations Proposed Action Scheduling Collaborative Planning Not Consulted On Seasonal Operations & Stanislaus Stepped Release Plan Stanislaus River pulse flows I Stanislaus River (East Side Division) Alteration of Stanislaus DO Requirement San Joaquin River r--- Conservation Measures ___J,._ Spawning and Rearing Habitat Restoration I San Joaquin Restorat ion Program I PA Conditions Conservation Measures --:::J...._ Temperature Management Study Lower SJR Habitat Figure 2.5.6-2. Deconstruction of the action for Stanislaus and San Joaquin rivers (East Side Division). In the San Joaquin River basin, the southern Sierra Nevada diversity group, there have been reports of adult "spring-running" Chinook salmon returning to San Joaquin River tributaries, February through June (Franks 2015, National Marine Fisheries Service 2016a), or present in the Stanislaus River in spring and summer (Kennedy and CallllOn 2002), indicating that a population (or populations) do(es) exist. Additionally, in 2014, spring-run Chinook salmon were reintroduced into the San Joaquin River; these reintroduced fish have been designated as a nonessential experimental population under ESA section lO(j) in the San Joaquin River from Friant Dam downstream to its confluence with the Merced River (78 FR 79622 2013). Just recently, eight returning SJRRP adults were confirmed in the restoration area, marking 65 years since CV spring-run Chinook salmon have completed their life cycle in this location (preliminary data Reclamation). The analysis of effects to species in the Stanislaus River focuses on effects to particular life history stages of CCV steelhead and (for informational purposes) any CV springrun Chinook salmon that may be present. Note that in the CV spring-run Chinook salmon Integration and Synthesis Section (Section 2.8.3), NMFS discusses the San Joaquin experimental population and associated 4(d) rule with respect to findings under this Opinion. Due to a continued high demand for limited water suppty in the Central Valley, numerous stressors continue to affect the viability ofsalmonid populations. Tabl e 2.5.6-1 provides a summary of which stressors from the "Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley Spring-Run Chinook Salmon and the Distinct Population Segment of California Central Valley Steelhead" (National Marine Fisheries Service 20 14b) will be analyzed under each PA component within this effects analysis for the Stanislaus River (East Side Division). 540 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-1. Summary of which stressors from the "Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley Spring-Run C hinook Salmon and the Distinct Population Segment of California Central Valley Steelhead" (NMFS 2014) will be analyzed under each PA component within this effects analysis for the Stanislaus River (East Side Division). An "X" indicates the stressor will be analyzed for at least one life-stage and species and a "-" indicates that the stressor iis not applicable for a particular PA component. Projject Component 2.5.7.1 Seasonal Operations and Stanislaus Stepped Release Plan X X 2.5.7.2 Alteration of Stanislaus DO requirement 2.5.7.3.1 Conservation Measures Spawning and Rearing Habitat Restoration 2.5.7.3.2 Conservation Measures Temperature Management Study X X X X X X X X X X X X X X X X X X X X A recent discussion of stressors in the Stanislaus River and potential effects is provided in Stanislaus River Scientific Evaluation Process (SEP) Team (20 19). Proposed operations will continue to affect flows and water temperatures in a way that will continue to negatively affect salmonids present in the Stanislaus and San Joaquin rivers. 2.5.6.1 Seasonal Operations and Stanislaus Stepped Release Plan Reclamation operates the CVP East Side Division for flood control, agricultural water supplies, hydroelectric power generation, fish and wildlife protection, and recreation. The New Melones 541 X X Biological Opinion for the Long-Term Operation of the CVP and SWP Dam operates in conjunction with Tulloch Reservoir and Goodwin Dam on the Stanislaus River. Goodwin Dam, completed in 1912, is an impassible barrier to upstream fish migration at RM 59. Water is released from New Melones to satisfy senior water right entitlements, instream and Vernalis salinity standards specified under D-1641 and D-1422, CDFG fish agreement flows, CVP water contracts and b(2) or CVPIA 3406(b)(3). Reclamation proposes to operate New Melones Reservoir to provide minimum releases at Goodwin Dam according to a Stepped Release Plan (SRP) with annual release volumes by year type as shown in Table 2.5.6-2. A summary of the PA is provided in Appendix A2 of this Opinion, with additional description provided in Appendix A (Facility Descriptions and Operations) ofthe ROC on LTO BA. The daily flow schedules (one for each water year type) of the proposed SRP are provided in Appendix K of this Opinion. When compared to minimum daily flow schedules from Appendix 2-E of the NMFS 2009 Opinion, the minimum daily flow schedules for the New Melones SRP are identical for critical, dry, and below normal year types; above normal and wet year types follow minimum daily flow schedules for below normal and above normal year types from Appendix 2-E of the NMFS 2009 Opinion, respectively (Table 2.5.6-2). Notably, Reclamation also proposes to determine year type using the "60-20-20" Index for the San Joaquin Valley Water Year Hydrologic Classification (based on the current water year's hydrology and the previous year's index), rather than the New Melones Index (NMI; based on end-of-February New Melones storage and March-September inflow to New Melones) used currently. Table 2.5.6-2. New Melones Stepped Release Plan annual releases by year type (based on San Joaquin Valley "60-20-20" Index). (Source: ROC on LTO BA: Modification of Table 4-14) (60-20-20 Index) SRP Annual Release {TAF) Equivalent to Appendix 2-E schedule from listed year type (New Melones Index) Critical 184.3 Critical Dry 233.3 Dry Below normal 344.6 Below normal Above normal 344.6 Below normal Wet 476.3 Above normal Water Year Type 542 Biological Opinion for the Long-Term Operation of the CVP and SWP Reclamation proposes to implement the SRP similar to current operations, in that seasonal flow volumes (as defined in the default daily flow schedules) may be shaped to meet specific biological objectives. The Stanislaus Watershed Team (successor to the Stanislaus Operations Group), which will include stakeholders (unlike the Stanislaus Operations Group, which includes only agency members) will provide input on shaping seasonal flows. Releases at Goodwin Dam to the Stanislaus River under the COS (current modeling representation of project operations at the time of consultation) or PA may exceed the proposed minimum fishery flows in Appendix 2-E (for COS) or the SRP (for PA) for a variety of reasons, including flood control, reservoir storage management, and other regulatory requirements. Some key uncertainties in the PA for the East Side Division relate to Reclamation' s assumptions about changes to regulatory requirements or agreements that are in flux or may not be fully within Reclamation's discretion to change. The assumptions in question include: Vernalis flows in D-1641: Modeling for the COS scenario assumes only the February through June "base flow" r,equirements at Vernalis (which might result in releases into the Stanislaus River above Appendix 2-E flows), and does not include the October and spring pulse flows at Vernalis in D-1641 17. Modleling for the PA scenario does not assume any Vernalis flow standard at any time of the year 18; Vernalis flows are simply the results of upstream contributions, including the SRP. Because of the SWRCB's efforts to update the Bay Delta Water Quality Control Plan, there is uncertainty about what Vernalis flow requirements will be in January 2020. NMFS analyzed the effects as modeled. Vernalis Electrical Conductivity (EC) in D-1641 : Modeling for the COS assumes the Vernalis EC standards in D-1641 (which might result in releases into the Stanislaus River above Appendix 2-E flows). Modeling for the PA scenario does not assume any Vernalis EC standard E9 ; Vernalis EC is simply the result of upstream contributions, including the SRP. Because ofthe SWRCB's efforts to update the Bay Delta Water Quality Control Plan, there is uncertainty about what Vernalis EC requirements will be in January 2020. NMFS analyzed the effects as modeled. Ripon Dissolved Oxygen (DO) standard in D-1422: One component of the PAis to shift the compliance location for the DO Standard (in D-1422) about 30 river miles upstream (from Ripon to Orange Blossom Bridge) during the summer. Modeling for the COS and 17 Reclamation's perspective on the Vernalis flow requirements is provided in an April 12, 2018, letter from Reclamation to the SWRCB: https://www. waterboards.ca.gov/waterrights/water_issues/programs/compliance_monitoring/ sacramento_sanjoaquin/docs/20 18/0 41220 18_ usbrltr.pdf 18 In a consultation meeting on May 24,2019, Reclamation clarified that some Vernalis flow standard may be in place by January 2020, but that the CVP contribution would be considered met by Stanislaus operations under the PA. 19 In a consultation meeting on May 24, 2019, Reclamation clarified that some Vernalis EC standard may be in p lace by January 2020, but that the CVP contribution would be considered met by Stanislaus operations under the PA. 543 Biological Opinion for the Long-Term Operation of the CVP and SWP PA do not differ (though the narrative acknowledges that flows might occasionally be lower during the summer due to this component of the PA). Neither NMFS nor Reclamation has the authority to approve a shift in this DO compliance location, so NMFS assumes that Reclamation will obtain any necessary approvals for this change before implementation of this PA component. The range of effects prior to implementation of the shift in DO compliance location is within the range of effects evaluated assuming the compliance location is changed, so coverage is provided both before and after the necessary approvals are obtained. " 1987 Agreement20" between Reclamation and (then) California Department ofFish and Game: Modeling assumptions include the "1987 Agreement" as a factor in the COS scenario (though the modeling assumes that the Appendix 2-E flows from the NMFS 2009 Opinion satisfy the " 1987 Agreement"). The PA scenario assumes that the SRP supersedes the "1987 Agreement." NMFS analyzed the effects as modeled and defers to Reclamation and the California Department of Fish and Wildlife to resolve the issue. 2.5.6.1.1 Review of Stanislaus River Flows under the PA Dam operations typically alter the downstream hydrograph from the unimpaired hydrograph, and this is true of the CVP's New Melones Dam, most notably by the reduction in annual peak flows due to capture of winter and snowmelt flood flows. Schneider et al. (2000) summarized the flattening of the hydrograph in both wet and dry years after construction ofNew Melones Dam. In wet year conditions, annual peak flows of 25,000 cfs to 30,000 cfs were reduced to <5,000 cfs. In dry year conditions, annual peak flows of7,000 cfs to 8,000 cfs were reduced to <1,500 cfs (Figure 2.5.6-3). 20 The 1987 Agreement is an agreement between California Department of Fish and Game and the United States Department of the Interior Bureau of Reclamation regarding interim instream flows and fishery studies in the Stanislaus River below New Melones Reservoir. 544 Biological Opinion for the Long-Term Operation of the CVP and SWP ly_W_e_ t 35.000 . - - - - - - - - -E:...x_tre_m-'e-'- .. _ _-----: 30,000 - Wf1904 - Wf1998 Wnter Floods u:;20.000 Spnng Snowmelt c: :310,000 " Summer 5,000 B-01 Apr-01 Jun-01 Sep-01 Jul-01 water Year Dale Dry Year Hydrograplils 9,000 . - - - - - - - - - - - - - - - - - - - 8.000 W( - -.;?.000 '0 r ·ooo u::s.ooo 1919 Wf1989 Wfnter Flood ---,. ' +--------r-----fl 0 ffi3.000 t--------+---tr-+----'T--------; Ill '!2.000 1,000 Oct-00 Baseflows Nov-00 Jan-01 Feb-01 Apr-01 Jun-01 Jul-01 water Year Dale Figure 2.5.6-3. Annual comparison of Wet and Dry year hydrographs before (I 904 and 1919) and after (1989 and 1998) construction of New Melones Dam. (Source: Figure 4 in Schneider et al. 2000). Further discussion of changes to the flow regime of the Stanislaus River after construction of New Melones Dam is provided in Kondolf et al. (200 1). While the hydrologic summary in Figure 2.5.6-3 does not include post-New Melones Dam operations under the NMFS 2009 Opinion, both current and proposed operations on the Stanislaus River show similar hydrologic characteristics, i.e. a flattened hydrograph with limited winter and springtime flows. While the average monthly flow output from CalSimll does not capture peak daily flow, model outputs for the PA scenario and COS scenario show that average monthly flows exceed 2,000 cfs only in March of Wet water year types and never exceed 750 cfs in Critical water year types (Table 2.5.6-3). The daily flow schedules in the SRP (Appendix K) include annual peak flows of725 cfs (Critical), 1,000 cfs (Dry), 2,000 (Below Normal and Above Normal), and 3,000 cfs (Wet). 545 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-3. Exceedance table of average modeled monthly flow in the Stanislaus River below Goodwin Dam for the PA scenario and COS scenario. (Source: ROC on LTO BA: Table 37-3 from Appendix D, Attachment 3-2) -_ Table 37-3. Stanislaus River Flow below Goodwin, Monthly Flow ..__.... Current Opontion• 011319 m - * m m It'll M m m m m m .... .... .... ........ .... 200 797 m m 200 200 21'6 m m m 219 100 ::100 21" 40:5 1- 1.521 1.$Sl M •• 238 200 I 400 1242 m m 812 767 918 m 229 705 :ut :100 Ttfl C53t m 1.565 1.089 318 363 54 275 2$$ 26S M2 1GS .:.2:.:.,e-...::.21:.:$_ _m _, m = 859 ............ (2"1 m llfiiM HctiUIItftt 7$2 m 871 200 __, 232 1/4 W8tel Y. .r Typo 205 m 814 Crilblptl£) Pre>,posed Action 011519 .. .... 21& eJO eJ$ It'll LM;T.,... ... Oct IK 1163 212 1,140 716 1.22'4 1140 959 m :13< 313 2.38 227 2$5 12'01 100 700 475 200 ,_..s. 1.030 742 »3 365 200 234 :169 278 272 37S 242 _ _ _ _!loo!!JflowJCfSf JM :100 .... "" ,....... .... .... 200 :100 308 m FM SS2 m 2)0 ,.. .._ ¥' Mit 1.$28 1.555 t.$2t I .57:1 11 .$$3 200 1.1 00 200 2)6 ' lOO 283 1212 3G3 203 243 243 243 200 m I 400 1 2.e2 lS3 :100 en aut 2$5 :>00 767 631 1'00 200 4C.O 400 400 400 m m ... .... 11'0 11'0 363 m 200 200 119 229 221 :100 200 200 200 21) 21) " " 214 '" 712 341 171 152 I 1"7 1.006 SU as< 508 202 735 100) 1.750 2.1119 t.eM ' 499 223 202 W4 $46 695 1.2$5 363 m 1 $10 1242' )1)3 243 2.09 236 571 2•1 200 ' 475 1,$7' 218 OM 14S 206 200 270 220 025 SOt 691 2SS 2SO 241 200 198 ·121 .ez 200 ""tn'OI ............... 1.691 &15 200 :>00 WIUr Y. .r Typn .c.1·:.:12;:. • _..;Gao=_ t.S36 610 ,... ,.,. 1.1!">9 2014 :).&0 :>00 :>00 IK _,m= 154 1.193 m ... Oct DOO tiOA _ _.26S 174 114 llry(IR) 826 Ctlllc.eiQl!l 578 200 200 m 228 222 100 200 e25 Pre>posod Action 011S19 minus Current Opontions 011319 .... Oct IK ... .. I "".... .... IK ,... '"" ,.,. 0 ltc llQ ·If 0 · Ill 0 .J 0 ...., 0 6 ·1 0 .7 ·I 0 .. IAOO""" . ..- . . . . J W1tt1 Yur Typn" .._""(2)!<) ........."' - - I IK I ·•0 _, 236 -.m..···.. ... .... ·101 ·1 129 • S.$7 ... ... -42 175 · 11 -17 ·114 .., .u 3$0 ·121 .. 11 31 20 ... 109 .$M 0 0 284 183 ... , . 150 .. , · 111 .JH .z•t .Ju -us . t lf llry( IR) 0 -10 .aa o 0 ·1 all · •• ..............,..,_.._._,,...,o I_, as.... ..... CNtlft* t'a. ... -...,... t 1li:M. ................. .......,... , _ fllfftlliCIIClttfM(II\ 546 .. .. 0 ->5 -14 ... ·•H .., ·I )I .... ·160 0 100 "*-'11'1!1 ... .... ""' ...ns .az 0 0 0 ....,, ... ...... ..... .. ... 0 · 11 -21 ·12 -64 ...... .. . -1 . .. ..,.. Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.1.2 Analysis of Proposed Changes in Operations and Year Type Method under the PA To understand the effects ofthe proposed changes in operations (due to the SRP and assumptions about other regulatory requirements) and changes in year type method, NMFS assessed the year type distributions for the year type method and operations combinations in Table 2.5.6-4. Table 2.5.6-4. Comparison of year type method and operations combinations. Name of scenario Operations scenario Year type method Comments COS-NMI Current Operations New Melones Index (with Appendix 2- (for operations and E flow schedules) year type assignment in modeling) Current Operations Scenario PA-60-20-20 Proposed Action (with Stepped Release Plan flow schedules) Proposed Action Scenario San Joaquin 60-20-20 Index (for operations and year type assignment in modeling) Table 2.5.6-5 describes how the distribution of year types changes under different year typemethod and operations combinations. There are more Critical, Above Normal, and Wet water year types and fewer Dry and Below Normal water year types in the PA scenario (PA-60-20-20) compared to the COS scenario (COS-NMI). 547 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-5. Distribution of year types under different year type method and operations combinations. Panel A Yeartype Critical 5 4 Dry 3 Below Normal Above Normal Wet Total 2 1 Panel B Yeartype 5 4 3 2 1 Comt of water years in each yeartype PA-60-20-20 18 24 20 10 21 9 14 20 9 19 82 82 Percent of water years in each yeartype PA-60-20-20 Critical 22 29 Dry 24 Below Normal Above Normal Wet Total 26 12 11 17 24 11 23 100 100 Because hydrology is the same; a change in PA-60-20-20 compared to COS-NMI is likely to be caused by a COMBINED change in the year type method and storage condition due to differing operations under the P A. Table 2.5.6-6 describes results ofthe comparison between the PA and COS in terms of"year type differential." 548 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-6. Results of the comparisons b etween PA and COS in terms of " year type differential." Critical, Dry, Below Normal, Above Normal, and Wet water year types are represented as 5, 4, 3, 2, and I, respectively. For example, a year with a PA-60-20-20 year type of Above Normal (3), and a COSNMI year type of Dry (4) would result in a "year type d ifferential" of 3 - 4 = -I. Pane l A Count of water years PA 60-20-20 minos COS i'1\D -3 4 -2 6 -1 18 0 38 1 14 2 2 3 0 Total 82 Yeartype differential min max -3 2 Percent of water years (in 82 year Pane iB Yeartype differential PA 60-20-20 minos COS 1'\1\D -3 5 -2 7 -1 22 46 0 1 17 2 2 3 0 Total 100 549 Biological Opinion for the Long-Term Operation of the CVP and SWP General conclusions based on Table 2.5.6-6 include: PA-60-20-20 to COS-NMI • • • Comparing PA-60-20-20 to COS-NMI controls only for hydrology and thus represents the effect of the COMBINED change in the year type method and storage condition due to differing operations under the PA. The combined effect is asymmetric, with 28 of 82 years (34 percent) being classified as wetter year types (which might trigger a higher flow schedule per the SRP) and 16 of 82 years (20 percent) being classified as drier water year types (which might trigger a lower flow schedule per the SRP). Because the SRP "downshifts" the two highest flow schedules in the NMFS 2009 Opinion's Appendix 2-E (i.e., PA's Wet water year type flow schedule is the same as the NMFS 2009 Opinion's Above Normal water year type flow schedule and PA's Above Normal water year type flow schedule is the same as the NMFS 2009 Opinion's Below Normal water year type flow schedule), a shift from Below Normal in COS to Above Normal in the PA (or from Above Normal in COS to Wet in the PA) doesn't actually trigger a flow schedule with higher releases. The PA's required minimum flows are lower in Above Normal and Wet water year types (based on SRP tables), so would be lower overall even if year type distribution was unchanged. The COS and PA's modeled flows (see Table 2.5.6-3), however, are more similar than might be expected based on this year type analysis and the required fishery minimum flow schedules (Appendix 2-E in the COS; SRP in the PA). The largest changes are that April and May flows during Dry and Critical water year types are about 200-250 cfs lower in the PA compared to the COS (probably due to the assumption that no Vernalis flow requirement is in effect in the PA, compared to an assumption of base Vernalis flows February through June in the COS). June flows are also lower in the PA except in Wet water year types. The greatest reduction in June flows in seen in Above Normal water year types; this is likely the signal from the SRP's implementation of the Appendix 2-E Below Normal flows in an Above Normal water year type. NMFS's interpretation of why larger changes are not observed in the PA flows compared to the COS flows is that in many Above Normal and Wet water year types (the years in which required flows in the PA are, in some months, lower than required flows in the COS), New Melones flood operations occur more often during February, March, and June in the PA, and thus modeled flows reflect releases higher than minimum flows, particularly during Wet water year types. Another reason is that the assumptions in the COS include only base Vernalis flows February to June, and not any of pulse flow elements in D-1641 (in October or mid-April to mid-May), so the PA assumption of no Vernalis flow requirements represents less of an operational change than if the COS assumed the D- 1641 Vernalis pulse flow requirements. 550 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.1.3 Review of Stanislaus River Temperatures under the P A Modeled water temperatures show much cooler conditions in Goodwin Canyon below Goodwin Dam (RM 59, Table 2.5.6-7) than at Orange Blossom Bridge (Table 2.5.6-8), about 11 river miles downstream of Goodwin Dam at RM 47. There is little difference in temperatlllres between the PA and COS at Goodwin Dam; water temperatures there are largely driven by the temperature of water released from New Melones Dam and any warming in Tulloch Reservoir and Goodwin Reservoir (with residence time not generally expected to change between the COS and PA scenarios). Air temperatures will warm or cool water between Goodwin Dam and Orange Blossom Bridge, and this warming or cooling is buffered at higher flows due to increased thermal mass. Results show that temperatures at Orange Blossom Bridge are often slightly warmer in the PA, particularly in June and July. 551 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-7. Exceedance table of average modeled monthly average temperature in the Stanislaus River below Goodwin Dam for the PA scenario and COS scenario. Interpretation of year type differences from these tables is complicated by the fact that both P A and COS flows are summarized by the 6020-20 year type, even though COS flows are modeled based on the NMI year type. (Source: ROC on LTO BA: Table 22-3 from Appendix D, Attachment 3-2) Table 22-3. Stanislaus River below Goodwin Dam, Monthly Temperature Current Operations 011319 0<1 ExcMiance IK ... 59.2 56.5 S4.6 5-3.3 su 50.3 5(1;,1 ss.s s...e: so • so.2 525 497 2.5 s•s S4.5 51.2 49.3 4ti 4&.4 $4.0 S3.5 51.0 46 0 479 S3.5 52.8 50.4 47.3 47..4 52.• 52.1 49 .8 46.4 46.7 56.0 54.9 51.8 46.7 48.7 50.2 52.9 52.4 50.6 47.9 47 1 4 9.2 55.2 5.4.9 56.7 59.4 5"5 54.2 .S.S.6 57.3 51 7 51.5 52.2 529 464 46.4 49.2 497 460 46.7 49.2 499 49 6 50.0 50.9 51.5 50.6 50.1 su 52.5 50.9 52.1 48.4 M.& s.ss s.. a $4,1 514 S42 5-4.0 sso ... ... ... 60,7 55.2 . .. 2 539 53.3 >22 SS.7 .... SS.J S4.2 53.7 >2.5 W_,tet Ye*' Types W«l23"l (2ft) Abo\11 Dl'yU' S.J tdtc:11(?7"1.1 Propo!!d Action 01151' 1... "" ..."" "" "" 58.8 57.1 S5.7 53.7 53.1 50.7 Si.... 55.8 55.0 S4.7 54.7 54.3 .53.9 52.5 49.5 51.8 49. 1 51 4 48.9 49.4 49.1 48 3 S4.3 53.9 53.4 52.3 S3.7 .53.3 52.8 52.2 51.2 50 8 50.3 49.5 48..4 460 47.4 46:9 S5.3 54.4 51.7 53.0 52.6 50.7 55.4 54.4 54.3 51.6 48.5 ss.e 53.8 54.7 48 5 57.4 56.3 51.3 51.9 527 50..2 52.0 50.6 5 1.8 50.3 51.4 48.4 479 47..5 47.0 so.o 51.2 50.8 50.1 ...9.4 53.1 52.9 52.8 52.2 52 0 51.5 50.6 48.7 48.3 50.3 51.3 525 $3 4 $4 4 55.2 47.9 47 9 48 2 48 7 49.t 498 49. 1 4 9.7 50. 1 50.9 516 so.o 5 1.4 51.7 52 4 !))0 50.6 5 1.9 5 22 52.8 S4 0 S2.S 53.8 .54.0 491 49.0 48.5 ss.o su .... Water Ye• r Typult.C ""lll"l BeiO,..NGMaiiiK ) 0tylli'4) 49.0 496 su 5U 527 Proposed Action 01151t minus Curr• nl Opentions 01131t 0<1 1... --"" ..."" "" "" W• ter Year Type.s' " Wttl23'4) Abo¥t NoiNI (2ft.) Bolow ...... llt"l ... · 1.9 -2.0 .t,e .o.s .o.e .o.e -0.5 -0.3 -0.2 -0.1 ..0.4 .0.3 -0.3 ..0.1 -0.1 .0.1 -0. 1 ..0.2 .0.1 -0.1 .0.1 0.1 0.0 .0.2 0.1 0.4 .0.7 .0.5 .0.2 0.0 0 .2 0 .2 0.0 0 .2 -0-2 ..0.4 0.1 ..() 1 .0.2 -03 0.0 ..02 - 1.0 -0.3 -0. 1 .o.• -1.1 ·2.0 ..0.9 .02 ..0.4 o.o .o. t -0..2 0.1 0.0 o.o o.o 0.1 529 53.9 55.6 54 8 56 7 0.1 o.o 0.1 0.0 0.0 0.0 0.0 .0.1 0.1 0.0 0.1 0 .0 S47 553 S70 Sl. l ... ... ... ..0.2 -0. 1 -0.1 0.1 -0.1 0.0 532 S5.5 5<,7 .... .... 0.2 .0.1 0.0 0.1 0.0 .0.1 0.1 0.1 ..0.6 .0.1 0.0 0.0 0 .1 .0.1 .(t2 ..0.8 .0.2 .0.3 .0.3 .0.1 o.o ·2.0 -0.7 -0.3 -0.4 ..0.3 0.0 0 .0 ..0. 1 0.2 0.2 0.2 ..0.1 0.2 0.2 0.1 0.1) 0.2 0 .0 .0.1 .0.1 0.3 0.2 0.1 0.4 0.3 ..0.1 0.3 0.0 0.1 0.0 0.0 0 .0 .0.1 .0.1 ..0.1 ..0.4 0..2 0..2 0..0 ..0.1 0.1 0.' 0 .1 0 .1 o.o 0.1 0 .1 0.1 0.0 0.1 0.0 -0.3- 00 0.0 00 -0.5 0.4 ..0.1 -0.3 -0.7 0.1 0.3 ..0.2 -0.7 0.3 ..0.4 .O.t 0.0 0.0 0.3 0.0 -0.4 ·1.4 -O.t 0.1 OA JII.BMia.hl2opt.lrYIW!b ...... .... .. l IM). ... - ..... ...... 552 o.o 0.0 0 .0 0..2 ..0.9 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-8. Exceedance table of average modeled monthly average temperature in the Stanislaus River at Orange Blossom Bridge for the PA scenario and COS scenario. Interpretation of year type differences from these tables is complicated by the fact that both PA and COS flows are summarized by the 60-20-20 year type, even though COS flows are modeled based on the NMI year type. (Source: ROC on LTO BA: Table 23-3 from Appendix D, Attachment 3-4) Table 23-3. Stanislaus River at Orange Blossom Bridge, Monthly Temperature Current Operltion.t 011319 61.6 59.3 "" ,.. "" .... ..."" "" .._....,.. , 57.5 568 564 53.4 52.6 s1.3 50.8 52.5 51.7 S5 8 55.1 560 52.2 515 50.1 496 51.2 507 54.6 540 54.9 StO 49 1 504 538 58.7 56.9 56.2 507 57.7 56.8 56.9 563 53J 52.7 560 544 63.7 62.4 61.6 606 59.3 65.5 64.6 64.1 637 632 62.6 62.1 65.4 64..2 63.4 62.9 62.5 62.2 64.5 63.3 62.0 617 61,2 50.5 50.1 48..3 47.9 49.6 49.2 52..1 51.0 52.2 53.6 55.9 55.3 61.9 54.9 54.0 54.1 53.7 607 60.4 527 49.7 471 48.4 496 50.8 52.6 54.4 58.6 61.5 59.8 58.1 57.2 56.3 5u 492 50.4 S3.2 53.2 561 59.0 629 62.7 50.5 s1.2 48.7 49.3 50.2 54.9 49.0 49.9 52.7 51.0 51.6 52.2 489 534 59.5 619 633 55.2 55.2 546 54 2 56.4 57.4 55.2 56.3 588 612 49.8 50.3 50.9 51.6 5U 52.4 52.9> 54 0 62.2 54 7 56.0 57.2 63.4 65.9 57.0 52.7 51.1 52.6 56.7 56.l 58.6 558 55.2 501 55.2 54.8 54.1 51.9 1 566 61.5 59.9 LOD!J Tfflll Wat« Year Typesb.C W.llll'l 56..7 558 54.8 63.3 61.9 60.0 6-5.4 64.1 63..5 64..7 63:.1 62.7 62.6 620 61.2 52.0 51.4 507 5o 540 53.4 5L8 59.3 58.7 56.2 54 7 632 62.8 61.9 609 62.1 619 61.6 60.4 60.8 602 60.0 583 53.2 53.3 SS.4 60.3 63.8 6)2 61.5 53.3 s.t.l S5.5 52.0 50.0 51.3 54.7 54.6 51.5 51.0 49..5 49.1 50.9 50.5 54.3 53.7 50.1 49.5 49.3 53.I 519 50 6 sa 50.5 50.6 504 50.0 532 484 47 9 U4 Lc.gltrlll 56.7 55.0 51.2 492 50.6 48.7 49.3 49.9 51.4 51.1 50.9 49.1 48.8 50.0 50.2 S2.9 53.5 51.91 52.8 ,c BllowMotrNij10"1f.) 01)11...) 56.7 55.6 54.8 54.4 54.7 59.7 59.7 58.0 59.3 59.4 63.2 63.4 62.6 62.3 61.5 60.9 &4.6 631.3 67.4 669 61.9 645 57.0 55.3 51.3 49.4 51.1 54..5 54.3 54.2 56.3 588 56.4 520 497 518 56.4 569> 585 62.6 650 .().1 0.1 0.1 0.3 1.0 0.9 1.5 2.4 1.8 .().1 0.8 0.5 1.3 0.7 2.2 1.9 1.3 0.4 1.4 1.2 (11.2 0.3 0.6 0.7 .0.1 0.1 - -0.2 -4.2 -4.2 -4.2 - --- r- r- r- (") ,..... Two Mile Knights Ferry Blossom -+-Valley Oak 0 C\J ,..... - C\J 0 0 C\.1 ....... (') ...- 0 0 C\J ....... (") r- (0 Leap Oakdale Rec. Figure 2.5.6-6. Average density of young-of-year 0. mykiss at eight sampling sites from February 2005 to July 2007. (Source: Figure 6 in Kennedy (2008)) 558 Biological Opinion for the Long-Term Operation of the CVP and SWP Steel head 1+ Density ... (/1 35 - 30 Q) Q) E ...ns 25 Q) ::J C" (/1 20 0 0 ..... 15 ... Q) a. ·c;; s::: Q) c 10 5 0 l{) l{) L{) 0 0 C\J 0 0 C\J 0 0 0 l{) l{) l{) 0 0 0 0 0 ?5 ,.... C\J ,..... -- - - - C\J C\J (") ,.... ?5 ,.... (") ,..... ?5 ,.... ?5 ,.... C\J "o:::t CD CO 0 ,..... ---....- Honolulu C\J <0 <0 <0 0 0 C\J CD 0 0 C\J (") ,.... (") ,.... (") ,..... ?5 ,.... C\J "o:::t CD co <0 C\J 0 0 C\J I'-0 0 C\J (") ,.... (") ,.... (") (;) 0 C\J ,..... C\J <0 I'-0 0 C\J I'-0 0 C\J ,..... (") ,.... "o:::t <0 -- -- -- - -- -- -- - -0 0 C\J 0 0 C\J 0 0 ..- Two Mile Knights Ferry -+-Orange Blossom --+- Valley Oak - ,..... Leap Oakdale Rec. Figure 2.5.6-7. Average density of yearling or older 0. mykiss at eight sampling. sites from February 2005 to July 2007. [Source: Figure 7 in Kennedy (2008)] There are no temperature control devices on any of the East Side Division facilities, so the only mechanism (aside from occasional flexibility to release from the gates at Tulloch Dam and the rare flexibility to use the low-level outlet at New Melones Dam) for temperature management is direct flow management. While it can take a lot of water to buffer temperature exceedances of long duration and large magnitude, less water would be required to buffer temperature exceedances of short duration and low magnitude. However, the PA does not commit to any temperature criteria for the Stanislaus River. As described above, CCV steelhead will be subjected to occasional sublethal and lethal temperature effects in the Stanislaus River from the egg through smolt stages and potentially as adults. Aceituno (1993) applied the instream flow incremental methodology to the Stanislaus River between Riverbank and Goodwin Dam (24 river miles) and determined that flows of200 cfs provided maximum WUA for steelhead spawning. The SRP flow schedules have minimum flows of at least 200 cfs from October through April in all water year types except Critical water 559 Biological Opinion for the Long-Term Operation of the CVP and SWP year types. The modeling results show that flows will not drop below 200 cfs, even in June through September of Critical water year types (Table 2.5.6-3), as a result of DO requirement. Because the existing dams prevent access to historical habitat, the proposed operations of the dams control the quality and quantity of available alternative habitat below Goodwin Dam and the suitability of the physical conditions to support CCV steelhead at various life history stages. Survival or growth of CCV steelhead may be affected by operations of the East Side Division in the foUowing ways: • Operational releases control extent of cool water habitat available below Goodwin Dam. • Operational release levels control the quantity and functionality of instream habitat for spawning, egg incubation, juvenile rearing and smoltification. • Operational releases are typically lower than flows under the natural hydrograph, requiring smelting juveniles to expend more energy to outmigrate and lower stream velocities increase the exposure of juveniles and smolts to predation. The proposed operation of the East Side Division modifies the hydrograph from the unimpaired flow pattern with which CCV steelhead evolved. Such modifications may affect survival, growth, and critical habitat for CCV steelhead in the following ways: • • • Peak flood flows are dampened, reducing floodplain and side-channel inundation and impairing rearing ability including production of food; Flow variability is muted, eliminating migratory cues that prompt migration and anadromy; Flow variabi1ity is muted, causing channel incision, reducing available rearing habitat, simplifying channel complexity and allowing land use encroachment into riverside habitats; and Channel forming flows are reduced or eliminated, resulting in fossilization of gravel bars and degradation of spawning habitat. 2.5.6.1.5.1 CCV Steelhead Response Now that the potential exposure of CCV steelhead to effects of seasonal operations and the SRP has been described, the next step is to assess how these fish are likely to respond to the PArelated stressors. Lite stage-specific responses to specific stressors related to the PA are summarized in and described briefly in this section. There may be other project stressors acting on Stanislaus River CCV steelhead than those identified in . However, this effects analysis intends to identify and describe the most important projectrelated stressors to these fish. 560 Biological Opinion for the Long-Term Operation of the CVP and SWP Dec-June Excessive fines in spawning gravel resulting from lack of overbank flow Excessive fmes in spawning gravel resulting from lack of overbank flow Stressor Egg mortality, Embryonic deformities Egg mortality from lack of interstitial flow; egg mortality from smothering by nestbuilding activities of other CCV steelhead or fall-run; suppressed growth rates Reduced suitable spawning habitat; For individual: increased energy cost to attempt to "clean" excess fine material from spawning site Response Reduced survival Reduced survival Reduced reproductive success Probable Fitness Reductiion Life Stage T iming Dec-Feb Dec-June Reduced growth rates; Reduced survival Reduced growth rates; Reduced survival Water temperatures warmer than life history stage requirements Year round Reduction in rearing habitat complexity due to reduction in channel forming flows Reduced growth rates; Reduced survival Year round End of summer water temperatures warmer than life history stage requirements Lack of overbank flow to inundate rearing habitat Year round, with temperature stress likely most acute JulySeptember Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Table 2.5.6-10. The temporal and spatial co-occurrence of CCV steelhead life stages and the stressors associated with the PA component of seasonal oper ations and the SRP. Life Stage/ Location Spawning Goodwin Dam to Orange Blossom Bridge Egg incubation and emergence Goodwin Dam to Orange Blossom Bridge Egg incubation and emergence Goodwin Dam to Orange Blossom Bridge Juvenile rearing Goodwin Dam to Orange Blossom Bridge Juvenile rearing Goodwin Dam to Orange Blossom Bridge Juvenile rearing Goodwin Dam to Orange Blossom Bridge 561 Life Stage Timing Jan-Jun Jan- Jun Stressor Response Suboptimal flow (March June) Water temperatures warmer than life history stage requirements (Mar- June) Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage/ Location Smoltification and emigration Stanislaus River at mouth Smolt emigration Stanislaus River Missing triggers to elect anadromous life history; failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of predation 562 Probable Fitness Reduced diversity. Reduced survival; Reduced diversity Biological Opinion for the Long-Term Operation of the CVP and SWP Water temperature can be a stressor in the Stanislaus River, particularly in summer months. The literature and scientific basis for life stage related temperature requirements for CCV steelhead are described in Table 2.5.6-1. A summary of those requirements relevant to CCV steelhead use of the Stanislaus River is presented in Table 2.5.6-11. Excelaent discussions of temperature suitability for salmonids in this region, and summary and evaluation of water temperature conditions at finer temporal scales are provided in SEP Group (2019) and Deas (2004). Information on maximum temperatures was not provided in the ROC on LTO BA; rather, the modeling results summarize monthly temperatures. So, this analysis evaluates modeled monthly temperatures at Orange Blossom Bridge under the PA (Table 2.5.6-8). The suitability of modeled temperatures under the PA for each CCV steelhead life stage is summarized below in Table 2.5.6-11. However, because the modeled monthly temperatures are lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to CCV steelhead on the Stanislaus River in the vicinity of Orange Blossom Bridge. Additionally, all the temperature model outputs are based on assumptions of daily flow equivalent to the monthly CalSimll inputs, so do not fully capture the flow (and associated temperature) variability expected during real-time operations. Table 2.5.6-11. Salmonid temperature requirements by life stage from Table 3 and Table 4 oftbe U.S. EPA's Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards (U.S. Environmental Protection Agency 2003). Temperature requirements are based on the 7-day average of the daily maximum temperature, or 7DADM. A rough evaluation of temperature suitability under the P A at Orange Blossom Bridge is provided based on monthly averages of daily average temperature; see caveats in the narrative. Life Stage & Timing Temperature Criterion Salmon/trout juvenile rearing (year-round) 61°F 7DADM Salmon/trout migration plus non-core juvenile rearmg (year-round) 64°F 7DADM Salmon/trout migration (OctoberMarch) 68°F 7DADM Rough evaluation of water temperature suitability at Orange Blossom Bridge based on monthly averages of daily average temperature rather than 7DADM Water temperatures are generally suitable (:S 61 °F) for juvenile rearing during October through May, but exceed 61 °F in the warmest 40 percent of years in June, 80 percent of years in July and August, and 50 percent of years in September. Water temperatures are generally suitable (:S 64°F) for migration and non-core juvenile rearing during October through May, but exceed 64°F in the warmest 20 percent of years in June, 40 percent of years in July, 30 percent of years in August, and 10 percent of years in September. Water temperatures are generally suitable (:S 68°F) for adult CCV steelhead migration into (and for kelt outmigration from) the Stanislaus River in all months. Water temperatures approach 68°F in July and August of the warmest 10 percent of years, but few, if any, 563 Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage & Timing Temperature Criterion Salmon/Trout Spawning, Egg Incubation, and Fry Emergence (December June) 55°F 7DADM21 Steelhead Smoltification (January- June) 57°F 7DADM Rough evaluation of water temperatur e suitability at Orange Blossom Bridge based on monthly averages of daily average temperature rather than 7DADM CCV steelhead are expected to be migrating in those months. Water temperatures are generally suitable (s 55°F) for spawning and incubation in December, January, and February. Water temperatures exceed 55°F in the warmest 20 percent of years in March and April , 40 percent of years in May, and 80 percent of years in June. CCV steelhead that spawn later in the season, or farther downstream will have reduced or even failed reproductive success, leading to reduced productivity and also reduce diversity in life-history timing by truncating the timing and area available for successful spawning. This life history stage is uniquely important for the expression ofanadromy in 0. mykiss. Water temperatures are generally suitable (s 57°F) for steelhead smoltification in January, February, March, and April. Water temperatures exceed 57°F in the warmest 20 percent of years in May and 70 percent of years in June. The proposed operations will truncate the successful smoltification of late developing smolts. Relative to temperatures at Orange Blossom Bridge (except during the winter when water may cool as it moves downstream), temperatures will generally be cooler at Goodwin Dam and warmer at the confluence to the San Joaquin River. Most spawning and core juvenile rearing occurs at or above Orange Blossom Bridge. CCV steelhead juveniles can likely avoid, to some degree, unsuitable rearing water temperatures at Orange Blossom Bridge by moving: farther upstream, but that does reflect a reduction of suitable rearing habitat and may result in increased competition for rearing habitat and food and reductions in growth or survival. Late-spawning CCV steelhead adults can likely avoid, to some degree, unsuitable spawning water temperatures at Orange Blossom Bridge by moving farther upstream. However, because conditions are generally suitable as far downstream as Orange Blossom Bridge from December to February, eggs spawned near Orange Blossom Bridge in those months may later experience unsuitable 21 Steelhead eggs incubating in the redds in the river may need colder temperatures than 55°F to have high survival. Martin et al. (2016) found strong evidence that significant thermal mortality occurred during the embryonic stage in Chinook salmon in some years due to a >5°F reduction in thermal tolerance in the field compared to laboratory studies due to differences in oxygen supply in lab and field contexts. This issue likely applies to what is known about the relationship between thermal tolerance and steelhead survival given that, like Chinook salmon, steelhead eggs incubate under the water column in spawning gravels. 564 Biological Opinion for the Long-Term Operation of the CVP and SWP water temperatures during egg incubation or as alevins that could lead to reductions in survival. CCV steelhead juveniles may be able to reach suitable smoltification temperatures in late spring upstream of Orange Blossom Bridge, but it is uncertain whether CCV steelhead juveniles rearing in the vicinity of Orange Blossom Bridge would seek cooler temperatures suitable for smoltification. Lindley et al. (2007) has identified the need for upstream habitat for salmonids, given predicted climate change in the next century. This may be particularly relevant for CCV steelhead on the Stanislaus River where Goodwin Dam blocks all access to historical spawning and rearing habitat and where the remaining population survives as a result of dam operations in downstream reaches that are historically (and occasionally even under the PA) unsuitable habitat because of high summertime temperatures. There are no temperature control devices on any of the East Side Division facilities, so the only mechanism (aside from occasional flexibility to release from the gates at Tulloch Dam and the rare flexibility-- during severe drought-- to use the low-level outlet at New Melones Dam) for temperature management is direct flow management. While it can take a lot of water to buffer temperature exceedances of long duration and large magnitude, less water would be required to buffer temperature exceedances of short duration and low magnitude. However, the PA does not commit to any temperature criteria for the Stanislaus River. As described above, CCV steelhead will be subjected to occasional sublethal and lethal temperature effects in the Stanislaus River from the egg through smolt stages and potentially as adults. As noted earlier, while Reclamation provided supplemental information on WUA for CCV steelhead fry and juveniles in various reaches of the Stanislaus River, those results are not evaluated in the Opinion due to time constraints. Additional information on rearing habitat as a function of Stanislaus River flow is provided in Bowen et al. (20 12). Past operations of the East Side Division have eliminated channel forming flows and geomorphic processes that maintain and enhance CCV steelhead spawning beds and juvenile rearing areas associated with floodplains and channel complexity (Kondolf et al. 2001). Since the operation of New Melones Dam, channel-forming flows above 8,000 cfs have been reduced to zero (as intended to avoid flooding), and mobilizing flows in the 5,000 to 8,000 cfs range occur very rarely. Channel-forming fl ows are important to rejuvenate spawning beds and floodplain rearing habitat and to recruit allochthonous nutrients and large wood into the river. Floodplain and side channel habitats provide important juvenile refugia and food resources for juvenile salmonid growth and rearing (Sommer et al. 200la, Sommer et al. 2005, Heady and Merz 2007, Jeffres et at. 2008). The SRP does not propose flows above 3,000 cfs, so flows of at least 5,000 cfs under the PA will only occur during flood control. Operations under the PA will result in continued degradation of spawning habitat and rearing habitat. Reduction and degradation of spawning gravels directly reduces the productivity of the species by reducing the amount of usable habitat area and causing direct egg mortality. Lower productivity leads to a reduction in abundance. Muting of winter storm flows and the spring/summer snowmelt in the seasonal hydrograph reduces the frequency and magnitude of flows that may cue anadromy, cue outmigration, and support more successful outrnigration by providing a "conveyance" flow that may increase 565 Biological Opinion for the Long-Term Operation of the CVP and SWP outmigration speed (or match an outmigration speed with lower energy expenditures) and survival. Zeug et al. (2014) documented a positive relationship between a survival index and flow for juvenile Chinook salmon on the Stanislaus River (Figure 2.5.6-8), based on data from rotary screw traps near Oakdale (RM 40) and Caswell (RM 8). However, a 3-year study using radio-tagged fall-run Chinook salmon on the Stanislaus River (Zeug et al. 2016) offered somewhat contrary results. The authors noted, "Flow did not have a significant effect on survival; however, because some fish exhibited holding behavior, the stationary detection models were biased toward actively migrating fish. The mobile detection models suggested that there was a greater probability offish transitioning out of the study reach when discharge was higher, which is supported by previous studies in this reach." The study years 2012 to 2014 had relatively dry hydrology and the variation in average flows tested ranged only from 12-77 ems (424-2,719 cfs), which does not include the highest flows required under the NMFS 2009 Opinion (short periods of 5,000 cfs in Wet water year types), and is slightly short of the highest flows required under the SRP (short periods of 3,000 cfs in Wet water year types). - 0.2 c -0.3 X R2 = 0.68 Ql "C • tU > -0.8 ·:;; Ill - 1.3 • QO 0 -1.8 0.0 2.0 4.0 6.0 8.0 10.0 Cumulative discharge x 108 m 3 Figure 2.5.6-8. Relationship between the juvenile Chinook salmon survival index and cumulative discharge in cubic meters per second (ems) for study years 2012-2014. Cumulative discharge was calculated as the sum of daily flow at the USGS gage near Ripon from January 17 to May 27. (Source: Top left panel of Figure 3 in Zeug et al. 2014.) 2.5.6.1.5.2 CCV Steelhead Risk Based on the effects to CCV steelhead associated with the P A component described above, fitness consequences to individuals include reduced reproductive success during spawning, reduced survival during embryo incubation, reduced survival and growth during juvenile rearing, and reduced survival and growth during smolt emigration (see ). Additionally, conditions may restrict the window of successful outrnigration of individuals and, thus, reduce the diversity of outmigration timing for the population. 566 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.1.6 CV Spring-run Chinook Salmon Exposure, Response, and Risk 2.5.6.1.6.1 CV Spring-run Chinook Salmon Exposure Temporal occurrence of any CV spring-run Chinook salmon that may be in the Stanislaus River is not well understood, though anecdotal information about observations of spring-running fish, adults holding over the summer, and early fry have been reported (Kennedy and Cannon 2002, Kennedy and Cannon 2005, Kennedy 2008). Based on adult and juvenile migration timing, egg incubation to fry emergence are assumed to occur from August through February and juvenile rearing from November through May for juveniles that emigrate as young-of-year; year-round for juveniles that emigrate as yearlings. The most likely windows of exposure for any CV springrun Chinook salmon that may be in the Stanislaus River and stressors are summarized in Table 2.5.6-12. NMFS expects any CV spring-run Chinook salmon life stages that may be in the Stanislaus River would experience similar exposure as CCV steelhead with the addition of oversummering adults being exposed to a greater degree to high water temperatures. 2.5.6.1.6.2 CV Spring-run Chinook Salmon Response Now that the potential exposure of any CV spring-run Chinook salmon that may be in the Stanislaus River to effects of seasonal operations and the SRP has been described, the next step is to assess how these fish are likely to respond to the PA-related stressors. Life stage-specific responses to specific stressors related to the PA are summarized in Table 2.5.6-12 and described briefly in this section. There may be other project stressors acting on any CV spring-run Chinook salmon that may be in the Stanislaus River than those identified in Table 2.5.6-12. However, this effects analysis intends to identify and describe the most important project-related stressors to these fish. Table 2.5.6-12. The temporal and spatial co-occurrence of CV spring-run Chinook salmon life stages that may be in the Stanislaus River· and the stressors associated with the PA component of seasonal operations and the SRP. Life Stage/ Location Spawning Goodwin Dam to Knights Ferry Spawning Goodwin Dam to Knights Ferry Life Stage Timing Stressor Response Aug-Oct Water temperatures warmer than life history stage requirements Egg mortality, Embryonic deformities Aug-Oct Excessive fmes in spawning gravel resulting from lack of overbank flow Reduced suitable spawning habitat; For individual: increased energy cost to attempt to "clean" excess fme material from spawning site 567 Probable Fitness Reduction Reduced reproductive success; Reduced survival Reduced reproductive success Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage/ Location Egg incubation and emergence Goodwin Dam to Knights Ferry Egg incubation and emergence Goodwin Dam to Knights Ferry Life Stage Timing Aug-Feb Aug-Feb Stressor Response Spawning habitat not likely limited during spawning, but fall-run may superimpose redds before springrun fry emergernce Reduced suitable spawning habitat Excessive fmes in spawning gravel resulting from lack of overbank flow Egg mortality from lack of interstitial flow; egg mortality from smothering by nest-building activities of CCV steelhead or fallrun; suppressed growth rates Egg mortality, Embryonic deformities Probable Fitness Reduction Reduced survival Reduced survival Egg incubation and emergence Goodwin Dam to Knights Ferry Aug-Feb Water temperatures warmer than life history stage requirements Juvenile reanng Goodwin Dam to Orange Blossom Bridge Nov-May forYOY; year-round for yearling Lack of overbank flow to inundate rearing habitat Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced growth rates; Reduced survival Juvenile rearing Goodwin Dam to Orange Blossom Br idge Nov-May forYOY; year-round for yearling Reduction in rearing habitat complexity due to reduction in channel forming flows Reduced food supply; suppressed growth rates; starvation; loss to predati·on; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced growth rates; Reduced survival Juvenile rearing Knights Ferry to Orange Blossom Bridge Nov-May forYOY; year-round for yearling June-September water temperatures warmer than life history stage requirements Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Reduced growth rates; Reduced survival 568 Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage/ Location Smolt emigration Stanislaus River Life Stage Timing Nov-May Stressor Response Probable Fitness Reduction Suboptimal flow (March - June) Failure to escape river before tempe ratures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of predation Reduced survival; Reduced diversity Many of the stressors affecting any CV spring-run Chinook salmon that may be in the Stanislaus River identified in Table 2.5.6-12 are similar to those discussed for CCV steelhead in and NMFS assumes that any CV spring-run Chinook salmon that may be in the Stanislaus River respond similarly as described for CCV steelhead unless described otherwise in this section. Water temperatures, however, are separately evaluated below since the expected spatial distribution of adults and timing of spawning through fry emergence is different for any CV spring-run Chinook salmon that may be in the Stanislaus River. Observations of adult Chinook salmon in the Stanislaus River during the summer are generally between Goodwin Dam and Knights Ferry, though adult Chinook salmon were observed as far downstream as Orange Blossom Bridge during snorkel surveys. During the summer and fall, when spawning and egg incubation for any CV spring-run Chinook salmon that may be in the Stanislaus River is expected, water temperatures are coolest near Goodwin Dam, intermediate near Knights Ferry, and warmest at Orange Blossom Bridge. Temperature data at Knights Ferry were not summarized in Appendix D of the ROC on LTO BA, but temperature data at that location were provided in raw modeling results. Therefore, the temperature evaluation is conducted a bit differently for CV spring-run Chinook salmon than in the evaluation for CCV steelhead to incorporate data from all three locations, which represent a range of potential effects experienced by any CV spring-run Chinook salmon that may be in the Stanislaus River, dependent on their in-river distribution. The modeling results presented below summarize monthly temperatures at Goodwin Dam, Knights Ferry, and Orange Blossom Bridge under the PA and COS, as reported in the raw modeling results provided with the ROC on L TO BA. The narrative summary focuses on the PA results. The summaries for Goodwin Dam and Orange Blossom Bridge are the same as those provided in Table 2.5.6-7 and Table 2.5.6-8. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to any CV spring-run Chinook salmon that may be in the Stanislaus River. Additionally, all the temperature model outputs are bas,ed on assumptions of daily flow equivalent to the monthly CalSimii inputs, so do not fully capture the flow (and associated temperature) variability expected during real-time operations. Suitable temperatures for each CV spring-run Chinook salmon life stage (with life-stage timing noted) are summarized in Table 2.5.6-13, and the evaluation of water temperatures under the PA 569 Biological Opinion for the Long-Term Operation of the CVP and SWP and COS are evaluated using these criteria at Goodwin Dam, Knights Ferry, and Orange Blossom Bridge for juvenile rearing (Table 2.5.6-14), migration plus non-core juvenile rearing (Table 2.5.6-15), migration (Table 2.5.6-16), and spawning, egg incubation, and fry emergence (Table 2.5 .6-17). Table 2.5.6-13. Salmonid temperature requirements by life stage from Table 3 and Table 4 ofthe U.S. EPA's Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards (U.S. Environmental Protection Agency 2003), along with life stage timing for any CV spring-run Chinook salmon that may be in the Stanislaus River. Temperature requirements are based on the 7-day average of the daily maximum temperature, or 7DADM. Life Stage & Timing Temperature Criterion Salmon/trout juvenile rearing (year-round, including yearlings) Salmon/trout migration plus non-core juvenile reanng (November- May for migration; year-round for rearing of yearlings) Salmon/trout migration (November- May) Salmon/Trout Spawning, Egg Incubation, and Fry Emergence (August- February) 61°F 7DADM 22 64°F 7DADM 68°F 7DADM 55°F 7DADM22 Steelhead eggs incubating in the redds in the river may even need colder temperatures than 55°F to have high survival. Martinet at. (20 16) found strong evidence that significant thermal mortality occurred during the embryonic stage in Chinook salmon in some years due to a >5°F reduction in thermal tolerance in the field compared to laboratory studies due to differences in oxygen supply in lab and field contexts. This issue likely applies to what is known about the relationship between thermal tolerance and steelhead survival given that, like Chinook salmon, steel.head eggs incubate under the water column in spawning gravels. 570 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-14. Evaluation of water temperature suitability under the PA (panel a) and COS (p.anel b) for juvenile core rearing of CV spring-run Chinook salmon (Temperature criterion = 61°F 7DADM). Data are modeled monthly water temperatures (not 7DADM), by San Joaquin "60-20-2(]1" year type, under the relevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to any CV spring-run Chinook salmon that may be in the Stanislaus River. Red shading indicates month/year type combinations in which monthly water temperatures exceed the temperature criterion. Juveniles may be rearing in the Stanislaus River year-round. a) PA scenario b) COS scenario 571 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-15. Evaluation of water temperature suitability under the PA (panel a) and COS (p.anel b) for migration and non-core juvenile rearing of CV spring-run Chinook salmon (Temperature criterion = 64°F 7DADM). Data are modeled monthly water temperatures (not 7DADM), by San Joaquin "60-20-20" year type, under the r elevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to any CV spring-run Chinook salmon that may be in the Stanislaus River. Red shading indicates month/year type combinations in which monthly water temperatures exceed the temperature criterion. The months of November through May are higltlighted in green to indicate that migration and non-core juvenile rearing are occurring in these months; juvenile rearing may occur year-round. a) PA scenario b) COS scenario 572 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-16. Evaluation of water temperature suitability under the PA (panel a) and COS (p.anel b) for adult immigration of CV spring-run Chinook salmon (Temperature criterion = 68°F 7DADM). Data are modeled monthly water temperatures (not 7DADM), by San Joaquin " 60-20-20" year type, under the relevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, t his analysis underestimates temperature-related impacts to any CV spr ing-run Chinook salmon that may be in the Stanislaus River. There are no month/year type combinations in which monthly water temperatures exceed the temperature criterion. Gray shading indicates month/year type combinations iin which the lifestage is not expected to be present in the Stanislaus River. a) PA scenario I OCT I NOV I DEC I JAN I FEB I:\1AR.I APR I I Wet 53.0 Above Normal 55.4 Below Normal 54.4 Dry 54.8 Critical 57.5 52.6 54.3 53.8 54. 1 56.4 50.7 5 1.6 51.3 51.4 52.8 52.8 54.3 53.8 54.1 56.3 50.6 51.3 51.1 51.1 52.5 53.6 54.8 54.4 54.7 56.6 50.6 51.1 50.9 50.9 52.1 I Wet 53.4 Above Normal Below Normal Dry Critical I 55.8 54.7 55.2 57.9 I Wet 54.5 Above Normal Below Normal Dry Critical 56.7 55.6 56.2 59.0 Good" ri:o Dam 47.9 49.1 50.0 48.2 49.7 50.6 49.0 50.3 51.7 48.8 50.7 51.7 49.8 51.5 52.7 Knights Ferry 48.0 48.2 49.3 50.4 48.6 48.7 50.6 51.0 48.7 49.4 51.3 52.0 48.5 49.3 51.7 52.4 49.6 50.3 52.6 53.6 Orange Blossom 48.7 49.3 49.9 51.4 49.1 50.0 52.9 51.9 49.1 50.5 53.8 52.9 48.9 50.8 54.3 54.1 49.8 5 1.8 55.3 55.9 47.9 48.5 48.7 48.5 49.7 573 y I JL"N I JUl.. I AGG I SEP 51.4 51.9 52.3 52.6 53.9 51.7 52.5 53.0 53.7 53.0 54.7 54.6 54.8 57.8 53.2 55.5 54.9 55.5 52.4 53.8 54. 1 54.5 56.7 52.0 52.6 52.9 53.7 55.3 52.6 54.7 55.1 56.6 58.7 54.8 56.9 57.3 57.6 60.3 55.1 57.3 57.1 60.8 54.7 57.4 56.8 57.0 60.2 53.3 54.1 54.3 56. 1 58.5 54.7 59.3 59.6 62.4 64.9 59.7 63.2 63.7 63.9 67.4 59.7 62.6 62.4 62.6 66.9 58.0 61.5 61.1 61.2 64.5 573 55.1 58.2 Biological Opinion for the Long-Term Operation of the CVP and SWP b) COS scenario I OCT INOV I DEC I JAN I FEB I:vrAR I APR I I Wet Above Normal Below Normal Dry Critical 52.9 55.2 54.9 55.6 59.6 52.4 54.2 54.8 57.5 50.6 51.7 51.5 51.7 53.1 53.3 55.6 55.1 55.9 59.9 52.6 54.5 54.2 54.8 57.3 50.5 51.4 51.2 51.4 52.7 5-t.3 56.6 56.0 56.8 60.7 53.4 54.9 54.7 55.3 57.4 51.2 51.0 51.2 52.4 54.5 I Wet Above Normal Below Normal Dry Critical I I Wet Above Normal Below Normal Dry Critical 50.5 Goodwin Dam 47.9 47.7 49.2 50.0 48.4 48.0 49.6 50.6 48.7 49.0 50.2 51.4 48.7 49.0 50.7 51.9 49.8 49.8 51.4 52.7 Knights Ferry 48.1 48.1 49.4 50.4 48.5 48.5 50.5 51.1 48.8 49.3 51.2 51.9 48.7 49.4 51.8 52.4 49.7 50.3 52.5 53.4 Orange Blossom 48.7 49.3 50.2 51.3 49.0 49.9 52 .7 52.4 49.2 50.5 53.7 53.0 49.1 50.7 54.3 53.8 49.8 51.6 55.2 55.2 574 y I JL"N I rur. I At;G I SEP 51.3 51.9 52.2 52.7 54.2 51.6 52.5 53.1 53.6 55.9 52.2 53.5 54.2 54.7 57A 52.8 54.5 54.9 55.3 58.3 53.0 51.9 52.7 52.8 53.4 55.1 52.7 53.7 54.8 56.2 58.3 54.6 56.3 57.3 57.7 60.1 54.9 57.0 57.3 57.7 60.6 54.5 57.0 57.2 57.6 61.1 53.2 54.6 54.4 55.2 57.3 55.2 56.3 58.6 61.3 63.3 59.5 61.9 63.5 63.9 65.8 59.4 62.2 62.6 62.9 65.6 57.8 61.1 61.3 61.6 64.7 55.2 55.3 55.8 59.7 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-17. Evaluation of water temperature suitability under the PA (panel a) and COS (p.anel b) for spawning, egg incubation, and fry emergence of CV spring-run Chinook salmon (Temperature criterion"" 55QF 7DADM). Data are modeled monthly water temperatures {not 7DADM), by San Joaquin " 60-20-20" year type, under the relevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this anaJysis underestimates temperature-related impacts to any CV spring-run Chinook salmon that may be in the Stanislaus River. Red shading indicates month/year type combinations in which monthly water temperatures exceed t he temperature criterion. Gray shading indicates month/year type combinations in which the lifestage is not expected to be present in the Stanislaus River. 575 Biological Opinion for the Long-Term Operation of the CVP and SWP 52.7 54.2 55.9 50.4 51.9 52.7 Under the PA, temperature conditions are: • Generally suitable for any CV spring-run Chinook salmon juvenile core rearing that may be occurring in the Stanislaus River except for June-September of most year types at the most downstream location, Orange Blossom Bridge. • Generally suitable for any adult CV spring-run Chinook salmon immigration that may be occurring in the Stanislaus River except (using the lower migration and non-core juvenile rearing criterion of 64°F 7DADM) for June-September of critical years at the most downstream location, Orange Blossom Bridge. • Generally not suitable for any CV spring-run Chinook salmon spawning that may be occurring in the Stanislaus River (in August to October) except in wet years or Novembers at Knights Ferry and Goodwin Dam. • Generally suitable for any CV spring-run Chinook salmon egg incubation and fry emergence that may be occurring in the Stanislaus River after October. Any CV spring-run Chinook salmon adults that may be in the Stanislaus River can likely avoid, to some degree, unsuitable water temperatures at Orange Blossom Bridge by moving farther upstream, but that does reflect a reduction of suitable spawning habitat. At a given location, the general seasonal trend in water temperatures means that water temperatures during egg incubation will likely be cooler than during spawning. Any juvenile CV spring-run Chinook salmon that may be in the Stanislaus River can likely avoid, to some degree, unsuitable rearing water temperatures at Orange Blossom Bridge or Knights Ferry by moving farther upstream, but that does reflect a reduction of suitable rearing habitat and may result in increased competition for rearing habitat and food and reductions in growth or survival. 576 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.1.6.3 CV Spring-run Chinook Salmon Risk Based on the effects to any CV spring-run Chinook salmon that may be in the Stanislaus River associated with the PA components described above, fitness consequences to individuals include reduced reproductive success during spawning, reduced survival during embryo incubation, reduced survival and growth during juvenile rearing, and reduced survival and growth during smolt emigration (see Table 2.5.6-12). Additionally, conditions may restrict the window of successful outmigration of individuals and, thus, reduce the diversity of outmigration timing. 2.5.6.2 Alteration of Stanislaus DO Requirement 2.5.6.2.1 Physical Description of the Alteration of Stanislaus DO Requirement Reclamation is required to meet DO standards on the lower Stanislaus River at Ripon for species protection as required by Reclamation's water rights in conjunction with the local basin plan. Reclamation currently operates to a 7.0 milligrams per liter (mg/L) DO requirement at Ripon year-round. Reclamation monitors and reports daily DO levels at Ripon, as required by the State Water Resources Control Board (D-1422, p. 32). Maintaining DO concentrations above 7.0 mg/L in the Stanislaus River at Ripon requires additional releases from New Melones Dam generally only during low flow, in the summer and early fall. Reclamation proposes to move the compliance location from Ripon to Orange Blossom Bridge, approximately 31 miles upstream, from June 1 to September 30. 2.5.6.2.2 Deconstruct the Action- Proposed Alternation of Stanislaus DO Requirement Changing the compliance point from Ripon to Orange Blossom Bridge from June 1 to September 30 would decrease DO at Ripon. Cramer Fish Sciences (2006a-d op. cit. ROC on LTO BA) indicated that DO concentrations at the Stanislaus River Weir (approximately 15 miles upstream from Ripon) can be 0.5 to 1 mg!L higher than those measured at Ripon. The DO is approximately 1.0 to 2.0 mg/L higher at Orange Blossom Bridge than at Ripon, so at this rate, if the DO standard of7.0 mg/L is moved to Orange Blossom Bridge, then the DO at Ripon (31 miles downstream) would be approximately 5.0 to 6.0 mg/L. 2.5.6.2.3 CCV Steelhead and CV Spring-Run Chinook Salmon Exposure, Response, and Risk 2.5.6.2.3.1 CCV Steelhead Exposure All current stocks of CCV steelhead have a winter run timing, although summer steelhead may have been present prior to the completion of major dams in the Sacramento River system (McEwan and Jackson 1996). The life history strategies of CCV steelhead are extremely variable between individuals, and it is important to take into account that CCV steelhead are iteroparous, and can spawn more than once in their lifetime. Therefore, timing of upstream and downstream migrating adult CCV steelhead (kelts) should be considered. San Joaquin River origin adult CCV steelhead peak in November through January in the Delta (CDFW California Department ofFish and Game 2007), and migrate up the San Joaquin River and its tributaries during a peak timing of November to January. There are limited data on the residence time and run timing of adult CCV steelhead of both Sacramento and San Joaquin River origin in the Delta. Data on the 577 Biological Opinion for the Long-Term Operation of the CVP and SWP frequency of occurrence and downstream run timing of CCV steelhead kelts throughout the Central Valley, and the Delta specifically, are very limited. Based on studies in the Stanislaus River from Oakdale to Goodwin Dam, CCV steelhead are primarily present upstream of Orange Blossom Bridge (Kennedy and Cannon 2002, Kennedy and Cannon 2005, Kennedy 2008) where temperatures and DO levels are suitable. During these snorkel surveys (in 2005, 2006, and 2007), young trout had the highest densities in September to October and April to July (Kennedy 2008). Therefore, juvenile steelhead may be present in the Stanislaus River when DO would be reduced to less than 7.0 mg/L. However, since juvenile steelhead are most abundant in the upper and middle reaches of the river, they are not expected to be present below Orange Blossom Bridge. Adult rainbow trout, including some that appeared to be steelhead, were observed sporadically in the river during summer surveys. All observations of adults were above Orange Blossom Bridge. Similar to juvenile, adult steelhead are not expected to be present below Orange Blossom Bridge during the warm summer months when DO would be less than 7.0 mg/L. 2.5.6.2.3.2 CV Spring-Run Chinook Salmon Exposure Although there is limited data on temporal occurrence of spring-run Chinook salmon in the Stanislaus River, observations of spring-running fish, adults holding over the summer, and early fry have been reported. Based on snorkel surveys (Kennedy and Cannon 2002, Kennedy and Cannon 2005, Kennedy 2008), Chinook salmon fry (which are likely primarily fall-run, but may be roughly representative of the distribution of occasional spring-run Chinook salmon fry that may be in the Stanislaus River) had a peak presence from January to March in the middle and lower reaches of the Stanislaus River study area, and juveniles were abundant in late winter and early summer throughout most of the river from Goodwin Dam downstream to Oakdale. Their distribution shifted downstream through the spring and their numbers declined sharply from mid-April to mid-June coincident with the Vernalis Adaptive Management Program (VAMP) experimental storage releases from New Melones Reservoir. The VAMP flows likely encouraged young salmon to leave the river and migrate to the Delta. All observations of adults were above Orange Blossom Bridge. Chinook salmon were most abundant near Goodwin Dam from July to October, where water temperatures remained around l2°C (54°F). Chinook salmon present in the Stanislaus River are mostly fall-run Chinook salmon, however, CV spring-run Chinook salmon are occasionally present. Since adults hold upstream over summer, they will not be affected by the change in DO requirement. Fry emerging in January to March are assumed to come from upstream spawning areas near Goodwin Dam. Any juvenile CV spring-run Chinook salmon that may be in the Stanislaus River may be exposed to the change in DO during early summer months as they are rearing or outmigrating. 2.5.6.2.3.3 CCV Steelhead and CV Spring-run Responses Since effects to CCV steelhead and any CV spring-run Chinook salmon that may be in the Stanislaus River are similar, discussion of responses are combined below. Adequate water quality, including temperature, salinity, DO concentrations, and other chemical characteristics necessary for normal behavior, growth, and viability of all salmonid life stages are 578 Biological Opinion for the Long-Term Operation of the CVP and SWP required for the proper functioning of salmonid species. Reduced levels of DO can impact growth and development of different steelhead and spring-run life stages. Such impacts can affect fitness and survival by altering embryo incubation periods, decreasing the size of fry, increasing the likelihood of predation, and decreasing feeding activity. Extremely low DO concentrations can be lethal to salmonids (California Regional Water Quality Control Board 2005). The upstream migration of adult salmonids requires swimming long distances and uses high expenditures of energy, which requires sufficient levels of DO. According to Hallock et al. ( 1970), migrating adult Chinook salmon in the San Joaquin River exhibited an avoidance response when DO was below 4.2 mg/L, and most Chinook salmon waited to migrate until DO levels were at least 5 mg/L. Salmonids may be able to survive when DO concentrations are low (<5 mg/L), but growth, food conversion efficiency, and swimming performance will be negatively affected (Bjornn and Reiser 1991 ). California Regional Water Quality Control Board (2005)referred to numerous studies and reported no impairment to rearing salmonids if DO concentrations averaged 9 mg/L, while DO levels of 6.5 mg/L result in symptoms of oxygen distress. Field and laboratory studies have found that juvenile salmonids consistently avoid DO concentrations of 5 mg/L and lower, and there is some indication that avoidance is triggered at concentrations as high as 6 mg/L. Changing the DO requirement location on the Stanislaus River from Ripon upstream to Orange Blossom Bridge would likely decrease DO downstream of the Orange Blossom Bridge by approximately 1 to 2 mg/L. This may result in juveniles avoiding the area during rearing or downstream migration. Adults would likely not be affected since they are not likely to avoid the area unless DO is below 4.2 mg/L, and adults are known to be present above Orange Blossom Bridge, where DO would be at least 7.0 mg/L. 2.5.6.2.3.4 Risk to CCV Steelhead Adult CCV steelhead may be present in the Stanislaus River during the summer months when DO may be lower at Ripon as a result of the PA, however, adult CCV steelhead have only been observed holding upstream of Orange Blossom Bridge, 31 miles upstream of the Ripon compliance point where DO is greater than 7.0 mg/L. Therefore, adult CCV steelhead are not expected to be exposed to the effects of altering the DO requirements at Ripon. Juvenile CCV steelhead may also be present in the Stanislaus River during the summer months while rearing or migrating downstream. Juvenile CCV steelhead observations during snorkel surveys were primarily upstream of Orange Blossom Bridge. Though a few juvenile CCV steelhead may be migrating past Ripon during the time the DO requirement is relaxed, the time of exposure to potentially lower levels (5 to 6 mg/L) of DO is expected to be short term. Juvenile salmonids are known to avoid migrating when DO is 5.0 mg/L or lower, and there may be oxygen distress from DO of6.5 mg/L or less (California Regional Water Quality Control Board 2005). Since most juvenile CCV steelhead will be upstream during summer months when DO is low, they would not be negatively affected by the PA component. However, the small number of juveniles migrating past Ripon during the summer months may avoid areas where DO is less than 5.0 mg/L, which would delay their outrnigration. Fish that pass through the area rather than avoid it would be exposed to short term oxygen distress. These responses would result in reduced fitness levels. 579 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.2.3.5 Risk to CV Spring-Run Chinook Salmon Adult Chinook salmon may be present in the Stanislaus River from March through September according to historical temporal occurrence (Table 2.5.7-12). All adult Chinook salmon snorkel survey observations were upstream of Orange Blossom Bridge. Some of these observed adults may be CV spring-run Chinook salmon. However, since any adult CV spring-run Chinook salmon that may be in the Stanislaus River are not expected to be present near Ripon during the summer months when DO would be lower than 7.0 mg/L (when flows are low and water temperatures are high), they would not be affected by the low DO as a result of the requirement at Ripon. Any juvenile CV spring-run Chinook salmon that may be present in the Stanislaus River could be present in the river year round while rearing, however they are likely to be migrating downstream in winter and spring, and into early summer months. Based on observations and seasonal timing, any juvenile CV spring-run Chinook salmon that may be in the Stanislaus River may be negatively affected by low DO as a result of the requirement at Ripon since a small proportion of late migrating juveni!les are expected to be passing Ripon during times when DO would be as low as 5.0 mg/L as a result of the PA. When DO is less than 5.0 mg/L, j uvenile salmonids are known to avoid the area, which would de1ay their outmigration and would affect fitness levels below Ripon. 2.5.6.3 Conservation Measures 2.5.6.3.1 Spawning and Rearing Habitat Restoration Reclamation proposes the following commitments to habitat restoration on the Stanislaus River: • Spawning Habitat: Under the CVPIA (b)(13) program, Reclamation's annual goal of gravel placement is approximately 4,500 tons in the Stanislaus River. • Rearing Habitat: Reclamation proposes to construct an additional 50 acres of rearing habitat adjacent to the Stanislaus River by 2030. A summary of restoration projects completed on the Stanislaus River since 2009 is provided in Table 2.5.6-18. 580 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.6-18. Summary of completed (since 2009) and potential habitat restoration projects on the Stanislaus River. Information from Table 2-3 of the WY 2018 Stanislaus Operations Group Annual Report (National Marine Fisheries Service 2018h). a) COMPLETED gravel augmentation projects (for spawning habitat at all locations; some gravel placed at the cable crossing in Goodwin Canyon intended for mobilization and downstream placement by river flows) COMPLETED Gravel Project Project extent Goodwin Canyon at cable crossing- 2011 Goodwin Canyon at float tube pool - 2012 2,941 cubic yards Goodwin Canyon at cable crossing- 2015 Main channel and floodplain bench at Honolulu Bar- 2012 Buttonbush- 2017 Rodden Road- 2018 4,706 cubic yards 8,000 cubic yards total used for spawning riffles in main channel and 0.7 acre floodplain bench 2,838 cubic yards 1,250 cubic yards b) 1,765 cubic yards COMPLETED floodplain and side-channel restoration projects (for improved rearing habitat, improved migratory habitat, improved connectivity to avoid stranding) COMPLETED Restoration Project Project extent Lancaster Road side-channel - 20U Side-channel at Honolulu Bar- 2012 Floodplain at Honolulu Bar- 2012 640 linear feet of side-channel and 2 acres of floodplain habitat Buttonbush - 2017 4.4 acres of side-channel and floodplain habitat and 2,400 linear feet of side-channel habitat. 4.9 acres of habitat Rodden Road- 2018 Improvement of existing side-channel to reduce stranding risk 2.4 acres c) Potential gravel and habitat restoration projects. POTENTIAL Project Two Mile Bar Project extent Anticipated gravel: 6,000 cubic yards. Anticipated habitat: TBD Kerr Park Restoration Anticipated gravel and habitat: TBD Migratory Corridor Rehabilitation Anticipated gravel and habitat: TBD Goodwin Canyon Anticipated gravel: TBD 581 Biological Opinion for the Long-Term Operation of the CVP and SWP In summary, in the 10-year period from 2009 through 2018, an average annual placement of 3,225 tons 23 was achieved, and a total of 13.8 acres and 3,040 linear feet of floodplain and side channel habitat was restored. Reclamation has been working to remove impediments to gravel augmentation in Goodwin Canyon (the easiest and least expensive option), however, restoration at the scale proposed will require partnerships with private landowners as well as funding, contracting, and permitting processes. Because it is not clear what assumptions Reclamation has made to conclude that restoration of 50 acres (over 3 times the restored acreage achi,eved in the past 10 years) is achievable by 2030, NMFS considers the full 50-acre target at a frameworklevel, with site-specific coverage within the limits identified below. In this consultation, NMFS assumes that: • • Reclamation can achieve, on average, 4,500 tons/year of gravel augmentation. If annual targets are not achieved in some years, NMFS assumes that Reclamation will make additional catch-up contributions in other years to meet the 4,500 tons/year average by 2030. Exemptions from take prohibitions are included under the Central Valley Restoration Programmatic Opinion, for any project that meets the guidelines; projects outside those guidelines need separate ESA consultation. Reclamation will restore up to 50 acres of rearing habitat by 2030. NMFS considers the effects of the full 50-acre target at a framework-level. Exemptions from take prohibitions are included under the Central Valley Restoration Programmatic Opinion, for any project that meets the guidelines; projects outside those guidelines need separate ESA consultation. 2.5.6.3.1.1 CCV Steelhead Exposure, Response, and Risk Habitat restoration activities would directly benefit CCV steelhead by increasing the quantity and quality of spawning habitat, creating side channel and floodplain rearing habitat, and increasing the quality and quantity of off-channel rearing habitat in the Stanislaus River. Habitat restoration activities within the Stanislaus River would yield benefits to CCV steelhead adults and juveniles by increasing existing riparian vegetation, providing instream and overhanging object cover, new shaded riverine habitat, and additional area for food production, and would also increase the aquatic habitat complexity and diversity within the Stanislaus River and provide additional predator escape cover. Additionally, the created side channel and floodplain habitat would provide additional refuge for outrnigrating juvenile CCV steelhead. These habitat benefits are expected to result in increased growth, fitness, and survival. Construction activities associated with spawning and rearing habitat restoration projects under this PA component are not expected to result in any direct effects to CCV steelhead adults, eggs or emerging fry, based on timing of in-water construction (July 15 through October 15 24), typical seasonal occurrence of these life stages in the Stanislaus River (December through June), and implementation of general avoidance and minimization measures. Construction activities associated with spawning and rearing habitat construction could result in minor, short-term, impacts to juvenile CCV steelhead (disruption to behavior, temporary displacement, increased 23 The total gravel volume from the projects listed in Table 2.5.6-1 8 is 21,500 cubic yards. Assuming a conversion of 1.5 tons/cy, the total is 32,250 tons over the I 0-year period which represents an annual placement rate of 3,225 tons per year. 24 While not specified in the P A, July 15 through October 15 is the window evaluated in the effects analysis of the ROC on LTO BA. 582 Biological Opinion for the Long-Term Operation of the CVP and SWP turbidity) for restoration projects upstream of Orange Blossom Bridge, since juvenHe CCV steelhead are present year-round in that area. Although not specified in the ROC on L TO BA, we assume standard avoidance and minimization measures typical for restoration work would be implemented, and therefore expect impacts limited to short-term behavioral changes not affecting fitness or survival. Habitat restoration would result in an overall benefit to the CCV steelhead. 2.5.6.3.1.2 CV Spring-run Chinook Salmon Exposure, Response, and Risk Habitat restoration activities would directly benefit any CV spring-run Chinook salmon that may be in the Stanislaus River, increasing the quantity and quality of spawning habitat for adults and eggs through fry emergence, and the quantity and quality of rearing and migratory habitat in the Stanislaus River for rearing and outmigratingjuveniles (see details in the discussion for CCV steelhead in Section 2.5 .6.3 .1.1 ). Any CV spring-run Chinook salmon adults and eggs that may be in the Stanislaus River would have tihe potential to be affected by construction activities associated with the restoration activities in the Stanislaus River given the proposed July 15 through October 15 in-water work window. Any CV spring-run Chinook salmon adults and eggs that may be in the Stanislaus River are most likely to be present during the work w indow in the coolest reaches of the Stanislaus River in or near Goodwin Canyon; projects located in warmer reaches may not overlap with any CV spring-run Chinook salmon adults that are present or spawning locations and implementation of avoidance and minimization measures will help to limit impacts. Construction activities associated with the restoration activities in the Stanislaus River are unlikely to affect any CV spring-run Chinook salmon fry that may be in the Stanislaus River (since that life stage is not expected during the in-water work window from July 15 through October 15) but restoration projects upstream of Orange Blossom Bridge could affect juveniles oversummering to outrnigrate as yearlings, resulting in minor, short-term, impacts (disruption to behavior, temporary displacement, increased turbidity). Effects can be minimized based on standard avoidance and minimization measures typical for restoration work. Habitat restoration would have an overall benefit to any CV spring-run Chinook salmon that may be in the Stanislaus River, resulting in increased growth, fitness, and survival. 2.5.6.3.2 Temperature Management Study Reclamation proposes that it "will study approaches to improving temperature for listed species on the lower Stanislaus River, to include evaluating the utility of conducting temperature measurements/profiles in New Melones Reservoir." NMFS supports this commitment and urges Reclamation to consider developing a simple temperature forecasting tool that could be used by the Stanislaus Watershed Team to screen alternate flow schedules when shaping seasonal flows. 2.5.6.3.2.1 CCV Steelhead Exposure, Response, and Risk The study itself will not affect CCV steelhead in the Stanislaus River. The study may improve management of temperatures and flows in the future, and help to inform decisions of the Stanislaus Watershed Team. 583 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.6.3.2.2 CV Spring-run Chinook Salmon Exposure, Response, and Risk The study itself will not affect any CV spring-run Chinook salmon that may be in the Stanislaus River. The study may improve management of temperatures and flows in the future, and help to inform decisions of the Stanislaus Watershed Team. 2.5.7 San Joaquin River (East Side Division) The analysis in this section, and references to "San Joaquin River", are limited in geographic extent to the San Joaquin River from the confluence with the Stanislaus River downstream past Vernalis to approximately Mossdale (as described in the Action Area section). While this reach of the San Joaquin River is in the statutory Delta, there are several reasons to consider it separately from the Delta effects section. First, conditions are primarity driven by upstream operations on CVP and non-CVP watersheds (including operations on the Stanislaus River) rather than Delta operations. Second, this reach of the San Joaquin River is primarily riverine, while further in the Delta the San Joaquin River is primarily tidal. The PA components being consulted on (Table 2.5.7-1) do not include any operational components that originate within this reach; conditions in the reach under the PA scenario ("PA conditions") are primarily affected by (1) San Joaquin River flow from upstream of the confluence with the Stanislaus Riv,e r (the boundary of the action area), (2) flow entering the San Joaquin River from the Stanislaus River as a results of East Side Division operations (described in detail in Section2.5.6), including assumptions made in the ROC on L TO BA about the flow requirement at Vernalis (a compliance location within this reach) per the Bay Delta Water Quality Control Plan that can affect East Side Division operations, and (3) accretions and depletions within the reach. NMFS evaluates the effects of East Side Division operations in this reach of the San Joaquin River, in combination with the baseline boundary flows, .accretions and depletions, under a project component named "PA conditions." The PA components being consulted on do include a conservation measure for Lower San Joaquin River Rearing Habitat. The analysis of effects to species in the San Joaquin River focuses on effects to particular life history stages of CCV steelhead, sDPS green sturgeon, and (for informational purposes) any CV spring-run Chinook salmon that may be present in this reach of the San Joaquin River. Note that in the CV spring-run Chinook salmon Integration and Synthesis Section (Section 2.8.3), NMFS discusses the San Joaquin experimental population and associated 4(d) rule with respect to findings under this Opinion. A summary of which stressors from the "Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley Spring-Run Chinook Salmon and the Distinct Population Segment of California Central Va11ey Steelhead" (National Marine Fisheries Service 20 14b) will be analyzed under each PA component within this effects analysis for the San Joaquin River is provided in Figure 2.5.6-1. 584 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-1. Summary of which stressors from the "Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-run Chinook Salmon and Central Valley Spring-Run Chinook Salmon and the Distinct Population Segment of California Central Valley Steelhead'' (NMFS 2014) will be analyzed under each PA component within this effects analysis for the San Joaquin River. An "X" indicates the stressor wiD be analyzed for at least one liife-stage and species and a "-" indicates that the stressor is not applicable for a particular PA component. Project Component 2.5.8.1 PA Conditions X X 2.5.8.2.1 Conservation Measures - Lower San Joaquin River Habitat X X X X X X X X X X X A summary of which stressors from the "Recovery Plan for the Southern Distinct Population Segment ofNorth American Green Sturgeon" (NMFS 2018) will be analyzed under each PA component within this effects analysis for the San Joaquin River is provided in TabJ,e 2.5.7-2. Table 2.5.7-2. Summary of which stressors from the "Recovery Plan for the Southern Distinct Population Segment of North American Green Sturgeon" (NMFS 2018) will be analyzed under each PA component within this effects analysis for the San Joaquin River. An "X" indicates the stressor will be analyzed for at least one life-stage and species and a "-" indicates that the stressor is not applicable for .a particular PA component. Project Component 2.5.8.1 PA Conditions X X X X X 585 X X X X Biological Opinion for the Long-Term Operation of the CVP and SWP Project Component 2.5.8.2.1 Conservation Measures - Lower X X X X X X X X X San Joaquin River Habitat 2.5.7.1 PA Conditions Effects of East Side Division operations in this reach of the San Joaquin River, in combination with the baseline boundary flows, accretions and depletions, are considered "PA conditions." See Section 2.5.6 for a detailed discussion of how East Side Division operations on the Stanislaus River affect the flows entering the San Joaquin River. Table 2.5.7-3 shows average monthly modeled flows at Vernalis in the PA and COS scenarios. 586 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-3. Exceedaoce table of average modeled monthly flow in the San Joaquin River at Vernalis for the PA scenario and COS scenario. Interpretation of year type differences from these tables is complicated by the fact that both PA and COS flows are summarized by the 60-20-20 year type, even though COS flows on the Stanislaus River are modeled based on the NMI year type. (Source: Table 39b-3 from Appendix D, Attachment 3-2, of the ROC on LTO BA.) Table 39b-3. San Joaquin River at Vernalis {60-20-20), Monthly Flow Current Operations 011319 NOY 10% 3,499 3,162 2.980 20% 2.795 2.602 2.401 2.247 1,995 1,849 Wilter Ye:tr Types Wet(23%) Aug 2,953 2.m 2.527 2,395 2.219 2,169 2.059 1,951 1,763 4,804 2.857 2 .401 2.216 2,101 2 ,046 1,979 1,829 1,669 11.236 4,812 3.611 2.629 2,402 2.293 2.114 1,883 1,699 5,079 14,G93 1M82 10,133 10,195 6.119 8.499 4,232 5,570 3,420 3,847 2,684 3,459 2.305 2.906 2,151 2,371 1,947 2.205 6,664 14,771 10,640 8.616 3.778 2.792 1,888 14,178 8.319 5.538 4,615 3,929 3,064 2.705 2_167 1,680 7,522 7,564 6,019 4,835 9.432 4,695 3.364 2,947 2.244 1,864 1,449 1,298 1,091 5. 8'il0 2. 634 1. 990 1, 741 1,493 1, 370 1, 163 1. 099 891 2.795 2,595 1.909 1,677 1,492 1,408 1,310 1,207 1,068 3.060 2,655 2.491 2,125 1,932 1,837 1,741 1,613 1.477 2,672 2,613 3,393 6,066 4,211 2. 630 1,850 2_225 3,611 2,947 2.518 2.289 1,864 4,025 2,582 2,133 2,153 1,849 6,134 11,463 2,953 4,898 2 .067 3.520 3,123 2.402 2,077 1,878 15,794 16,880 6,903 7,536 3,651 4,149 2,549 3.241 2,091 2.288 15,399 14,703 8,537 5.295 6.338 4,142 3.998 2.808 2.310 1,932 11,398 3.282 2,077 1,685 1,119 6. 693 1. 996 1,466 1, 200 932 3,136 1,979 1,448 1,351 1,064 3,417 2,347 1,838 1,778 1.489 3.500 3.146 2.996 2.628 2,975 2.778 2.483 2,395 2.219 4,804 2,904 2.321 2.204 2_101 12.398 4,838 3,613 2.681 2.371 11,192 15,482 10.122 10,324 6.806 8,470 4.232 5.306 3,071 3,847 15,015 10,641 8 .980 7.921 6 .437 15.004 8,327 5.767 4,655 4,131 9,433 4,781 2,704 2.370 2.069 5, 780 2. 503 1, 957 1. 730 1. 507 2,744 2.602 1,894 1.679 1.497 3,060 2.635 2.486 2.128 1.933 2,402 2,137 2,170 2,060 2 .046 1.979 2.290 2,084 2,910 2,305 1.866 1,473 1.757 1,351 1.217 978 1. 362 1. 153 994 874 1.407 1,319 1,136 1,029 1.830 1,743 1,575 1,452 5,982 4 ,102 2. 619 1,831 2.214 15,339 14,678 8 ,887 5,409 6.497 4.189 3.795 2.537 2.071 1.680 11,759 2,691 1,974 1,570 1.040 6,815 1.915 1, 473 1. 245 864 3,125 1,976 1,454 1,349 1.003 3,417 2,340 1,836 1,776 1.457 Ju Au; 7.282 $ AJ>ov.N'"""'(24%) S.l o w - (10%) Dry(1S%) Critical!n%1 Proposed Action 011619 Au; 1"" 20% 2.835 .._..... Full Simulation periocf' 2,614 2,305 3,440 2,906 1,978 1,951 1,829 1,883 2,128 2,372 1.807 1,763 1.669 1.699 1,891 2.205 4.786 3,212 2.500 1,765 2,669 2,607 3.368 5,109 6.792 7.290 7,513 3,607 2,994 2.542 2.239 1.829 4,001 2,579 2,133 2,153 1.849 6,006 11,466 2,954 4,928 2.067 3.784 3.132 2.393 2.077 1.871 Wilttr Yt:tr Typts.._e Wet(23%) ............ (24%) S..lowNonnal (10%) Dry(l&ov. N'"""'f24%) 47 23 Dry(1&'11) ·50 Criticalf27%) -36 0 ·23 ·56 245 826 39 <>577 0 344 357 419 202 ·175 -48 · 15-' · 107 0 -666 -400 ·301 ·208 ·113 0 ·123 1 &111 7 87 229 -660 -98 -131 -33 ·11 14 ·9 -10 ·61 ·105 -62 7 ·15 ·1 ·8 ·17 2 -38 ·25 -11 127 8 ·10 -64 -110 · 11 -20 171 -61 ·25 362 -11 19 -68 349 114 --.591 122 -60 183 •117 1S9 47 •lo;l 7 ·203 ·271 ·114 ·15 ·1 -15 -239 -253 ..ao -68 -61 ·128 11 31 0 0 264 ·9 -7 -33 ·85 ..... ... 587 -20 ·5 9 ·71 -39 550 -24 -3 0 0 ·100 128 -4 6 Biological Opinion for the Long-Term Operation of the CVP and SWP The largest reductions in flow in the PA relative to the COS occur in April to June, likely related to some combination of changes in the assumed Vernalis requirements and the SRP. In a Critical year, for example, the average 239 cfs decrease in April flows in the PA represents a 10 percent decrease from the average April COS flows of 2,310 cfs; the average 253 cfs decrease in May flows in the PA represents a 13 percent decrease from the average May COS flows of 1,932 cfs; the average 80 cfs decrease in June flows in the PA represents a 7 percent decrease from the average June COS flows of 1,119 cfs. Higher flows tend to result in cooler water temperatures at Vernalis. Water temperatures are also highly affected by air temperature (Figure 2.5.7-1). Higher flows and cooler temperatures typically extend into summer in wetter years. 80 90 92 en ...... 75 -- 919292 89 87 90 0 88 M e 9SI2 'I :1_7 >..... 70 ...-, 91 b 1 Q) 00 m65 ... ·-· I I II I I 1111 u I I Q) 11 111111 l1 1 60 -- a Q) 88 I, I -- - cd 88 7 77 Q) 87 1111 11111111 I I I Q) E-< 55 - - 50 ,1111111!1!:111111 524 751 1150 1600 1750 1890 2130 3290 3840 8640 1090031000 Streamflow (cfs) at Vernalis Figure 2.5.7-1. Range in daily water temperature relative to streamflow in the San Joaquin River at Vernalis from the period of May 13-17 in 1962, 1963, 1970, and 1973 to 1994. (Source: Figure 11 from Mesick (2001)) Monthly average water temperatures at Vernalis by month and San Joaquin ("60-20-20") year type are provided in Table 2.5.7-4 to show the range of temperatures expected under the PA and COS. 588 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-4. Monthly average water temperatures at Vernalis by month and San Joaquin ("60-20-20") year type for PA and COS scenarios. I OCT I NOV I DEC Wet Above Normal Below Normal Dry Critical Dry &.. Critical 62.4 63.1 62.1 63.4 65.3 64.7 55.6 56.1 56.9 56.6 49.1 Wet Above Normal Below Normal Dry Critical Dry &.. Critical 62.4 63.2 62.2 63.4 65.5 64.9 55.9 55A 55.7 56.1 56.9 56.1 48.9 48.6 48.7 49.3 49.1 55.9 55A 49.5 48.9 48.6 I I I APR JAN Y ern a lis water temperatures under PA 51.9 55.5 59.3 6U 52.7 56.9 59.3 65.4 53.2 58.5 60.1 53.8 58.5 63.7 68.1 48.6 5U 61.1 65A 69.9 48.5 54.5 60.3 69A Vernalis water tewperatnres under COS 52.0 55.6 59.3 48.7 52.7 56.9 59.6 65.7 53.1 58.4 60.3 64.2 48.4 53.8 58.5 63.0 66.8 48.6 54.8 61.1 64.6 68.7 48.5 54.5 60.3 64.1 68.1 I JUNI 68.0 73.3 73.3 75.3 75.5 JUL 12.0 75A 77.4 78.2 78.4 78.8 78.7 68.3 70.4 72.2 74.8 74.9 74.9 72.2 76.6 78.1 78.3 78.3 78.3 I AUG I 73.8 76.0 76A 76.5 77.6 77.3 SEP 70.4 72.4 72.8 73.1 73.7 73.6 73.8 70.4 75.8 72.3 76A 76.5 77.1 76.9 72.8 73.1 73.6 73.4 2.5.7.1.1 CCV Steelhead Exposure, Response, and Risk 2.5.7.1.1.1 CCV Steelhead Exposure Life history timing of CCV steelhead adults and juveniles in the mainstem San Joaquin River is described in Table 2.5.7-5. Additionally, CCV steelhead may exit the Stanislaus River during winter storm flows [similar to juvenile Chinook salmon as described in Sturrock et al. (2015)] and rear in the mainstem San Joaquin River from roughly December to May. Some CCV steelhead in the mainstem San Joaquin River may residualize and not exhibit the sea-going life history, but water temperatures in the mainstem San Joaquin River are unsuitable for juvenile CCV steelhead in the summer and fall, so juveniles would not be expected to be present in those seasons. Table 2.5.7-5. Temporal occurrence of (a) adult and (b) juvenile California Central Valley Relative Abundance Low (a) Adult migration Location Jan Feb Mar Sacramento River near Fremont W eir1 Sacramento R. at Red Bluf£2 Delta3•4 San Joaquin River4 (b) Juvenile migration Location Sacramento River near Fremont Weir1.2 Sacramento River at Knights Landing2•5 Chipps Island (clipped)6 Chipps Island (unclipped) 6 589 Apr May Jun Jul Dec Biological Opinion for the Long-Term Operation of the CVP and SWP Relative Abundance Low 6 San Joaquin R. at Mossdale Stanislaus R at CasweW Sources: 1(Hallock et al. 1957); 2(McEwan 2001); 3 (Hallock et al. 1961, Moyle 2002); 4(Califomia Department of Fish and Game 2007); 5NMFS analysis of 1998-2011 CDFW data; 6NMFS analysis of 1998-2018 USFWS data; 7 0 akdale RST data (collected by Fishbio) summarized by John Hannon (Reclamation) 2.5.7.1.1.2 CCV Steelhead Response Expected effects from the PA Conditions in the lower San Joaquin River will expose CCV steelhead to limited rearing habitats and potential migrational delays, leading to increased vulnerability to factors including poor water quality, which reduce survival, including predation. Life stage-specific responses to specific stressors related to the PA Conditions are summarized in Table 2.5.7-6. This effects analysis identifies and describes the most important proj ect-related stressors to these species. All project-related stressors acting on San Joaquin River CCV steelhead are identified in Table 2.5.7-6. Table 2.5.7-6. T he te mporal a nd spatial co-occurrence of CCV steelbead life sta ges a nd the stressors associated with PA Conditions in the San Joaquin River between the confluence of the Stanislaus River and Mossdale. Life Stage/ Location Life Sta ge Timing Stressor Response Probable Fitness Reduction Juvenile rearing Dec-May Lack of overbank flow to inundate rearing habitat Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced g rowth rates; Reduced survival Juvenile rearing Dec-May Reduction in rearing habitat complexity due to reduction in channel forming flows Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced growth rates; Reduced survival Juvenile reanng Dec-May Springtime water temperatures warmer than life history stage requirements, primarily MarchMay Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Reduced growth rates; Reduced survival 590 Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage/ Location Life Stage Timing Stressor Response Probable Fitness Reduction Juvenile outmigration Feb-Jun Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; Reduced survival; Reduced diversity in outmigration timing Juvenile outmigration Feb-Jun Water temperatures warmer than life history stage requirements, primarily in May and June Suboptimal flow Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of predation Reduced survival; Reduced diversity in outmigration timing Many ofthe flow-related stressors affecting CCV steelhead in this reach of the San Joaquin River identified in Table 2.5.7-6 above are similar to those discussed for CCV steelhead in the Stanislaus River in Section 2.5.6.1.5.1. Water temperatures, however, are separately evaluated below since water temperatures are higher on the San Joaquin River than the Stanislaus River. Suitable temperatures for each CCV steelhead life stage (with life-stage timing noted) are summarized in Table 2.5.7-7 and the evaluation ofmonthly average water temperatures at Vernalis under the PAusing these criteria is summarized in. Because the modeled monthly temperatures are lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to CCV steelhead on the San Joaquin River. 591 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-7. Salmonid temperature requirements by life stage from Table 3 and Table 4 of the U.S. EPA's Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards (U.S. Environmental Protection Agency 2003), along with CCV steelhead life stage timing in the San Joaquin River. 7DADM is 7-day average of the daily maximum temperature. Because the modeled monthly temperatures are lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to CCV steelhead on the San Joaquin River. Life Stage & Timing Temperature Criterion Salmon/trout juvenile rearing (December- May) Salmon/trout migration plus non-core juvenile rearing (Combined: year-round) Adult migration: July-March Juvenile migration: February-June Non-core juvenile rearing: December -May Salmon/trout migration (Combined: year-round) Adult migration: year-round Juvenile migration: February-June 61 °F 7DADM 592 64°F7DADM 68°F7DADM Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-8. Evaluation of water temperature suitability under the PA (panel a) and COS (panel b) for CCV steelhead for various lifestages. Data are modeled monthly water temperatures (not 7DADM), by San Joaquin "60-20-20" year type, under the relevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to CCV steelhead on the Stanislaus River. Red shading indicates month/year type combinations iin which monthly water temperatures exceed the temperature criterion. Gray shading indicates month/year type combinations in which the lifestage is not expected to be present in the San Joaquin River. a) PA scenario b) COS scenario 593 Biological Opinion for the Long-Term Operation of the CVP and SWP Water temperatures at Vernalis are mostly unsuitable for rearing in late spring, especially in drier years. Water temperatures at Vernalis are likely to be stressful to outmigrating CCV steelhead, or even serve as a barrier to migration, in May through September. According to Deas (2004), in April, May and particularly June, San Joaquin River water temperatures can reach stressful levels and may be limiting to young salmonids. 2.5.7.1.1.3 CCV Steelhead Risk Based on the effects to CCV steelhead associated with the PA Conditions described above, fitness consequences to individuals include reduced survival and growth during juvenile rearing, and reduced survival and growth during juvenile outmigration in the lower San Joaquin River (see Table 2.5.7-6). Additionally, conditions may restrict the window of successful outmigration of individuals and, thus, reduce the diversity of outmigration timing through the lower San Joaquin River for all the San Joaquin River steelhead populations. 2.5.7.1.2 CV Spring-run Chinook Salmon Exposure, Response, and Risk 2.5.7.1.2.1 CV Spring-run Chinook Salmon Exposure Any adult CV spring-run Chinook salmon that may be in this reach of the San Joaquin River may be affected by warm water temperatures, primarily in June to September, that have not reached tributaries before temperatures rise at lower river reaches. This will result in thermal stress and mortality of individuals .. Warm water temperatures in the springtime may also affect any juvenile CV spring-run Chinook salmon that may be in this reach of the San Joaquin River by causing metabolic stress, starvation, and loss to predation, resulting in reduced growth and survival. Juveniles may also be affected by decreased flow since this would reduce inundated rearing habitat, channel complexity, and may increase predation as they are less able to avoid them. Life history timing of any CV spring-run Chinook salmon adults and juveniles that may be in the mainstem San Joaquin River is described in Table 2.5.7-9, and stressors and responses are described in Table 2 .5.7-10. 594 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-9. Temporal occurrence of adult (a) and juvenile (b) CV spring-run Chinook salmon in the Central Valley, including the San Joaquin basin. Relative Abundance High Low (:1) Adult M igration Location Nov Dec Delta• San Joaquin Basin Sac. River Basinb,c Sac. River Mainstem<.d b) Adult Holdingb.c c) Adult Spaw1lingb.c.d (b) Juvenile M igratio n Location Jun Jul Aug Sep Oct Sac. River at RBDDd Sac. River at KLi San Joaquin basin De Sources: •(CDFW 1998); b(Yoshiyama et al. 2001); c(Moyle 2002); d(Myers et al. 1998); •(Lindley et al. 2004). r(CDFG 1998); &(McReynolds et al. 2007); h(Ward et al. 2003); ;(CDFW 1998-2019); j(USFWS 2000-20 19) Note: Yearling CV spring-run Chinook salmon rear in their natal streams through the first summer. Downstream emigration generaLly occurs the foLlowing fall and winter. Most young-of-year CV spring-run Chinook salmon emigrate during the first spring after they hatch. 2.5.7.1.2.2 CV Spring-run Chinook Salmon Response Expected effects from the PA Conditions will expose any CV spring-run Chinook salmon that may be in this reach of the San Joaquin River to limited rearing habitats and potential migrational delays, leading to increased vulnerability to factors such as poor water quality, which reduce survival, including predation. Life stage-specific responses to specific stressors related to the PA Conditions are summarized in Table 2.5.7-10. This effects analysis identifies and describes the most important project-related stressors to these species. All project stressors acting on any CV spring-run Chinook salmon that may be in this reach ofthe San Joaquin River are identified in Table 2.5.7-6. 595 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-10. The temporal a nd spatia l co-occurrence of any C V spring-run C hinook salmon life stages that may be present a nd the stressors associated with PA conditions in the Sa n J oaquin River between the confluence of" the Stanislaus River and Mossdale. Life Stage Life Stage Timing Stressor Response Probable Fitness R eduction Adult migration Mar-Sep Failure to enter tributary before temperatures rise at lower river reaches; thermal stress; mortality Reduced survival; reduced reproductive success; Reduced diversity in Lifehistory timing Juvenile rearing Dec-May Water temperatures warmer than life history stage requirements, primarily in JuneSeptember Lack of overbank flow to inundate rearing habitat Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced growth rates; Reduced survival Juvenile rearmg Dec-May Reduction in rearing habitat complexity due to reduction in channel forming flows Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced growth rates; Reduced survival Juvenile rearing Dec-May Springtime water temperatures warmer than life history stage requirements, primarily MarchMay Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Reduced growth rates; Reduced survival Juvenile outmigration Nov-May Water temperatures warmer t han life history stage requirements, primarily in May Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress Redluced survival; Reduced diversity in outmigration timing Juvenile outmigration Nov-May Suboptimal flow Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through D elta leading to increased residence time and higher risk of predation Redluced survival; Reduced diversity in outmigration timing Many of the flow-related stressors affecting any CV spring-run Chinook salmon that may be in this reach of the San Joaquin River identified in Table 2.5.7-6 are similar to those discussed for CCV steelhead in the Stanislaus River in Section 2.5.6.1.5. 1. Water temperatures, however, are separately evaluated below since water temperatures are higher on the San Joaquin River than the Stanislaus and need to be linked to CV spring-run Chinook salmon life-history timing. 596 Biological Opinion for the Long-Term Operation of the CVP and SWP Suitable temperatures for each CV spring-run Chinook salmon life stage (with life-stage timing noted) is summarized below in Table 2.5.7-11 and the evaluation of monthly average water temperatures at Vernalis under the PAusing these criteria is summarized in Table 2.5.7-12. Table 2.5.7-11. Salmon temperature requirements by life stage from Table 3 and Table 4 ofthe U.S. EPA's Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards (U.S. Environmental Protection Agency 2003), along with life-stage timing of any CV spring-run Chinook salmon in the San Joaquin River. 7DADM is 7-day average of the daily maximum temperature. Life Stage & Timing Temperature Criterion Salmon juvenile rearing (December- May) Salmon migration plus non-core juvenile rearing (Combined: November- September) Adult migration: March - September Juvenile migration: November - May Non-core juvenile rearing· December -May Salmon migration (Combined: November- September) Adult migration: March - September Juvenile mif!ration: November - May 61°F7DADM 597 64°F7DADM 68°F7DADM Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-12. Evaluation of water temperature suitability under the PA (panel a) and COS (p.anel b) for CV spring-run Chinook salmon for various lifestages. Data are modeled monthly water temperatures (not 7DADM), by San Joaquin "60-20-20" year type, under the relevant scenario. Because the modeled monthly temperatures, averaged by water year type, will be lower than the maximum daily temperatures most relevant for evaluating 7DADM criteria, this analysis underestimates temperature-related impacts to any CV spring-run Chinook salmon that may be in this reach of the San Joaquin River. Red shading indicates month/year type combinations in which monthly water temperatures exceed the temperature criterion. Gray shading indicates month/year type combinations iin which the lifestage is not expected to be present in the San Joaquin River. Water temperatures at Vernalis are most unsuitable for rearing in April and May, and unsuitable in March as well during drier years. Water temperatures at Vernalis are likely to be stressful to any outmigrating CV spring-run Chinook salmon that may be in this reach of the San Joaquin 598 Biological Opinion for the Long-Term Operation of the CVP and SWP River, or even serve as a barrier to migration, in May through September, and in April during drier years. 2.5.7. 1.2.3 CV Spring-run Chinook Salmon Risk Based on the effects to any CV spring-run Chinook salmon that may be in this reach of the San Joaquin River associated with the P A Conditions described above, fitness consequences to individuals include reduced survival and growth during juvenile rearing, and reduced survival and growth during juvenile outmigration (see Table 2.5.7-10). Additionally, conditions may restrict the window of successful outmigration of individuals and thus reduce the diversity of outmigration timing for any CV spring-run Chinook salmon in the San Joaquin River basin.. 2.5.7.1.3 sDPS Green Sturgeon Exposure, Response, and Risk Catch of sDPS green sturgeon in the San Joaquin River on Sturgeon Fishing Report Cards25 and the verified observation of an sDPS green sturgeon on the Stanislaus River (Anderson et al. 2018) indicate opportunistic use of the San Joaquin River basin when conditions are favorable. No spawning on the San Joaquin River has been verified. Life history timing of sDPS green sturgeon adults and juveniles in this reach of the San Joaquin River is described in Table 2.5.7-13 and Table 2.5.7-14. 25 Available at: http://www.dfg.ca.gov/delta/data/sturgeonlbibliography.asp 599 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-13. The temporal occurrence of (a) spawning adults (see row for "Sac-SJ-SF Estuary"), (b) larval, (c) young juvenile, (d) juvenile (see row for " Sac-SJ Delta, Suisun Bay"), and (e) sub-adult/non- spawning green sturgeon in California's Central Valley. (a) matm·e indhidu als. em TL 120 em TL males), including pre- and post- Jan Sac River (< rkm 332. Sac-SJ-SF Location SAC-SJ-SF Estuaty Pacific Coast Coas tal Bays & Estuaries 1 Relative Abundance: =High = Medium Sources: (a) Heublein et al. 2008; Klimley et al. 2015; Poytress etal. 2015; Mora et al. 2015; (b) Poytress etal. 20 15; Heublein et aL in review; (c) Heublein eta!. in review; B. Poytress unpublished; (d) Radtke 1966; CDFG 2002; Heublein et al. in review; B. Poytress unpublished; (e) Erickson and Hightower 2007; Moser and Lindley 2006; Lindley eta!. 2008; Lindley et aL 2011; Huff et aL 2011. Outside of Sac-SJ-SF estuary (e.g. Columbia River, Grays Harbor, Willapa Bay). 600 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.7-14. Summary of green sturgeon catch and length statistics from Sturgeon Fishing Report Cards for observations in the San Joaquin River from Stockton to the Highway 140 Bridge. Seasons were detined as follows: Winter"" December-February, Spring"" March-May, Summer"" June-August, Fall= September-November. R eport Card Year 2007 Number of .J\uglers Winter Catch Spring Catch Summer Catch Fall Catch I Total Catch Number l\Ie asured Minimum Length (inches) l\Ia1-imnm Length {inches) Avera ge Length (inches) - 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 TOTAL - - 2 - - 1 24 - - 1 - - - - - - - 1 6 18 - - - 0 2 - - 1 2 5 29 - - - - - 25 - - - - - - - - - - - - - - - - - - - - 8 1 7 0 1 9 13 4 10 - - - - - . - 2 16 - - - - 9 16 - - - 49.0 47.0 - - 66.0 62.0 - 58.1 54.3 - - 1 I Data sources: (California Department ofFish and Game 2008, Gleason et al. 2008, California Department ofF ish and Game 2009, 2010a, 2011 , 2012, California Department of Fish and W ildlife 20 13a, 2014a, 2015a, 2016a, 2017a, DuBois and Danos 2018) SDPS green sturgeon presence and behavior in the San Joaquin River is poorly understood and use of this reach of the San Joaquin River is likely opportunistic. Operations under the PA Conditions could lead to changes in the stressors identified in Table 2.5.7-2; mechanisms and probable change in fitness would generally be similar to those discussed in the Sacramento Division and Delta Division analyses for green sturgeon. 2.5.7.2 Conservation Measures 2.5.7.2.1 Lower San Joaquin River Habitat The ROC on LTO BA describes the "Lower SJR Rearing Habitat" conservation measure as "Reclamation may work with private landowners to create a bottom-up, locally driven regional partnership to define and implement a large-scale floodplain habitat restoration effort in the Lower San Joaquin River. ... Such a large scale effort along this corridor would require significant support from a variety of stakeholders, which could be facilitated through a regional partnership." NMFS supports both regional partnerships and multi-benefit floodplain habitat restoration projects in the San Joaquin basin and expects that such a project would provide benefits to CCV steelhead and any CV spring-run Chinook salmon that may be in this reach of 601 Biological Opinion for the Long-Term Operation of the CVP and SWP the San Joaquin River and could provide benefits to juvenile sDPS green sturgeon26• Acknowledging that the full scope of the effort is outside Reclamation and DWR's discretion and would require regional partners, in this Opinion, NMFS considers the benefits of this proposed conservation measure at the framework level. 2.5.8 Effects of the Action on Southern Resident Killer Whales The primary potential impact of the PA on SRKW that has been identified in the ROC on LTO BA (U.S. Bureau of Reclamation 2019) and in this Opinion is through potential reductions in availability of preferred prey, Chinook salmon, in the coastal waters where Chinook salmon from the Central Valley of California may be encountered by SRKW. The Quantity and Quality ofPrey portion of the Factors Affecting the Prey ofSRKW in the Action Area section (Section 2.4. 7.4) describes the evaluation by the Science Panel (Hilborn et al. 201 2) ofthe state ofthe science ofthe effects of salmon fisheries on SR.KW. While there is uncertainty in the extension of the statistical correlations to precise predictions of the effect of Chinook salmon abundance on the SRKW population, to date there are no data or alternative explanations that contradict fundamental principles of ecology that wildlife populations respond to prey availability in a manner generally consistent with the analyses that link Chinook salmon abundance and SRK.W. As a result, and based on evidence discussed in the Rangewide Status of the Species section (Section 2.2.9 and Appendix B) and the Factors Affecting the Prey ofSRKW in the Action Area section (Section 2.4.7.4), NMFS concludes that the best available science suggests that relative Chinook salmon abundance in the ocean throughout their range and any changes in prey availability resulting from natural and man-made factors are likely to influence the SRKW population. 2.5.8.1 Impacts to the Abundance of Chinook as a Result of the Proposed Action 2.5.8.1.1 Central Valley Chinook Salmon Abundance and Productivity 2.5.8.1.1.1 Escapement of Central Valley Chinook salmon In terms of productivity and abundance, the vast majority of CV Chinook salmon is comprised of non-ESA-listed fall-run Chinook salmon, and to a lesser degree non-ESA-listed late fall-run Chinook salmon and ESA-listed populations of CV spring-run Chinook salmon, and least of all ESA-1 isted winter-run Chinook salmon. This is reflected in estimates of annual spawning escapement for the Sacramento and San Joaquin rivers and their associated tributaries provided by CDFW; fall-run Chinook salmon escapement estimates are typically on the order of several hundred thousand adults, compared to tens of thousands each for late fall-run and CV spring-run Chinook salmon, and several thousand adults for winter-run Chinook salmon (CDFW 2018 GrandTab; Figure 2.5.8-1). Our approach to analyzing the effects of the P A on SRKW in this Opinion includes analysis of impacts to fall-run and late fall-run Chinook salmon, in addition to impacts to ESA-listed winter- 26 Green sturgeon presence and behavior in the San Joaquin River is poorly understood and floodplain rearing has not been documented. However, there are a number of benefits that floodplain habitat could provide j uvenile green sturgeon such as increased growth opportunity and refuge from predators. 602 Biological Opinion for the Long-Term Operation of t he CVP and SWP run and CV spring-run Chinook salmon in the Central Valley since individuals from all populations are potential prey for SRKW along the U.S. West Coast. (a) 1000000 Q) ..... ro E ..... ..... c 1/) 900000 Fall Run Chinook Salmon 800000 700000 UJ Q) E Q) c. ro u 600000 500000 UJ 300000 ro ..... 200000 1/) • Hat chery 400000 • In-River 100000 0 I I I I I I II I I I I I I I I II I I 1998200020022004 200620082010201220142016 Escapement Year (b) 45000 40000 Late-Fall Run Chinook Salmon 35000 Q) ..... ro 30000 E ·..... 25000 UJ ..... c 1/) Q) E Q) • Hatchery 20000 • In-River c. 15000 ro u 1/) UJ -ro ..... 10000 5000 II 0 • 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 Escapement Year 603 Biological Opinion for the Long-Term Operation of the CVP and SWP (c) 35000 <1) +-' 30000 Spring Run Chinook Salmon ro E tl w +-' c 25000 20000 <1) a. ro u Vl • Hatchery 15000 • In-River 10000 UJ 1998 2000 2002 2004 2006 2008 2010 201 2 2014 2016 Escapement Year (d) 20000 <1) +-' ro E 18000 16000 Vl 14000 +-' 12000 +-' w c <1) E <1) a. ro u Vl w ro +-' g Winter Run Chinook Salmon 10000 8000 • Total 6000 4000 2000 0 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 Escapement Year Figure 2.5.8-1. Total annual escapement of adult Chinook Salmon to river systems in the Central Valley from 1998-2017 for each run of Chinook salmon, distinguished by escapement totals back to natural production areas in-river and to hatchery areas, as appropriate. (a) Fall-run Chinook salmon; (b) Late fall-run Chinook salmon; (c) CV spring-run Chinook salmon; and (d) winter-run Chinook salmon. Source data: CDFW 2018 GrandTab 604 Biological Opinion for the Long-Term Operation of the CVP and SWP Over the last 20 years (1998-20 17), the total annual adult escapement of each Chinook salmon run in the Central Valley has varied considerably; especially the total annual escapement for the predominant fall-run Chinook salmon population which has ranged from just over 50,000 adults to almost 900,000 adults during that time period. Using analysis of variance (ANOVA) linear regression, trends indicate that the average total annual adult escapement has significantly declined over the last 20 years for fall-run Chinook salmon (F=8.54; a=0.009), late fall-run Chinook salmon (F=14.3; a.=0.001), and CV spring-run Chinook salmon (F=4.59; a.=0.046). The trend for winter-run Chinook salmon over this time is negative as well, but not significantly so (F=l.99; a.=O.l75). There are likely many factors that contribute to the trends in abundance and productivity of CV Chinook salmon, including variation in natural and human-caused mortality and other influences on the quantity and quality of available habitat, survival, and ultimate reproductive success throughout their life cycle in both the freshwater and marine environment (Michel2018). As described in Section 2.2 Rangewide Status ofthe Species, Appendix B, and Section 2.4 Environmental Baseline for ESA-Iisted Chinook salmon, these include significant influences such as harvest, hatchery production, and habitat alterations. Included among the major influences for all Chinook salmon in the Central Valley is the ongoing operation of water projects that are subj ect to consultation as part ofthis PA. 2.5.8.1.1.2 Hatchery Production The production and release of hatchery Chinook salmon of different run-types from various hatcheries represents a substantial proportion of overall Chinook salmon productivity in the Central Valley. Table 2.5.88-2.5.8-1 describes the general release goals for each Central Valley hatchery and run-type, as well as the average proportions of releases made directly in-river and releases transported directly into San Francisco Bay based on production and release activity 2007-2013 (Palmer-Zwahlen et al. 2019 and 2018, and Palmer-Zwahlen and Kormos 2015). The number of hatchery-produced fish released each year for all CV Chinook salmon runs combined during that time averaged 35,059,237; ranging from 30,455,664 to 38,510,728 (Appendix L). The proportion of hatchery fish released in-river and in the Bay varies from year to year based on water year conditions and other factors. 605 Biological Opinion for the Long-Term Operation of the CVP a nd SWP Table 2.5.88-2.5.8-1. Central Valley Chinook salmon hatchery release goals and proportion released in-river and in Bay areas. Hatchery annual Chinook releases Coleman fall Coleman late fall LSNFH Winte,r General Proportion Number inriver goal Proportion bay in-river 12,000,000 0 1 12,000,000 1,000,000 1 0 1,000,000 200,000 1 200,000 0 Feather Fall 6,000,000 0.7 0.3 1,800,000 Feather Spring 2,000,000 0.5 0.5 1,000,000 1 Feather enhancement 2,000,000 0 0 Nimbus 4,000,000 0.33 0.67 2,680,000 Mokelumne 5,000,000 0.7 0.3 1,500,000 Mokelumne enhancement 2,000,000 1 0 0 Merced 300,000 0 1 300,000 Total release 34,500,000 In-river release 20,480,000 Proportion released in-river 0.59 f Analysis of Chinook salmon otoliths in 1999 and 2002 found that the contribution of hatcheryproduced Chinook salmon made up approximately 90 percent of the ocean fishery offthe central California coast from Bodega Bay to Monterey Bay (Barnett-Johnson et al. 2007). More recently, estimates based on data from the 2012-2014 Central Valley coded wire tag recovery indicated the proportion of CV Chinook salmon in the ocean associated with hatchery proportion in was 70 percent (Palmer-Zwahlen et al. 2019, Palmer-Zwahlen et al. 2018, and PalmerZwahlen and Kormos 2015). The large influence of hatchery fish on the productivity of CV Chinook salmon likely results from numerous factors that may include decreased survival rates of natural production in the system, and increasing survival rates of hatchery production as hatchery release practices have been modified over time to improve survival of hatchery fish through the system (e.g., release of hatchery production directly into San Francisco Bay to avoid the Delta). Consequences of this increasing influence of hatchery production include increasing the number of returning adults that stray to non-natal watersheds, further diminishing the genetic integrity of those watersheds' natural population, which likely weakens the viability ofthe natural stocks to persist. 2.5.8.1.2 Effects of the Proposed Action on Chinook Salmon Individuals Detailed descriptions regarding the exposure and response of individuals from each of the ESAIisted Chinook salmon ESUs found in the action area and affected by the PA (winter-run Chinook salmon and CV spring-run Chinook salmon) to stressors associated with the PA are described in Section 2.5 Effects ofthe Action (and summarized in Section 2.8 Integration and Synthesis). Given that the potential effect of the PA on SRKW is mediated through reduced prey availability associated with effects to all Chinook salmon runs in the Central Valley affected by the PA, the effects analysis for SRKW needs to include analysis of effects to all Chinook salmon populations in the Central Valley that are affected by the PA, including non-listed populations. 606 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.8.1.2.1 Winter-run Chinook salmon As described elsewhere (by Division) in Section 2.5 and shown in Table 2.8.1-1 in the Integration and Synthesis section, FA-related stressors for winter-run Chinook salmon are expected to reduce the fitness of individuals during the adult, egg, fry, and juvenile life stages. While the entire suite of adverse and potentially beneficial effects associated with the PA are described in Section 2.5 and summarized in Table 2.8.1-1, focus in thiis section is placed on water temperature management, operations of the DCC gates, and Delta export operations, because among all the CVP/SWP operational components, these have the largest effects on winter-run Chinook salmon viability. While the modeling results suggest that the PA would protect winter-run Chinook salmon eggs better than under COS (see Table 2.5.2 3 for a comparison of the actual current operations to the COS and PA for major CVP action components), there is a high amount of uncertainty with that conclusion. For example, depending on how the fall Delta smelt habitat PA component is implemented, the modeled Shasta storage gains (which assume no augmentation of Delta outflow in the fall) that are primarily responsible for the improvements in egg-to-fry survival may not be realized under real-world implementation of the PA. Regardless of whether the PA improves egg survival relative to current operations, the PAis expected to result in concerning levels ofwinter-run Chinook salmon mortality. DCC gates could be open for up to 5 days for up to two events in December through January, but only if drought conditions are observed (i.e., fall inflow conditions are less than 90 percent of historic flows), and after Reclamation and DWR coordinates with USFWS, NMFS and the SWRCB on how to balance D-1641 water quality and ESA-listed fish requirements. If the gates are opened in December or January (expected in less than 1 in 10 years), a substantial proportion ofthe juvenile winter-run Chinook salmon cohort could enter the migratory routes through the Delta interior and be subject to a much lower rate of survival. Based on projected loss under the PA, thousands of winter-run Chinook salmon juveniles are expected to be lost at the south Delta export facilities under the PA in almost every water year type. Export operations modify hydrodynamics in the south Delta and may lead to far-field migratory impacts as well, particularly in the OM and Middle River corridors, which would negatively affect winter-run Chinook salmon in those corridors.. Reduced survival for juveniles from routing changes and increased transit time resulting from operation of the DCC is also listed as high magnitude stressor for winter-run Chinook salmon. 2.5.8.1.2.2 CV Spring-run Chinook salmon As described elsewhere (by Division) in section 2.5 and summarized in Table 2.8.2-2, PA-related stressors are expected to reduce the fitness of CV spring-run Chinook salmon individuals during all life stages. Therefore, each life stage will be harmed to some degree by the PA, with lethal impacts expected to eggs, fry, and juveniles. The most significant PA-related stressors to CV spring-run Chinook salmon are those that are related to water temperature management, operations of the DCC gates, and Delta export operations. Water temperatures unsuitable for lifestage requirements are expected to occur under the P A in the Sacramento River below Shasta Dam. Tiered temperature management based on a presumed critical period for winter-run Chinook salmon egg incubation could result in lethal effects to CV spring-run Chinook salmon eggs and fry, and sublethal effects to holding and spawning CV spring-run Chinook salmon adults. Under the PA, DCC gates may be operated in less than 1 in 10 years for water quality control management in December and January (see above discussion for winter-run Chinook 607 Biological Opinion for the Long-Term Operation of the CVP and SWP salmon). DCC gate opening results in increased routing of migrating Chinook salmon into the Delta interior through the open DCC gates, where survival is reduced. The more negative OMR flows predicted under the PA are a direct response to increased exports, particularly in April and May. This action potentially affects all life stages ofCV spring-run Clhinook salmon, and increases the risk of entrainment, particularly juveniles, into the export facilities, increasing the risk ofmortality to exposed fish (s·ee Table 2.8.1-3). Export operations modify hydrodynamics in the south Delta and may lead to far-field migratory impacts as well, particularly in the Old and Middle River corridors, which would negatively affect CV spring-run Chinook salmon in those corridors. 2.5.8.1.2.3 Fall-run and Late Fall-run Chinook salmon In general, all of the stressors that ·exist for CV spring-run and winter-run Chinook salmon also exist for CV fall-run and late fall-run Chinook salmon in the action area. We recognize there are differences how various Chinook salmon ESUs are exposed to the stressors based on variations in run timings, locations within the system where migrations and spawning may occur, and how/where the PA impacts the system in relation. In some cases, the exposure and response of fall-run and late fall-run Chinook salmon to certain stressors may be more or less given these variations, and in some cases the exposure and response is likely very similar. For example, increased exports under the PAin April and May coincide with the majority of fallrun and late fall-run Chinook salmon emigrating through the Delta region. The proposed increase in exports will increase the number offish from these populations entrained into the fish collection facilities as indicated by the substantial increases in loss predicted using the salvage density model. Increased exports under the PA operations will increase the number offish lost during the salvage process, as more fish are entrained from the surrounding Delta waterways. Export operations modify hydrodynamics in the south D elta and may lead to far-field migratory impacts as well, particularly in the Old and Middle River corridors, wlhich would negatively affect fall-run and late fall-run Chinook salmon in those corridors. Likewise, as in the COS, under the PA the DCC gates begin to be intermittently operated starting May 21, and generally fully open by mid-June, which would allow late emigrating fall-run Chinook salmon from the Sacramento River basin to be routed into the Delta interior, where their survival is predicted, based on previous studies, to be substantially lower. 2.5.8.1.3 Effects of the Proposed Action on Chinook Salmon Populations In this Opinion, we have not conducted identical analysis of each stressor on non-ESA-listed Chinook salmon populations throughout the action area. Given that the potential impact of the PA on SRKW is on the availability of all potential Chinook prey sources from the Central Valley, we will focus on the overall impact of the proposed action on Chinook productivity from the entire system and ultimate abundance of CV Chinook salmon in the ocean that may be available as prey for SRKW using available information that characterizes overall population levels effects of the proposed action. To do this, we consider the available quantitative and qualitative information that describes the underlying and ongoing effects of water operations on Chinook salmon populations under the proposed action. Where possible, we explore this Chinook salmon population level analysis quantitatively drawing upon available models of sources of mortality related to the proposed project in comparison to the COS to gauge how productivity is affected by the operational changes that have been proposed. Finally, where 608 Biological Opinion for the Long-Term Operation of the CVP and SWP necessary, we consider additional qualitative assessment of stressors tlhat cannot be captured directly through these models. 2.5.8. t .3. t Winter-run Chinook Salmon As described in section 2.5 and summarized in Table 2.8.1-1, habitat conditions in the Sacramento River and Delta are adversely affected by the PA in a number of ways, including but not limited to: (1) releasing warm water temperatures for eggs in all years, resulting in particularly high mortality in drier years; (2) decreasing flows during the juvenile rearing period, which increases the likelihood that juveniles using floodplain and side-channel habitats when flows are high will be isolated from the river when flows are decreased; and (3) routing more water and juvenile salmon into the Central and South Delta, and into the export facilities, which creates detrimental outmigration conditions and decreased survival by increasing the exposure of juveniles to predation and poor water quality. In these ways, the PA reduces habitat quantity and quality, which increases the risk of extinction of the winter-run Chinook salmon population, and consequently the ESU. As described in Section 2.5.9, results from the winter-run Chinook salmon life cycle model (WRLCM) support that expectation by indicating that while the WRLCM shows a very slight increase in CRR for the P A, the abundance for PA operations is on average less than for the COS. The effects of the operations of the PA would not increase abundance or productivity of winter-run Chinook salmon, but assumes that results would be similar to those of current operations. 2.5.8.1.3.2 CV Spring-run Chinook salmon As described in section 2.5 and Table 2.8.3-2, conditions in the Sacramento River and the Delta for CV spring-run Chinook salmon are negatively affected by the PA by delaying adult immigration through the DCC operations, affecting water temperatures that are stressful to CV spring-run Chinook salmon, entrainment of juveniles into the Central and South Delta and at fish salvage facilities. Spawning and egg incubation habitat for CV spring-run Chinook salmon in the mainstem Sacramento River is often adversely affected by operation of the CVP through warm water releases from Shasta Reservoir. The PA produces stressors to spawning, rearing, and migratory habitats in the mainstem Sacramento River. Those stressors include changes in water temperature management, exposure to warm water temperatures during egg incubation and juvenile rearing, increased exports, and loss of natural river function and morphology, affecting all habitat types and rearing habitat quantity and quality in particular. In these ways, the PA reduces habitat quantity and quality, which increases the risk of extinction of CV spring-run Chinook salmon populations, and consequently the ESU. Under the P A, DCC gates may be operated more frequently for water quality control management in December and January. When this operation occurs (expected in less than 1 in 10 years), listed fish may route into the interior Delta through the open DCC gates. During the months of potential DCC gate operation in December and January, approximately 5 percent of the current brood year's juvenile CV spring-run Chinook salmon population has migrated into the upper Delta region adjacent to the location of the DCC gates and may be subjected to routing into the Delta interior where survival is reduced compared to remaining in the Sacramento River migratory route. Reclamation also proposed to increase exports at the CVP and SWP during drier years from February through June and in all water year types in April and May in the original PA (Appendix Al ). Delta exports potentially affect all life stages and populations ofCV spring-run 609 Biological Opinion for the Long-Term Operation of the CVP and SWP Chinook salmon, and increasing exports increases the risk of entrainment (particularly juveniles) into the export facilities, increasing the risk of mortality to exposed fish (see Table 2.8.3-2). The salvage density modelling showed that the increased exports under the PA will lead to more loss at the CVP and SWP (loss is 4.33 times salvage, on average, at SWP, and 0.66 times salvage at the CVP). There are expectations for revised PA elements such as OMR management and performance objectives intend to limit impacts (i.e., salvage loss) under the PA to levels comparable to what would occur under the COS. However, as described in 2.5.8.2 Supplemental Analysis ofJune 14, 2019, there are some uncertainties in how new approaches will be implemented and uncertainties associated with effects. 2.5.8.1.3.3 Fall-run and Late fall-run Chinook Salmon In the NMFS 2009 Opinion, we analyzed freshwater mortality sources that included high water temperature and low flow upstream, and direct entrainment in the Delta, to evaluate an overall change in freshwater mortality for CV fall-run and late fall-run Chinook salmon attributed to project operations. Impacts from project operations that were not included in our assessment were mortality from fish stranding, redd dewatering and predation. In 2009, we determined that Project operations in the Central Valley reduced the total abundance of hatchery and natural CV fall- and late fall-run Chinook salmon available to SRKW compared to other basic operation scenarios by between 1.9 and 2.3 percent annually (average) over the project duration (range: 1.1 to -13.5 percent), although we identified interrelated and interdependent hatchery production that offset those overall losses at that time (National Marine Fisheries Service 2009b). Because natural-origin salmon are important to the long-term maintenance of salmon population distribution and diversity, both important factors for retaining population viability (McElhany et al. 2000) and buffering environmental variation (Lindley et al. 2009), we also quantified the prey reduction specific to natural-origin fall and late fall-run Chinook salmon in the SRKW analysis. We determined that project operations in the Central Valley reduced the abundance of naturalorigin fall and late fall-run Chinook salmon compared to a "maximum salmon production" scenario by between 9.8 and 10.7 percent annually (average) over the project duration (range:0.7 percent to -41.9 percent), depending in part on environmental variability (National Marine Fisheries Service 2009b). During consultation on this PA, there has not been an update to these analyses of overall impacts of water operations on the productivity ofnon-ESA listed CV Chinook salmon provided (see below for comparison of current operations following the NMFS 2009 Opinion and the PA). We recognize that the NMFS 2009 Opinion contained numerous RP A actions designed to avoid jeopardy to ESA-listed Chinook salmon species, as well as measures that were expected to benefit non-ESA-listed Chinook salmon species, and ultimately the prey base ofSRKW. At this time, it is unclear if there have been significant changes in the impact of water operations on the productivity and overall survival of CV fall-run and late fall-run Chinook salmon as a result of RPA implementation, changes in the status of these Chinook salmon populations, or other factors. Without any more specific information, we assume that water operations under the P A will continue to reduce the productivity of both ESA listed and non-listed Chinook salmon each year and have significantly higher impacts to natural origin fall- and late fall-run Chinook salmon that can be especially acute during some years when environmental stress on the Central Valley system is greatest. We also assume that other sources of mortality associated with water 610 Biological Opinion for the Long-Term Operation of the CVP and SWP project activities that remain unquantified further continue to exacerbate the reduction and limitation of productivity ofboth ESA listed and non-listed CV Chinook salmon. 2.5.8.1.4 Changes in Chinook Salmon Productivity under the PA compared to COS During this consultation, analyses of the relative change in Chinook salmon productivity for all CV Chinook salmon populations (ESA listed and non-listed) under the PA compared to current operations (COS) was provided. Ultimately, these results were used to assess the relative change in the number of adult Chinook salmon in the ocean available as prey for SRKW under the COS. The complete analyses are presented as SRKW Prey Appendix L to this Opinion; here we will summarize the analyses and key results. 2.5.8.1.4.1 Upstream Sacramento River The Salmod model (Bartholow 2003) was used to estimate effects to fall-run, late fall-run, and CV spring-run Chinook salmon in the Sacramento River upstream of Red Bluff. Factors in the model affecting survival include water temperature effects on each life stage present in the upper Sacramento River (adult through emigrating juveniles), flow versus spawning habitat area relative to adult spawner distribution, flow versus rearing habitat area relative to juvenile fish distribution, and the adult escapement input to the simulation. Redd dewatering is a factor not assessed in the Salmod model, and is a potentially significant stressor to fall-run Chinook salmon in particular. Results for Sacramento River fall-run Chinook salmon show a median change in production (outmigrants past Red Bluff) under the proposed action compared to COS of -0.34 percent (average is -1.19 percent) with a range of -30 percent to 17 percent change over the CalSirnll simulation period (82 years: 1920-2002). Salmod estimates that late fall-run Chinook salmon productivity would have a medium change under the PA compared to COS of -0.68 percent (average is -0.15 percent) with a range of -12.7 percent to 8.7 percent. The median change in productivity under the PA compared to COS for CV spring-run Chinook salmon is -1.08 percent (average is 3.1 percent increase) with a wide range in both the positive and negative directions (100 percent to 600 percent), acknowledging that CV spring-run Chinook salmon abundance/productivity in the upper Sacramento River is small and variations appear relatively large in comparison (Table 2.5.8-2; Appendix L). 611 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.8-2. Change in survival from COS to PA scenarios for each Central Valley (CV) Chinook salmon population, by area, and model source of estimate. The relative proportion of total CV escapement for each population is also provided. Negative values indicate a decrease; positive values indicate an increase. Note: for winter-run Chinook salmon the lOS model is applied for ocean abundance and incorporates freshwater survival factors. River and run Sacramento Rive r winter-run Sacramento River spring-run Sacramento River fat1-ru n Sacramento River late fall-run Clear Creek fall and spri ng-run American Riverfall-run Stanislaus Riverfall-run Feather River fall and spring-run Other Sac Runs (spring) Other Sac Runs (fall) San Joaquin Basin Mokelumne Proportion Upstream effects· Sal mod Delta effects· Delta ofCV juvenile production Passage Model Life cycle effects · lOS Abundance median 97.5%ite 2.5%ite median 97.5 %ite 2.5%ile median 97.5%ile 2.5 %ile O.D15 0.50073 · 0.4495 0.0141 · 0.0108 15L8044 · 99.787 ·0.0051 0.015145 · 0.014 0.0003 ·0.0034 0.0734 · 0.2004 · 0.0032 0.021709 · 0.017 0.0970 0.0807 ·0.0787 ·0.0023 0.008336 ·0.0715 0.0259 ·0.0068 ·0.0032 0.021709 ·0.017 0.0228 -0.0333 -0.0032 0.021709 -0.017 0.2233 ·0.1042 0.0099 0.0032 0.016971 ·0.0217 0.2397 ·0.0051 0.015145 · 0.014 0.0218 ·0.0032 0.021709 · 0.017 0.2915 not evaluated 0.0264 not evaluated 0.0284 Upstream effects· Egg !Mortality Model median 97.5 %ile 2.5%ite -0.0001 0.0037 00389 0.1542 2.5.8.1.4.2 Sacramento River Winter-run Chinook Salmon Effects ofthe PA on the relative productivity ofwinter-run Chinook salmon were quantified using the lOS model (Section 2.5.9). lOS is a lifecycle model that provided an estimate of the change in life stage survival and ultimate ocean abundance and escapement throughout the CaiSimii simulation period. In the upper Sacramento River the model integrates the effects of temperature, flow, fish abundance, and habitat availability to arrive at production of juvenile winter Chinook salmon emigrating down the Sacramento River, through the Delta, and to the ocean. Ocean survival factors are included through the range of years in the ocean until the fish come back and spawn. lOS differs from the Salmod model in that it includes the entire lifecycle with each generation seeding fish to the next. The change in abundance from the beginning to the end of the simulation period from a starting abundance of 5,000 escapement used to seed the model in the first four years showed a 92 percent increase in ocean abundance (age 3 and 4) for COS and a 125 percent increase for PA. The difference in median ocean abundance between the two scenarios was a 1.5 percent increase in abundance in PA compared to COS (Table 2.5.8-2; Appendix L). In contrast, the Winter-run Life Cycle Model (WRCLM) developed by NMFS, estimated a decrease in abundance (-3.05 percent) between the PA and COS, with a 95 percent confidence interval of -8.07 to 0.137 percent change in productivity. There was less than a 0.03 percent chance that the PA average abundance was greater than the average abundance in the COS. Typically the WRLCM predicted lower smolt survival based on habitat origin, except for wet water year conditions, where greater survival of smolts utilizing the Yolo Bypass during the January through March period enhanced overall survival under the PA compared to the COS. 2.5.8.1.4.3 American River The Salmort egg survival model (DWR and Reclamation 20 16) was used to estimate the change in fall-run Chinook salmon survival from the American River from changes in early lifestage survival attributable to water temperature. This model uses the water temperature model outputs along with Chinook salmon spawning distribution and abundance to estimate water temperature 612 Biological Opinion for the Long-Term Operation of the CVP and SWP effects to pre-spawned eggs, incubating eggs, and alevins. Survival is decreased slightly (median value of -0.012 percent) under the PA compared to COS. During most years in current and future scenarios the effect of high water temperature on egg survival is significant, ranging: from around 15 percent - 35 percent mortality due to water temperature (Table 2.5.8-2; Appendix L). 2.5.8.1.4.4 Stanislaus River The Salmort egg mortality model was used to estimate water temperature related mortality of early life stages of fall-run Chinook salmon in the Stanislaus. Mortality is typically decreased under the PA compared to COS in a majority of years, but in about 10 percent of years mortality is estimated to be higher under the PA (Table 2.5.8-2; Appendix L). Water temperatures during spawning are reduced on average and New Melones storage is maintained at a higher level in PA, although egg survival is probably not the most limiting factor in t!he Stanislaus (Appendix L). 2.5.8.1.4.5 Clear Creek There were no appreciable differences in water temperature in Clear Creek or release from Whiskeytown Dam into Clear Creek to compare between the PA and COS; therefore, no modeling of change in fall-run or CV spring-run Chinook salmon survival in Clear Creek was conducted. 2.5.8.1.4.6 Overall Central Valley Upstream Productivity In order to calculate the overall change in upstream survival and productivity for all CV Chinook salmon under the PA compared to COS, the change in upstream survival for each Chinook salmon population described above (with the exception of winter-run Chinook salmon life cycle model results) was scaled by the relative proportion of CV Chinook salmon productivity represented by each population through escapement totals in Grand Tab (Appendix L; CDFW 20 18). The median aggregate change in survival from upstream areas was a slight reduction (0.05 percent) for PA compared to COS, and a 97.5 percentile to 2.5 percentile range from an increase of over 6 percent to a decrease of 6 percent. This value represents expected change in upstream survival and productivity for natural production from all upstream areas that were modeled, in total. 2.5.8.1.4.7 Delta Survival The Delta Passage Model (Cavallo et al. 2011) was used to estimate survival of fall-run, late fallrun, and CV spring-run Chinook salmon from the Sacramento River side emigrating through the Delta. This model uses results from acoustic tagged salmon survival studies along with relationships between flow and routing through delta channels and survival rate to estimate through-Delta smolt survival. Results for fall-run and CV spring-run Chinook salmon indicate that both populations will experience slight reductions in productivity as a result of reduced through-Delta survival under the PA compared to COS; -0.3% and -0.5% change in median surviva1 rates, respectively (Table 2.5.8-2; Appendix L). Late fall-run Chinook salmon show more years with reduced throughDelta survival than increased survival and a median reduction of0.2 percent under the PA compared to COS (Appendix L). Since the Delta Passage Model does not incorporate data from 613 Biological Opinion for the Long-Term Operation of the CVP and SWP the San Joaquin River basin into its development, no Delta survival ch.anges were modeled for Chinook from the San Joaquin or Mokelumne rivers. A total reduction in CV Chinook salmon productivity as a result of reduced through-Delta survival under the PA compared to the COS was calculated in a similar manner as the upstream aggregated upstream productivity by weighting each CV Chinook salmon population by their relative proportions of overall escapement. The overall median change in delta survival under the PA compared to COS was -0.0014 with 2.5 percentile to 97.5 percentile values ranging from0.0 I 81 to 0.0184, so the range is less than a 2 percent change in the positive or negative directions (Appendix L). 2.5.8.1.4.8 Hatchery Production and Survival to San Francisco Bay Hatchery-produced Chinook salmon releases are included in the analysis by using the average release of hatchery juveniles for 2007-2013 for all CV Chinook salmon runs combined (average total of35,059,237; Table 2.5.8-1), and the average in river release proportion (0.59; Table 2.5.8-1). In-river mortality was applied to the in-river released hatchery fish using a static river survival value for survival from release to the delta of 0.5 that comes from acoustic telemetry survival studies using late fall-run Chinook salmon (National Marine Fisheries Service 20 I 9d). The Delta Passage Model was used to estimate Delta survival for the COS and PA scenarios for all hatchery produced Chinook salmon that travel through the Delta (Appendix L). The resulting median change in survival for hatchery produced Chinook salmon released in-river to San Francisco Bay under the P A is 0.003, which leads to a median change of -1.5 percent in the number of juveniles that survive to San Francisco Bay (Appendix L). Finally, the in-river released hatchery Chinook salmon surviving through the Delta were added to the number of hatchery fish released directly into San Francisco Bay to calculate the total number of hatchery Chinook salmon that make it into San Francisco Bay (Appendix L). The resulting median change in productivity for all Central Valley hatchery production into San Francisco Bay under the PA is that 0.2% less hatchery produced juveniles survive to San Francisco Bay under the PA compared to COS (Appendix L). 2.5.8.1.4.9 Combined Upstream and Delta Survival to San Franc:isco Bay for Natural Production Aggregate freshwater survival change under the PA compared to COS is based on the upstream change in survival multiplied by change in Delta survival under the PA, resulting in an overall median PA value of 0.999 of the COS value with the 2.5 percentile to 97.5 percentile values of 0.982 to 1.018 (Appendix L). 2.5.8.1.4.10 Linking Hatchery and Natural Production in San Francisco Bay to Ocean Abundance Tn order to relate the comparative i1mpact ofthe PA to COS in terms of the overall ocean abundance of CV Chinook salmon, we first examined the relative contribution of hatchery production (released in-river and directly into San Francisco Bay as described above) and natural production to recent ocean abundances of CV Chinook salmon, in order ultimately relate the relative impact of the PA compared to COS to each component as described above. The hatchery and natural proportions ofCV Chinook salmon were estimated based on data from the 2012614 Biological Opinion for the Long-Term Operation of the CVP and SWP 2014 Central Valley coded wire tag recovery reports (Palmer-Zwahlen et al. 2019, PalmerZwahlen et al. 2018, and Palmer-Zwahlen and Kormos 2015). Over these years, the proportion of fish recovered that were of hatchery origin averaged 0.70 (range 0.65- 0.75). Using: the median ocean abundance of CV Chinook salmon for the period 2001 - 2018 of 454,052 (age 3+), along with the assumed hatchery proportion of0.7, and the median number of hatchery-produced Chinook salmon that survive and/or are released into San Francisco Bay under COS ( 16,831,019), the estimated survival rate of juvenile Chinook salmon smolts in San Francisco Bay to the adult stage in the ocean (age 3+) is 0.0189 (Table 2.5.8-3; Appendix L). In addition, using this same information we can estimate that contribution of naturally produced CV Chinook salmon in San Francisco Bay would have been 7,213,294 juvenile smolts. From this point, it is possible to combine the combined upstream and delta survival effects under the PA compared to COS for all hatchery and naturally produced CV Chinook salmon and project these results in terms of changes in the adult (age 3+) ocean abundance of CV Chinook salmon under the PA compared to COS, including results from winter-run Chinook salmon lOS model runs. Using estimates of ocean abundance from 2001-2018, the percent change in abundance is a 0.21 percent decrease adult Chinook salmon) at the median value, and a 2.21 percent ( 700 adults) decrease at the 2.5 percentiile and 2.43 percent increase ( 12,600 adults) at the 97.5 percentile (Table 2.5.8-3; Appendix L). 615 Biological Opinion for the Long-Term Operation of t he CVP and SWP Table 2.5.8-3. Abundance of Central Valley Chinook salmon available as prey for Southern Resident killer whales under the COS and PA scenarios and change in abundance between scenarios. Natural Chinook smolts in Bay baseline (COS) median 97.5 %ile 7,213,294 7,345,971 Natural Chinook smolts in Bay in PA 7,199,260 2.5 %ile 7,212,754 7,829,734 6,654,245 Hatchery juvenile Chi nook total in Bay COS 16,831,019 19, 710,070 16,082,252 Hatchery juve nile Chi nook total in Bay PA Total juvenile Chinook in Bay (COS) 16,792,102 19,647,691 24,044,313 27,056,041 16,135,970 23,295,006 Total juvenile Chinook in Bay (PA) Bay to ocean adult survival 23,991,362 27,477,426 0.0189 0.0189 22,790,215 0.0189 Ocean Adult Chinook Abundance (COS), not including wint er-run Ocean Adult Chi nook Abundance ( PA), not includi ng wi nter-run Adjustment for w inte r-run f rom lOS model 454,052 453,052 510,925 518,882 Winter-run Chinook COS {lOS model )* 3,293 9,345 Winter-run Chinook COS t o PA (proportional lOS model changes) Winter-run Chinook PA {lOS model changes) 0.015 3,342 0.501 14,024 457,345 456,393 520,270 532,907 440,347 430,615 -951 12,637 -9,733 -0.21% 2.43% -2.21% Ocean Adult Chinook Abundance (COS) Ocean Adult Chinook Abundance (PA) 439,902 430,369 446 -0.450 245 Change in median number of Adult Chinook in the Ocean COS to PA Percent abundance change in adult Chinook in the Ocean from COS to PA Change in Chinook Biomass (pounds) COS to PA** -16,067 213,435 -164,386 *The median wi nter-run Chinook ocean abundance for 2001-2018 was used as the baseline in COS and proportional changes over the lOS modeling period are applied to that value **median adult weight of 16.89 pounds 2.5.8.1.4.11 Limitat ion of Model Estimates of Productivity Changes under PA Compared to cos The models used to construct the estimated changes in the overall productivity of CV Chinook salmon described above are limited to evaluating the impacts that are quantifiable within those models. As described above in Section 2.5.8.1.2 Effects of the Proposed Action on Chinook Salmon Individuals, there are numerous other stressors on various segments of Chinook salmon populations as a result of the PA that are not quantified or accounted for in these models. Table 2.5.8-4 lists the models used above in estimating changes in survival and productivity for CV Chinook salmon populations under the PA compared to COS. 616 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.5.8-4. List of models used to estimate changes in Central Valley Chinook salmon productivity under the P A compared to COS. Model or Analytical Method DPM CalSim II lOS X Salmod SacSalMort/ Reclamation Egg Mortality Model Winter-Run Life Cyde Model Salvage Density Model X X X X X X X X X X X X X X X X X X X X X X X X X X X X Although not included in the Salmod model, flow modeling shows that flows will drop in September prior to fall-run Chinook salmon spawning, and general the extent of potential dewatering that might occur for fall-run Chinook salmon in the Sacramento River will be reduced in the proposed action compared to current operations (Appendix L). However, this could shift dewatering effects from fall-run to winter-run Chinook salmon depending on how real time operations interact with winter-run Chinook salmon redds (Appendix L). The survival of juvenile Chinook salmon emigrating out of the Stanislaus River, down the San Joaquin River, and through the Delta is generally approximately 2 percent, although changes in survival between current and futur·e scenarios has not been quantified. March through May flows in the Stanislaus River are slightly lower under the PA scenario, so juvenile emigration survival through the Delta and into San Francisco Bay should be slightly reduced (Section 2.5.6-7; Appendix L). Under the original PA, Delta pumping would increase under the PAin April and May during the primary outmigration season for fall-run Chinook salmon (Appendix L). Salvage-density analysis assumes changes in salvage (and loss) occur in proportion to the change in amount of water pumped between scenarios. The effects of increased pumping in April and May on winterrun Chinook salmon and spring-run Chinook salmon are described in detail in Section 2.5.6.7.2.1 617 Biological Opinion for the Long-Term Operation of the CVP and SWP ("South Delta Salvage and Entrainment"); similar effects are expected for fall-run Chinook salmon during April and May. The projected combined loss at the CVP and SWP in the COS and PA scenarios are summarized in Table 2.5.8-5. Except for late fall-run Chinook salmon in wet years, projected loss is higher under the P A. While loss is still expected to occur under the final P A, NMFS notes that the revised loss thresholds in the June 14, 2019 PA are expected to limit risks associated with the near-field effects (entrainment into and loss at the export facilities) to levels less than estimated using the Salvage Density Model. The intent of the loss thresholds is to limit loss to levels comparable to loss observed under the COS. However, because the only loss threshold in effect during AprilJune 15 is for natural steelhead, the revised loss thresho1ds in the final PA only indirectly provide protections for outmigrating young-of-year fall-run Chinook salmon and CV spring-run Chinook salmon during this period. The final P A includes triggers for review and technical assistance anytime observed loss exceeds average annual historical loss, which provide some assurance that species risks will be conservatively managed. The Salvage Density Model shows the greatest differences in the PA vs. the COS during April and May, when fall-run Chinook salmon are migrating through the Delta, and the revised loss thresholds are expected to provide an incremental level of additional protection relative to the original P A during this period. 618 Biological Opinion for the Long-Term Operation of the CVP a nd SWP Table 2.5.8-5. Projected combined loss at the CVP and SWP for the February 5, 2019, COS and PA scenarios, by Chinook salmon run and water year type. Positive differences in the final column represent increases in projected loss in the PA relative to the COS. Revised loss thresholds in the June 14, 2019 PA may limit Chinook salmon loss to be more comparable with the COS scenario, though there are not specific loss thresholds for fall-run, late fall-run, or CV spring-run Chinook salmon. Run Fall-run Yeartype (Sacramento "40-30-30" Index unde r ELT Q5 hydrology) Wet AboveNonml BelowNonml Dry Late fall-run Sprimgerun Winter-run Critical Wet AboveNonml BelowNonml Dry Critical Wet AboveNonml BelowNonml Dry Critical Wet AboveNonml Below Nonnal Dry Critical Predicted loss under COS Predicted loss underPA 86,601 32,188 I8,341 27,353 6,966 357 312 33 178 45 42,532 23,057 5,814 13,885 7,628 12,417 6,369 5,830 4,106 1,230 130,431 60,387 29,905 51,530 11,405 351 336 38 188 50 86,606 59,659 1I ,679 24,118 12,474 13,788 6,805 6,812 5,070 I,702 Difference in o;o predicted loss (PA Change COS) 11 51% 88% 63% 88% 64% -2% 8% 13% 6% 4 44,074 36,603 5,865 10,233 4,845 1,371 437 982 965 472 9% 104% 1590/o 101% 74% 64% 11% 7% 17% 23% 38% 43,830 28,198 II ,563 24,177 4,439 -6 25 4 This salvage-density analysis estimates loss, but does not estimate that loss as a proportion of all CV fall-run Chinook salmon, so we are unable to determine a population level effect at this time. The loss estimates from the salvage-density analysis are not explicitly factored into the models of changes in Chinook salmon productivity described above. With respect to the Delta Passage Model, salvaged salmon do not enter the interior Delta and are not influenced by the survival relationships described by that model. Delta exports more strongly affect Chinook outrnigrating from the San Joaquin River tributaries than those from the Sacramento River side. The increase in pumping would most strongly affect the approximately 2.6 percent of all CV Chinook salmon that come from the San Joaquin side of the Delta, particularly at the CVP facility. The Delta Passage Model was not adapted to the San Joaquin River so there is no assessment in the difference in survival between scenarios for San Joaquin River fall-run Chinook salmon. Ultimately, we assume that salvage rates will increase for CV Chinook salmon, especially for fall-run Chinook salmon populations. 619 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.8.1.4.12 Restoration Activities Reclamation identified a number of these restoration actions or programs that have been occurring, and which are expected to continue into future. An analysis of any negative and/or beneficial effects to fish and their habitat has been completed for those actions or programs that previously underwent separate ESA section 7 consultations, and are therefore described in the environmental baseline section. For those programs or actions Reclamation identified as linked to the P A, and will continue into the future, we consider any expected continued negative and/or beneficial effects to listed fish and habitat at a broader scale- or "framework-level" only. For any identified new restoration programs or actions that lack sufficient detail to analyze and quantify level of impact at the level of incidental take, the program or action would require a separate section 7 consultation when sufficient details are available. Reclamation has proposed to conduct habitat restoration projects in the Sacramento River, American River, and Stanislaus River through 2030. Projects would occur annually with a goal to complete at least one habitat improvement project on each of these rivers each year. Cumulative habitat creation is proposed as 40-60 acres on the Sacramento River, 40 acres on the American River (based on 4.0 acres/year from among the identified sites), and 50 acres on the Stanislaus River. By 2030, an estimated 15,273 additional Chinook salmon could be available, assuming that habitats are otherwise at carrying capacity and that any new habitat translates directly into more fish (Appendix L). However, water operational factors are not figured into these estimates so these estimates cannot be directly aggregated with the prey estimates above. While the specific level impact of restoration benefits that may be realized is uncertain, we anticipate that the increase in habitat should help to offset impacts to populations from water operational factors and improve conditions for naturally produced Chinook salmon in California's Central Valley. 2.5.8.1.5 Summary of Project Effects on Central Valley Chinook Salmon Productivity Proposed action-related stressors are expected to reduce the fitness, survival, and abundance of Chinook salmon individuals from all CV Chinook salmon populations during all life stages, through direct impacts as well as reduced quality and quantity of available habitat within the action area. While there are numerous adverse and potentially beneficial effects associated with the PA for Chinook salmon, impacts associated with water temperature management and Delta export operations are especially acute for all CV Chinook salmon populations. For ESA-listed winter-run and CV spring-run Chinook salmon ESUs, we have concluded that the PA is likely to increase the risk of extinction for the populations due to reduced viability across several VSP parameters. For non-ESA-listed species, we conclude that continued water operations will likely continue to lead to diminished productivity ofthese populations, including reducing the abundance of natural-origin fall- and late fall-run Chinook salmon by significant amounts that can vary widely depending in part on environmental variability. There is no estimate in terms of the overall reduction in the number of adult Chinook salmon that may be in the ocean as a result of water operations, but we note the ongoing apparent decline in the relative abundance of Chinook salmon over time for most Chinook salmon ESUs in the Central Valley, especially the dominant fall-run Chinook salmon populations, that has been occurring in concert with ongoing water operations along with other significant factors described in Section 2.4 Environmental Baseline. With respect to COS, available models suggest the PAis expected to lead to an additional increased reduction in productivity of CV Chinook salmon due to reduced survival ofjuveniles 620 Biological Opinion for the Long-Term Operation of the CVP and SWP in upstream areas and through the Delta into San Francisco Bay during the majority of years, which equates to an overall additional reduction in the number of Chinook salmon that survive to the ocean in subsequent years. In particular, results suggest that fall-run, late fall-run, and CV spring-run Chinook salmon populations will experience decreased productivity on average under the PA compared to COS, with fall-run Chinook salmon representing the bulk of CV Chinook salmon productivity. There are conflicting model results about the expected impact of the PA on the productivity of winter-run Chinook salmon, but winter-run Chinook salmon make up a very small percentage ofthe total amount ofCV Chinook salmon productivity. The reductions in Chinook salmon productivity that are estimated by the models through various portions of their life-stage, and in-total through the Central Valley system to the ocean, are not necessarily large for most years (overall < 1 percent median estimate), including variable impacts on natural and hatchery production released into the Central Valley. Expectations are that there will be several hundred less adult CV Chinook salmon on average in the ocean under the P A compared to what might be available under COS. While the available models do incorporate some of the key stressors identified for CV Chinook salmon populations, some stressors are not readily quantifiable and/or cannot be incorporated into these models, and some portions of the Central Valley system could not be evaluated given the available data (all stressors for ESA-listed Chinook salmon summarized in Tables 2.8.2.1 and 2.8.3.1). As a resuh, we conclude it is likely that the models have not fully captured all of the potential difference between CV Clhinook salmon productivity. As discussed above, Reclamation identified a number of these restoration actions or programs that have been occurring, and which are expected to continue into future, in addition to proposing restoration actions linked to the PA. These ongoing and new restoration actions are expected to improve Chinook salmon habitat. Effect of Reduced Prey for SRKW The information described previously in this Opinion suggests that the health of individual animals and the overall population dynamics of SRKW are related to the abundance of Chinook salmon available as prey throughout the range of SRKW. Reductions in availability of preferred prey (Chinook salmon) would be expected to influence the behavior and potentially affect the fitness of individual SRKW, and may affect the survival and reproductive success of SRKW. As described in the Section 2.2.9 Rangewide Status ofSRKW and Appendix B, and the Section 2.4.7.4 Factors Affecting the Prey ofSRKW in the Action Area, during the winter and spring, SRKW (particularly members ofK and L pod) are likely to spend at least some time in coastal waters where they would be affected by reductions in CV Chinook salmon (especially fall-run Chinook salmon) abundance due to the proposed action. As described in Factors Affecting the Prey of SRKW in the Action Area section (Section 2.4.7.4), SRKW (particularly members ofK and L pod) are linked to consumption of Chinook salmon from California based on the contaminant signatures discussed above. As described in Factors Affecting the Prey of SRKW in the Action Area section (Section 2.4.7.4), CV Chinook salmon, especially fall-run Chinook salmon, can constitute a sizeable proportion of the total abundance of Chinook salmon that is available throughout the coastal range ofSRKW 20 percent on average, but varying substantially 10 and 30 percent during any given year). As described in the Factors Affecting the Prey ofSRKW in the Action Area section (Section 2.4.7.4), CV Chinook salmon become an increasingly significant portion of prey source during any southerly movements of SRKW along the coast of Oregon and California that may occur during the winter and spring, and CV fall-run Chinook salmon can be expected to constitute at least 25 percent local 621 Biological Opinion for the Long-Term Operation of the CVP and SWP abundance in many places throughout this area at any time (Bellinger et al. 20 15), and are expected to constitute well over 50 percent of local abundance of Chinook salmon in some areas off California when SRKW are present there (Shelton et al. 20 19). With respect to short-term effects, SRKW could abandon particular areas where prey resources are limited and/or have been reduced in search of more abundant prey or expend substantial effort to find prey resources in response to a decrease in the amount of available Chinook salmon due to the proposed action. These changes in behavior can result in increased energy demands for foraging individuals as well as reductions in overall energy intake, increasing the risks of being unable to acquire adequate energy and nutrients from available prey resources (i.e., nutritional stress). SRKW are known to consume other species offish, including other salmon, but the relative energetic value of these species is substantially less than that of Chinook salmon (i.e., Chinook salmon are larger and thus have more energy value). Reduced availability of Chinook salmon would likely increase predation activity on other species (and energy expenditures) and/or reduce energy intake. With respect to longer-term effects, numerous studies have demonstrated the effects of energetic stress (caused by incremental increases in energy expenditures or incremental reductions in available energy) leading to reduced body size and condition and lower reproductive and survival rates for adults (e.g., Daan et al. 1996, Gamel et al. 2005) and juveniles (e.g., Trites and Donnelly 2003, Noren et al. 2009}. In the absence of sufficient food supply, adult females may not successfully become pregnant or give birth and juveniles may grow more slowly. Any individual may lose vitality, succumb to disease or other factors as a result of decreased fitness, and subsequently die or not contribute effectively to future productivity of offspring necessary to avoid extinction and promote recovery of a population. Ultimately, the effect of reduced prey for SRKW could lead to behavior changes and nutritional stress over the short term that could negatively affect the animal's growth, health, reproductive success, and/or ability to survive over the long term. 2.5.8.1.5.1 Project-Related Impacts of Reduced Prey Base for SRKW Based on the analyses of expected effects of the PA to CV Chinook salmon populations, reductions in the survival and productivity of CV Chinook salmon populations (especially fallrun Chinook salmon) are expected to occur throughout the proposed action, and the greatest effects will occur during the drier water years when effects of the proposed action are most pronounced. These reductions would decrease the abundance of Chinook salmon populations in the ocean and the availability of these Chinook salmon populations as prey for SRKW in the southern portion of their coastal range. The reduced abundance of prey could be detected by all members ofK and L pod during foraging on a reduced prey field, leading to increased expenditures of energy during foraging. The exposure of members of J pod to reduced Chinook salmon abundance in coastal waters is not as clear based on the available data regarding their distributions and contaminant signatures as described in Section 2.4.7.4 Factors Affecting the Prey ofSRKWin the Action Area, but available information suggest their exposure may be much more limited or nonexistent. The expected consequences of biologically significant reductions in the abundance of preferred prey for these SRKW are reductions in the fitness of individuals because impaired foraging behavior and increased energy expended to find sufficient prey and nutritional stress, which can diminish health, lower growth rates, lower reproductive rates and increase mortality rates. Based on the general relative analyses that have been described in 622 Biological Opinion for the Long-Term Operation of the CVP and SWP Section 2.5.8.1.2 Effects ofthe Proposed Action on Chinook Salmon Individuals, all members of K and L pod are expected to be adversely affected, or "harmed,"27 through the increased risk of impaired foraging due to decreased Chinook salmon abundance in the ocean resulting from effects of the proposed action. Based on the analyses of expected effects of the proposed action to CV Chinook salmon, we generally cannot fully quantify the overall impacts due to the operational effects ofthe PA on SRKW in terms of the absolute reduction in Chinook salmon in the ocean that is attributable to the PA. As described above, the productivity of CV Chinook salmon populations as measured by escapement has been decreasing over the last 20 years. This is especially true for the dominant fall-run Chinook salmon populations, where escapement during most of the last 10 years has been substantially lower than previous time periods. Previous analysis of water operations suggested that the natural production of fall-run and late fall-run Chinook salmon is about -10 percent less on average than it could be under other operation scenarios that aim to maximize Chinook salmon production, although this could vary widely and include much higher productivity reductions under certain environmental conditions. Currently, hatchery fall-run Chinook salmon production represents a significant portion of the overall CV Chinook salmon productivity (-70 percent), and significant effort is required to implement hatchery release programs designed to overcome low survival rates for juveniles through a large portion ofthe Central Valley system resulting from habitat conditions and stress created in part by ongoing components of the P'A. With respect to the PA compared to COS, our expectations are that the productivity of most CV Chinook salmon populations, espe.cially fall-run Chinook salmon, and the total Chinook salmon productivity of the entire system, will experience even further reduction and limitations on average/during the majority ofyears under the PA. Although the difference between COS and PA overall is estimated to be relatively small (<1 percent), these results may not be representative ofthe total extent of relative changes in impacts under the PA. What is more certain is that under the PA is that fewer Chinook salmon would be expected survive to the ocean than was has been occurring under COS. Additional stressors that cou1d not be quantified suggest the relative impact of the P A compared to the COS could be larger than model estimates generated. In general, our overall qualitative assessment indicates that the conditions for CV Chinook salmon as a result of water project operations will result in continued reductions and limitations in juvenile Chinook salmon survival and fitness that are expected to reduce the abundance of CV Chinook salmon populations in the ocean. In particular, decreased and limited abundances resulting from the proposed action are expected for CV fall-run Chinook salmon, which constitute a significant portion of all Chinook salmon adults in the ocean in the action area, and generally throughout the ocean range of SRKW. In addiition, we anticipate that under the PA there will commonly be years when at least several hundreds or thousands less adult Chinook salmon could be available as prey for SRKW in the action area compared to COS, especially during years when environmental conditions may provide the most potential stress on juvenile CV Chinook salmon broods when their survival on the way to the ocean would already be 27 As harm is defined in ESA implementing regulations (50 CFR § 222.102), we associate changes in foraging behavior and increased risk of nutritional stress as causing injury to Southern Residents "flJLsignificantly impairing essential behavioral patterns, including, breeding, spawning, rearing, migrating, feeding or sheltering"; specifically, in this case, feeding. 623 Biological Opinion for the Long-Term Operation of the CVP and SWP heavily impacted. Even if the reduction in productivity under the PA compared to COS is not large, the overall trend toward increasing the impact of water operations on CV Chinook salmon productivity will exacerbate conditions that are challenging for Chinook salmon survival to the ocean. For ESA-listed CV Chinook salmon species, the PAis expected to increase the risk of extinction for these ESUs, potentially placing even further limitations on the future productivity ofthe Central Valley system and the abundance of Chinook salmon in the ocean as prey for SRKW. 2.5.8.1.5.2 Consequences of Reduced Prey Base for SRKW Based on the analysis above, NMFS expects that the proposed action will generally reduce the productivity and abundance of CV Chinook salmon (especially fall-run) available in the ocean for SRKW to forage, especially during time periods when environmental conditions are creating additional stress on the productivity and survival of CV Chinook salmon. Reduced abundance, in a range of magnitudes dependent upon other environmental factors, will continue to extend throughout the duration of the PA, which is indefinite. These reductions in available prey are most likely to be detected by all members ofK and L pod, during foraging on a reduced prey field. The result is that SRKW, especially forK and L pod whales, are expected to periodically face conditions where individuals present in the action area are required to spend more time foraging, which incr,eases energy expenditures and the potential for nutritional stress, which can negatively affect the animal's growth, body condition, and health. 2.5.8.1.5.3 Short-term Effects As described in Section 2.4. 7.4 Factors Affecting the Prey ofSRKW in the Action Area, CV Chinook salmon (especially fall-run) are expected to constitute a significant component of the diet of SRKW in coastal waters within the action area where they overlap. In the short term, SRKW are expected to detect and respond to reduced CV Chinook salmon abundance and a reduced prey field during foraging, likely resulting in SRKW searching for other Chinook salmon and more abundant prey fields, either within the action area and/or other parts of their range. While Chinook salmon are expected to be the preferred prey with high nutritional value, SRKW are capable of taking advantage of other prey sources to supplement their nutritional needs and are assumed to do so in the immediate absence of sufficient Chinook salmon resources. Based on the distribution ofCV Chinook salmon described in Section 2.4.7.4 Factors Affecting the Prey ofSRKW in the Action Area, any nutritional and energetic stress impacts caused by the proposed action are most likely to occur in the more southerly range of SRKW. Based on research and the known distribution of SRKW described in Section 2.2.9 Rangewide Status ofSRKW and Appendix B, and Section 2.4. 7.4 Factors Affecting the Prey ofSRKW in the Action Area, we conclude that while SRKW are known to occasionally use the southerly end of their range where CV Chinook salmon are a predominant prey source, it is also likely that this population may limit or avoid use of this area altogether during some years as a result of limited prey availability. The harm created by the PA in the short term is the anticipated changes in the foraging behavior of SRKW in the action area and increased risks of nutritional stress that are perpetuated, and potentially exacerbated, by the PA. Ford and Ellis (2006) report that SRKW engage in prey sharing about 76 percent of the time during foraging activities. Prey sharing presumably could distribute more evenly any short-term effects of prey limitation across individuals ofthe 624 Biological Opinion for the Long-Term Operation of the CVP and SWP population than would otherwise be the case (i.e., if the most successful foragers did not share with other individuals). We also recognize the ability ofSRKW to take action to search out other areas with more abundant Chinook salmon prey fields or take advantage of other prey sources to supplement their nutritional needs in the immediate absence of sufficient Chinook salmon resources and the likelihood that SRKW may avoid the southern end of their range in some years (where CV Chinook salmon are most important as a prey source). As a result, we conclude it is likely that the relative magnitude of short-term adverse effects resulting from the behavioral changes and nutritional stress that may occur in response to reduced abundance of CV Chinook salmon prey in the ocean available to SRKW in the ocean at any one particular time during of the proposed action would likely be limited in extent and moderated to some degree by the factors discussed above. Consequently, we do not anticipate severe short-term adverse effects such as immediate mortality or reproductive incapacitation directly as a result of short term exposure to the effects of the P A. Long-term Effects While the overall absolute impact of the PA on the survival and abundance of CV Chinook salmon is not quantified, there is information that suggests the effects of the PA will likely exacerbate the existing reductions and limitations on CV Chinook salmon productivity as a result of the PA, especially for the larger populations of Chinook salmon (fall-run Chinook salmon in particular) that contribute a substantial amount of overall Chinook salmon production and abundance in the ocean range of SRKW, and are increasingly significant in large stretches of that range. Over the long term, we expect the extent of this impact to be persistent over time, and increasingly acute during years when environmental conditions are increasingly challenging for Chinook salmon survival throughout the Central Valley system, further amplifying the significance of the reductions in Chinook salmon productive expected to occur as a result of the PA. The future projections of climate-related impacts and conditions that present challenges for CV Chinook salmon are described in Section 2.4 (Environmental Baseline), which suggests that these challenges are likely to increase and/or emerge on a more frequent basis moving forward in the coming decades. In addition to the immediate reduction of CV Chinook salmon in the ocean as a result of diminished survival directly as a result of the PA, we conclude that the increased extinction risk for some CV Chinook salmon populations created by the PA potentially limits the long term future productivity and diversity of prey sources for SRKW. As a result, over time, we expect the effect of reduced Chinook salmon abundance and productivity will likely not relent under the PA, but to continue and escalate as the productive capacity of the Central Valley system is diminished as some Chinook salmon populations head to extinction. Although SRKW may have the ability to take action to search out other areas with more abundant Chinook salmon prey fields or take advantage of other prey sources to supplement their nutritional needs in the immediate absence of sufficient Chinook salmon resources, the significance of the contribution of CV Chinook salmon to the overall total available prey resources within the action area and total abundance of Chinook available in the ocean for SRKW across their range on an annual basis suggests that over the course of a given season, and persistently year after year, SRKW may have to consistently and persistently expend this additional energy to overcome limitations in available prey and any nutritional stress that is created by effects of the PA. Recently, as described in Section 2.2.9 Rangewide Status ofSRKW and Appendix B, a number of individuals from the SRKW population have been showing signs of poor body condition, nutritional stress and overall diminished health. Based on the analysis, it 625 Biological Opinion for the Long-Term Operation of the CVP and SWP is likely that conditions under the PA where SRKW are exposed to and affected by reductions and limitations in the abundance of Chinook salmon available as prey as a result of the PA will increase over time. As a whole, as described in Section 2.2.9 Rangewide Status ofSRKWand Appendix B, the population has recently been experiencing low fecundity rates and projections are that the population will decrease in the future as a result. The effect of perpetual and/or additional nutritional stress over time for individual SRKW that are already experiencing and showing signs of nutritional stress is an additional reduction in fitness that increases the probability of reduced survival and/or reproductive success for at least some members of the SRKW population that are already compromised, or potentially contributing to diminishing the fitness of individuals to a compromised state over time where reduced survival and/or reproductive effects become increasingly likely to occur. 2.5.8.2 Supplemental Analysis of June 14, 2019, Final PA During consultation for this Opinion, discussions between NMFS and Reclamation resulted in revisions to the PA that were not captured in the February 5, 2019, BA that was used for the majority of the analysis in this Opinion. Also during the consultation for this Opinion, the Sacramento River Settlement Contractors (SRSC) drafted for adoption a resolution for activities involving recovery projects, actions related to annual operations, and engagement in ongoing science partnership. It was not possible to include these revisions in any modeling due to the White House memorandum that mandated issuance of final biological opinions within 135 days of January 31, 2019 (June 17, 2019, and subsequently extended to July 1, 2019), and limitations in the capability to quantitatively assess their influence on PA effects. The effects description above (Section 2.5.8.1.2-2.5.8.1.4) was based on the modeling associated with the f ,ebruary 5, 2019 PA (Appendix Al, the original PA) and associated modeling that NMFS requested. The following subsection provides a supplemental effects analysis to assess the effects ofthe June 14, 2019 PA revisions reflected in the final PA (Appendix A3), including a discussion of whether and how the PA revisions modify the effects analyzed above. 2.5.8.2.1 Upstream Productivity Revisions to the Cold Water Pool Management section of the fmal PA include the addition of Section 4.10.1.3.3 Upper Sacramento Performance Metrics, described in more detail in Section 2.5.2.6.1 Revisions to the PA Relevant to the Shasta/Upper Sacramento Division. The objective of these performance metrics is to ensure that the performance falls within the modeled range, and shows a tendency towards performing at least as well as the distribution produced by the simulation modeling of the PA. This addition to the Cold Water Pool Management section contributes to increasing the certainty that the central tendency of the analyzed results is what the species will experience when these operations are implemented. That is, the analysis characterized exposure and risk based on the central statistics of modeled TDM for each Tier type and the long-term projected likelihood of occurrence of each year type. However, the TDM results included a broad range for each Tier due to the variability of conditions included in each Tier type. With this change, we consider our previous analysis of the modeled outcomes of temperature management - which is based on the central tendency to capture the most likely conditions - to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.8.1.4 Changes in Chinook Salmon Productivity under the PA compared to COS do not change quantitatively due to the revisions included in the final PA, as 626 Biological Opinion for the Long-Term Operation of the CVP and SWP this commitment to assess cold water management does: not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. The final PA includes a number of commitments for funding and improvements at Livingston Stone National Fish Hatchery, described in more detail in Section 2.5.2.6.1 Revisions to the PA Relevant to the Shasta/Upper Sacramento Division. Most of these actions are expected to benefit winter-run Chinook salmon to some degree, but it is unclear if any benefit would extend to other Chinook salmon populations, or if these actions could influence the overall analysis of Chinook salmon productivity given their focus on a small part of the overall abundance of Chinook salmon. The final PA includes revisions to the Governance section ofthe PA that include the addition of Section 4.12.5 Drought and Dry Year Actions to develop a toolkit of actions to be taken in drought conditions, and a process by which early warnings of drought conditions may allow for clear and swift development of a drought contingency plan. Compared to the previous analysis, the addition of the drought and dry year actions decreases the uncertainty associated with high mortality values modeled for Tier 3 and Tier 4 years. NMFS expects that any actions taken in this instance would increase the likelihood that resulting mortality values would be minimized to the exil:ent possible. With this change, we consider our previous analysis of the modeled outcomes of temperature management to still apply as a conservative characterization of projected and expected operations. The results described in Section 2.5.8.1.4 Changes in Chinook Salmon Productivity under the PA compared to COS could slightly over-represent a high mortality event that could be prevented by this Drought and Dry Year Action; however, the results ofthe modeling would not notably change the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. The final PA includes revisions to the Governance section of the PA that include the addition of Section 4.12.6 Chartering oflndependent Panels and Section 4.12.7 Four-Year Reviews to charter reviews either at set dates or as triggered. The review topics are expected to include the Upper Sacramento Performance Metrics and associated topics in that section. While the reviews will be greatly informative in increasing the understanding of effects of temperature conditions and operational decisions on species response, they are post-hoc evaluations that alone do not afford additional protections to the species or alter the quantitative analysis already completed based on the modeling results. The results described in Section 2.5 .8. 1.4 Changes in Chinook Salmon Productivity under the PA compared to COS will not change quantitatively, as this commitment to assessing the performance of the PA does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. The actions and commitments within the draft SRSC Resolution, described in more detail in Section 2.5.2.6.1 Revisions to the PA Relevant to the Shasta/Upper Sacramento Division, are expected to benefit Chinook salmon populations. NMFS expects that any actions taken in response to Tier 3/Tiier 4 conditions would increase the likelihood thatt resulting mortality values would be minimized to the extent practicable, particularly for winter-run Chinook salmon. Additionally, delayed diversions for rice decomposition during the fall months could provide increased reliability that target flows would be met and reducing the effects of flow fluctuations. 627 Biological Opinion for the Long-Term Operation of the CVP and SWP The continuation of the recovery actions by the SRSC is expected to result in long-term benefits for CV Chinook salmon populations, including fall-run Chinook salmon. The commitment to establish and implementation of the Mainstem Sacramento River Integrated Water and Fish Science and Monitoring Partnership is expected to improve the science that is used to protect and support the recovery ofCV Chinook salmon populations, including fall-run Chinook salmon. However, it is not possible to describe their benefits more specifically or quantitatively at this time based due to limited information on their effectiveness and/or uncertainty on how these actions will ultimately be incorporated into future project operations. On June 19,2019, USFWS sent a letter to NMFS providing an update on efforts that USFWS has been engaged in, largely in partnership with BOR, regarding CNFH and LSNFH and their contribution to the management and restoration of CV Chinook salmon. With respect to improving the overall productivity of Chinook salmon, these efforts include design of a fish trapping and sorting facility at CNFH to minimize handling and migration delay of listed species during CNFH's fall-run Chinook salmon spawning operations, and to allow for passage, monitoring, and management of fish passage during times when spawning operations are not taking place. Design is underway, but funding to complete construction has not yet been secured. Notable efforts also include studies of alternative release strategies for CNFH produced fall-run Chinook salmon that have potential for increasing juvenile survival to the ocean and adult returns to the Sacramento River without unacceptable levels of straying. To date, USFWS has completed one year of a three-year study, and is close to securing funding to complete the project. At this time results are not yet available to inform any long term alternative release strategies moving forward, although we do expect any successful strategies implemented as a result of these studies to benefit CV Chinook salmon populations in the future. 2.5.8.2.2 Delta Productivity The revised PA includes revisions to the OMR Management component of the PA that are described in detail in Section 2.5.5.11.1 Revisions to OMR Management. The cumulative and single-year loss thresholds for CV salmonids proposed were developed to limit loss for key (and reliably measurable) populations to loss rates observed under implementation of the NMFS 2009 Opinion. The intent of these PA revisions was to limit direct loss at the south Delta export facilities as a way to limit some ofthe higher-magnitude effects under the original P Aspecifically, effects associated with DCC operations, OMR Storm Flexibility, and increased exports in April and May. The concept was that, rather than use the hydrodynamic metric of OMR to manage species risks, we could use a metric of historical loss rates to keep risks comparable to risks under the NMFS 2009 Opinion. NMFS concludes that this approach is a reasonable way to limit risks associated with the near-field effects (entrainment into and loss at) the export facilities. While there are some uncertainties in how this new approach will be implemented, the final PA includes triggers for review and technical assistance anytime observed loss exceeds average annual historical loss, which provide some assurance that species risks will be conservatively managed. While loss is still expected to occur under the final PA, NMFS notes that the loss thresholds are expected to limit loss to levels less than estimated using the Salvage Density Model results described in Section 2.5.5.8.3.1, and to levels comparable to loss observed under the COS. The Salvage Density Model showed the greatest differences in the PA vs. the COS during April and May, and NMFS expects that the benefits of the revised loss thresholds (relative 628 Biological Opinion for the Long-Term Operation of the CVP and SWP to the original PA) will be greatest during this April-May period during outmigration of CCV steelhead (particularly from the San Joaquin basin) and young-of-year CV fall-run and springrun Chinook salmon. It is less certain whether this approach will fully limit risks associated with the far-field effects (potential disruptions to migration rate or route) of the export facilities. Because NMFS assumes that far-field effects are correlated with exports (both footprint and magnitude of hydrodynamic effect greater at higher exports), limiting near-field effects to historical rates could be assumed to limit far-field effects to historic rates. However, it is likely that OMR (and associated Delta hydrodynamics) may still be more negative under the final PA than observed under the COS, especially in April and May. IfOMR (and associated Delta hydrodynamics) is more negative under the final PA than observed under the COS, far-field effects under the final PA are expected to be intermediate between the COS and the original PA. The revised PA also clarified that DCC openings in December through January would be limited to occasions when drought conditions are observed and gate opening will help to address water quality concerns, which is expected to occur less than 10 percent of the time. The final PA also includes a new commitment to reduce combined CVP/SWP exports to health and safety levels (NMFS assumes that this is I ,500 cfs) during any DCC gate opening in December or January. This may have some benefit for juvenile winter-run Chinook salmon during their migration in December and January, but may not offer much additional protection for other Chinook salmon beyond the anticipated effects that were previously analyzed. 2.5.9 LifeCycle Models Life cycle models of winter-run Chinook salmon were used to analyze population abundance, cohort replacement rate, habitat use distribution, and juvenile survival differences between the COS and PA. These models characterize the dynamics of multiple lifestages, including eggs, fry, smolts, juveniles in the ocean, and mature adults in the spawning grounds. The two life cycle models considered in this opinion are the Interactive Object-Oriented Simulation (lOS) Model, the results for which were provided by Reclamation (as supplemental ROC on LTO BA modeling information), and the Southwest Fisheries Science Center's Winter-run Chinook Life Cycle Model (WRLCM). Both the lOS model and the WRLCM provide a more holistic evaluation in their examination of the effects of the action because both models consider the collective effects of disparate action components across the entire life-cycle. And while it is acknowledged that the underlying modeling (CalSirnll and HEC-5Q temperature modeling) for both tlhe lOS model and WRLCM does not capture or reflect the entirety of conditions associated with the COS and PA, the lOS model and WRLCM are considered the best available tools for assessing the effect of those conditions on winter-run Chinook salmon. Given the unique set of results provided by the life cycle models, they are presented here instead of being integrated into, and possibly attributed to, an individual PA component. The results affect the population-level attributes of abundance, productivity, and population trend, rather than just an individual's response described as a relative change in fitness. The analysis presented in this section is comparative in nature and incorporates uncertainties in PA and COS modeling discussed in other effects sections. The comparative analysis is useful in terms of understanding the overall direction of modeled effects and assessing predicted trends on population structure and viability. However, as discussed in Section 2.1 Analytical Approach, 629 Biological Opinion for the Long-Term Operation of the CVP and SWP this comparative analysis should not be conflated with an analysis of the full effects of proposed project operations on species. Section 2.8 Integration and Synthesis discusses how NMFS considers the life cycle model results, in addition to other information, in evaluating the operational effects of the PA to species in aggregate with the effects of components of the baseline. 2.5.9.1 Interactive Object-Oriented Simulation (lOS) Model Structure The lOS Model is composed of six model stages defined by a specific spatiotemporal context and are arranged sequentially to account for the entire life cycle of winter-run Chinook salmon, from eggs to returning spawners. In sequential order, the lOS Model stages are listed below. • Spawning, which models the number and temporal distribution of eggs deposited in the gravel at the spawning grounds in the upper Sacramento River between Red Bluff Diversion Dam and Keswick Dam. • Early Development, which models the effect of temperature on maturation timing and mortality of eggs at the spawning grounds. • Fry Rearing, which models the relationship between temperature and mortality of fry during the river rearing period in the upper Sacramento River between Red Bluff Diversion Dam and Keswick Dam. • River Migration, which estimates mortality of migrating smolts in the Sacramento River between the spawning and rearing grounds and the Delta. • Delta Passage, which models the effect of flow, route selection, and water exports on the survival of smolts migrating through the Delta to San Francisco Bay. • Ocean Survival, which estimates the effect of natural mortality and ocean harvest to predict survival and spawning returns by age. 2.5.9.1.1 lOS Model Results For the first four years of the 82-year simulation period, the starting population of spawning adults for both scenarios is 5,000, of which 3,087.5 are female. In the fifth year, the number of female spawning adults is determined by the model's probabilistic simulation of survival to this life-stage. The model assumes all winter-run Chinook salmon entering the Delta are smolts and that there is no flow- or temperature-related mortality for the river migration (RBDD to Freeport); a mean survival for this stage of23.5 percent is applied with a standard error of 1.7 percent. Once in the Delta, the survival of smolts is characterized by the Delta Passage Model (DPM) component in which flow, route selection, and water exports determine survival. In lOS, only timing into the Delta is altered from the standalone DPM as spawning events and temperature determine migration towards the Delta. lOS results show that egg survival is generally very high in most water year types but decreases substantially in critical years. Results for the two scenarios were similar, with median egg survival of0.99 for both the COS and the PA (Figure 2.5.9-1). 630 Biological Opinion for the Long-Term Operation of the CVP and SWP 09 .,. . · -=- • • 08 0.7 06 OS 04 03 0.2 0 I 0 w AN BN 0 c Figure 2.5.9-1. Box plots of annual egg survival for the COS and the PA for winter-run Chinook salmon estimated by the lOS Model by water year type. The x-axis is water year type (Wet, Above Normal, Below Normal, Dry and CriticaUy Dry) and they-axis is the proportion of egg survival. Note the results are intended to be used in a manner that compares different scenarios. Likewise, fry survival from Keswick Dam to Red Bluff Diversion Dam is temperature dependent and was very similar for the two scenarios with median fry survival for COS at 0.94 and for the PA at 0.95 (Figure 2.5.9-2). 631 Biological Opinion for the Long-Term Operation of the CVP and SWP • PA_Fry_S • COS_Fry_S 1 0.9 ......... • • • • • ...• • 0.8 • 0.7 • 06 0.5 04 0.3 0.2 0.1 0 w AN BN D c Figure 2.5.9-2. Box plots of annual fry survival for winter-run Chinook salmon from Keswick Dam to Red Bluff Diversion Dam estimated by the I OS Model between the COS and the P A separated by water year type. Here the x-axis is water year type (Wet, Above Normal, Below Normal, Dry and Critically Dry) and the y-axis is the proportion of fry survival. Note the results are intended to be used in a manner that compares different scenarios. 2.5.9.1.2 lOS Through-Delta Survival (From Freeport to Chipps Island) Results Across all years, the lOS model's median predicted through-Delta survival was 0.41 for the COS and 0.42 for the PA (Figure 2.5.9-3). 632 Biological Opinion for the Long-Term Operation of the CVP and SWP • PA_Delta_S • COS_Delta_S 0.6 0 .5 0.4 0.3 0.2 0.1 0 w AN BN D c Figure 2.5.9-3. Box plots of annual through-Delta survival for the COS and PA for winter-run Chinook salmon estimated by the lOS Model by water year type. The x-axis is water year type (Wet, Above Normal, Below Normal, Dry, and Critically Dry) and they-axis is the proportion of juvenile survival through the Delta. Note the results are intended to be used in a manner that compares different scenarios. 2.5.9.1.3 lOS Escapement Results In the lOS model, the probability of survival in the ocean is almost identical for both the PA and COS. The model predicts COS median adult escapement at 3,864 and PA median escapement of 3,909, a population difference of 1.2 percent (Figure 2.5.9-4). In other words, the model predicts a 1.2 percent increase of adult spawners for the P A. Throughout the life cycle of winter-run Chinook salmon, the lOS model identifies very little difference in results between the COS and the P A Based on the lOS model, fry survival is the stage most affected by the PA, with an increase of 1.2 percent. lOS results show survival probabilities are similar for both scenarios for all stages, attributing the 1.2 percent increase in escapement to the increased fry survival for the PA. The differences in escapement based on 633 Biological Opinion for the Long-Term Operation of the CVP and SWP water year type is not a reflection of hydrologic conditions for the outmigrating juveniles; instead, it is a classification of hydrology for the time when adults returned to spawning grounds. • PA_escapement • COS_escapement 18000 16000 14000 uooo • • 10000 8000 6000 4000 2000 0 w BN AN [) c Figure 2.5.9-4. Box plots of annual escapement for the COS and the PA for winter-run Chinook salmon estimated by the lOS Model by water year type. The x-axis is water year type (Wet, Above Normal, Below Normal, Dry, and Critically Dry) and they-axis is the number of returning adults. Note the results are intended to be used in a manner that compares different scenarios. 2.5.9.2 Sacramento River Winter-run Chinook Salmon Life Cycle Model A state-space life-cycle model for winter-run Chinook salmon in the Sacramento River (WRLCM) developed by the Southwest Fisheries Science Center was used to analyze differences between the COS and PA. The model has multiple stages, including eggs, fry, smolts, juveniles in the ocean, and mature adults in the spawning grounds. The model is spatially explicit and includes density-dependent movement among habitats during the fry rearing stage. It also incorporates survival from the habitat of smoltification to Chipps Island by applying equations from analysis of reach specific survival in the Delta (Newman 2003). The model operates at a monthly time step in the freshwater stages and at an annual time step iin the ocean stages. Parameter estimates for the model were obtained from external analyses, expert opinion, and estimation by statistical fitting to observed data. The observed data included winter-run Chinook salmon natural origin escapement, juvenile abundance estimates at Red Bluff Diversion Dam, and juvenile abundance estimates at Chipps Island. To evaluate alternative management actions, 634 Biological Opinion for the Long-Term Operation of the CVP and SWP 1,000 Monte Carlo parameter sets were run that incorporated parameter uncertainty, process noise, and parameter correlation. For survival in the Delta, the WRLCM uses Newman (2003) survival results, which are based on a statistical model and environmental covariates that occurred over the time frame 1979-1995. We also note that the Newman model was developed using juvenile fall-run Chinook salmon reared in hatcheries and released in April and May, which is later than the peak outmigration for winter-run Chinook salmon. While there are more recent evaluations of survival through the Delta, these approaches have yet not been incorporated into the development of the WRLCM and were therefore not available at the time of the evaluations for this Opinion. NMFS acknowledges that a level of uncertainty is introduced by using the older information ofNewman (2003), and consider this when evaluating the multiple lines of evidence of the WRLCM and other analytical tools. The COS and the PA were run for each of the 1,000 parameter sets. It is important to note that the COS and PA should be evaluated in a relative sense using the WRLCM, because relative comparisons are more robust than the absolute predictions from the WRLCM. Moreover, it would be incorrect to equate outputs of the model as equating to actual numbers of fish in the Sacramento River. This perspective is adopted for several reasons: I) the underlying hydrology of the COS and the P A are based on CalSimll model outputs that are a combination of historical hydrology and future expected hydrological conditions, but do not represent actual historic or future hydrology; 2) the WRLCM model and the models used to provide input to the WRLCM that use the CalSimli results [HEC-RAS, DSM2, and Newman (2003)] require assumptions that would all need to be true; and 3) the WRLCM was not calibrated to produce forecasts of actual abundances. As a result, the WRLCM should be viewed as a tool that can provide guidance on the relative performance of the two sets of operations, and the percent difference (i.e., (P ACOS)/COS * 100 percent) was computed for each of the 1,000 model runs. A detailed description of the model methods and assumptions, as well as all the scenario results, are contained in the Appendix H of this Opinion. The model was applied in a scenario that compared the PA to the COS using an initial abundance of 10,000 spawning adults as a representative population of winter-run Chinook salmon. This initial abundance is not meant to refl ect current, historical, or projected population trends, but instead is used to seed the model. The standard hydrology used in this evaluation represents the 82-year historical CalSimll record from 1922 to 2002. However, prior to 1926, the WRLCM is initializing; results from these years may disproportionately reflect the initial conditions. To control for this potential artificial skew in results, only annual percent differences from the 1926 abundance value (which may differ slightly between the PA and the COS due to the initialization period) and afterward are used to calculate the abundance and cohort replacement rate (CRR) metrics. 2.5.9.2.1 Results of the Scenario Evaluation Overall, the WRLCM results indicate higher abundances and lower CRR for the COS relative to the PA. Mean abundance is 3.05 percent less for the PA relative to COS through the modeled time series (Figure 2.5.9-5). The probability that average abundance for the PA would be greater than average abundance for the COS in the 82-year time series is approximately 0.03. That is, of the 1,000 paired runs ofthe COS and PA, there were 30 in which the average modeled 635 Biological Opinion for the Long-Term Operation of the CVP and SWP abundance for the PA was greater than the average modeled abundance for the COS, leading to a probability of0.03. 0 l() I () c .... & 6 :::e. 0 0 ,...- I l() ,- I 0 C\1 I 1920 1940 1960 1980 2000 Figure 2.5.9-5. Difference in abundance ((PA- COS)/COS X 100 percent) for 1,000 paired runs of the WRLCM incorporating parameter uncertainty and ocean variability. Results show median (red line), 50th percentile interval (dark grey) and 95th percent interval (light gray). The CRR is a key metric to understand population dynamics, since it characterizes the ability of a population to replace itself. In the model runs, estimates of the difference in CRR for 1,000 paired runs of the WRLCM indicate that there is a 0.993 probability that CRR would be higher for the PA than the COS over the 82-year model period. There is, therefore, a consistent difference over the model period. However, density dependence in the spawning stages will cause the CRR to decrease for situations with higher spawner abundance. In the WRLCM the spawner density-dependence relationship is a Beverton-Holt function where density-dependent effects begin to occur at spawner abundances below the carrying capacity. This densitydependent function directly influences the production of eggs in the model such that when the 636 Biological Opinion for the Long-Term Operation of the CVP and SWP spawner abundance is above approximately half the carrying capacity, the production of eggs per spawner will start to decrease as abundance increases. The loss of productivity of eggs per spawner affects the CRR negatively, leading to reduced CRR for higher abundances. Furthermore the mean CRR of the PAis only 0.55 percent greater than the mean CRR of the COS (Figure 2.5.9-6). This number indicates that the population's ability to replace itself is, numerically, slightly improved for the PA, but that is partially driven by the relative decrease in abundance for the P A. Overall, the mean difference in CRR between the PA and COS may be so small that it does not represent a biologically meaningful difference. 0 T""" Q.) (.) c Q.) ..... 0 0 0 0 T""" I 0 C\1 I 1920 1940 1960 1980 2000 Figure 2.5.9-6. Difference in CRR (i.e., (PA- COS)/COS X 100 percent) for 1,000 paired runs of the WRLCM. Results show median (red line), 50th percentile interval (dark grey) and 95th percent interval (light gray). 637 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.5.9.2.1.1 Dynamics Leading to Differential Abundance and Productivity The lower abundance in the PA relative to the COS are largely due to conditions in the non-wet water year types and the month of April in certain lifestages/locations. There is little difference between the PA and COS in the egg-to-fry mortality that occurs in the reach from Keswick Dam to RBDD, except for minor differences in the months of June - August in Critical water year types (Figure 2.5.9-7). During Critical water year types, the model shows that the PA has a decreased median survival, specifically in August (a reduction of 5.6 percent). Egg Survival for Spawning in Apr Egg Survival for Spawnirng in May " ci ci eLl E8 <0 ci ..r ci I I I I C\1 ci ..1.. ..1.. 0 G.fS$ I I I I I I ..1.. ..1.. ci I I I I cts• c!sl I I I I t:g gg ..1.. ..1.. <0 ..1.. ..1.. I ci ..r ci I C\1 ci ..1.. AN BN ci :; - ..1.. I I ..1.. ..1.. I I I I I I S8 ..1.. ..1.. I AN BN II II I I I ' ..1.. ..... I ..1.. ..1.. I I D c Upper River Smolt Survival (origin to Chipps) in Apr ro ci - C\1 00 w c D Upper River Smolt Survival (origin to Chipps) in Mar d- I I ci I w I I ..1.. 0 ..1.. cts• eLl cls' ' I I I I I I I I I I E8 ...... S$ ..1.. ..1.. ..1.. ..1.. w AN !1 I ' ..... ..... BN D <0 eLl ' ci I I I C\1 ci ..1.. cts+ ..r ci I I I ..1.. 0 93 ..1.. ..... ..1.. ..... ..... ..1.. .......... ' ......... BN D c ci w c AN Upper River Smolt Survival (origin to Chipps) In May d- dC\1 I ci 0 ci Sliil cis' .......... ..1.. ..1.. ..1.. ..1.. ..1.. ..1.. I I I I I w AN BN D c ..1.. ..L Figure 2.5.9-8. Monthly survival ofsmolts originating from the Upper River habitat under COS and PA. (In general, survival results of the PA are lower than the COS for a given water year type and month except Jan- March of Wet water year types.) Results are shown for Jan-May for aU habitat types and do not imply equal distribution of presence in that habitat type for the full period. 639 Biological Opinion for the Long-Term Operation of the CVP and SWP Similar to the analysis of survival of smolts originating in the Upper River habitats, survival of smolts originating in the Lower River habitats is genera11y lower for the PA than the COS (Figure 2.5.9-9). The Lower River habitat begins below RBDD and ends at the Delta. Survival for the PA was lower than COS in all months and water year types except for January through March ofwet years, when PA survival is slightly greater than COS survival (Figure 2.5.9-9). Of the months examined, April has the greatest difference in survival of smolts originating in the Lower River habitats; in this month, PA survival is 3.6 to 7.5 percent lower than COS survival. Lower River Smolt Survival (origin to Chipps) in Jan co 0 "53.5°F for IOO%of the populati on of eggs/fry Large (33.1% of days >53.5°F for 100%of the populati on) Medium (4568%of years) Frequen cy of Exposur e High High Magni tude of Effect High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. W eight of Evidence Reduced survival probabilit y(5% 6% temperatu re dependent mortality with standard deviations of +/- 8 percent [Anderso n] and+/9 percent [Martin]). Reduced survival probabilit y (12% 15% temperatu re dependent mortality with standard deviations of +!- 13 percent [Anderso nl and +/- Probable C h.ange in F itness Low to Medium (17 35%of years) High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. medium magnitude benefits, low magnitude stressors, low magnitude benefits, uncertain stressorslbenefits. Table 2.8.1-1 Summary of proposed action-related effects on winter-run Chinook salmon organized by division component. Within each division, components are listed top to bottom in the following order: high magnitude stressors, high magnitude benefits, medium magnitude stressors, Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Tier2 (Shasta Cold Water Pool Mgmt.) Temperatures higher than 53.5°F would result in reduced survival ( increase in mean temperature dependent mortality of 12 percent [Anderson] and 15 percent [Martin]; the standard deviations are +/13 percent 694 Action Com pone nt Tier3 (Shasta Cold Water Pool Mgmt.) Stressor/Facto r Water Temperature under Tier 3 management Water Temperature under Tier 4 management Life Stage (Location) Eggs/Pry (Keswick Dam- CCR gauge) Eggs/Fry (Keswick Dam - CCR gauge) MayOctober (May IS - October) MayOctober (May IS - October) Life Stage Timing (Work Window Intersection) Individual Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Tier4 (Shasta Cold Water Pool Mgmt.) [Anderson] and +/- 16 percent [Martin]) Temperatures higher than S3.S°F would result in reduced survival (increase in mean temperature dependent mortality of28 percent [Anderson] and 34 percent [Martin]; the standard deviations are +/25 percent (Anderson] and +/- 31 percent [Martin]) Temperatures higher than 53.5°F would result in reduced survival probability (increase in mean temperature dependent mortality of79 percent [Anderson] and 81 percent [Martin]; the standard deviations are +/- 695 Severity of Stressor/ Level of Benefit Lethal Lethal Proport ion of Populat ion Expose d Large (6S% of days >53.S°F for 100%of the populati on) Large (86% of days >53.5°F for 100%of the populati on) e Frequen cy of Exposur Low (7% - 1S% of years) Low (5% - 7% of years) Magni tude of Effect High High Probable Ch.ange in F itness Reduced survival probabilit y (28% 34% temperatu re dependent mortality with standard deviations of+/- 25 percent [Anderso n] and +/31 percent [Martin]). Weight of Evidence High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. Reduced survival probabilit y (79%81% mean temperatu re dependent mortality with standard deviations of+/- 14 percent [Anderso 16 percent [Martin]). High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. Action Compone nt Fall and Winter Refill and Redd Maintena nee Spring Pulse Flow Stressor/Facto r Life Stage (Location) Juveniles (Upper Sacramento River) Eggs/Fry (Upper Sacramento River) May October (NA) JulyDecember (October, November) Life S tage Timing (Work Window I ntersection) Summer temperatures higher than 53.5°F would result in increased egg/fry mortality. Decreased month-to-month flows resulting in stranding and decreased floodplain inundation and side-channel habitat. 14 percent [Anderson] and +/- 16 percent [Martin]). Individua l Response and Rationa le of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division To build storage for the subsequent year class, fall flows are reduced from the high summer flow. This reduction of flows is likely to influence Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function. Reduced storage caused by spring pulse releases (May I - May 15), reduces Reclamation's ability to provide suitable spawning and incubation 696 Severity of Stressor/ Level of Benefit Lethal Lethal P roport ion of Populat ion Expose d Medium (<50% of the populati on) Small Medium (<2 6%) Frequen cy of Exposur e Low (20% of years) Medium (<75% of years) Weight of Evidence Proba ble C h.ange in F itness Reduced survival probabilit y Magni tude of Effect High Medium: Supported by technical publication s specific to the region and species. Quantitativ e results include WUA analysis and monthto-month floodplain inundation. Decreased survival probabilit y(<2% 6% egg/fry mortality) n) and+/16 percent [Martin)). Mediu mHigh Medium: High level of understandi ng of the relationship between temperatur e and egg/fry survival, but limited Action Compone nt Shasta Cold Water Pool Mgmt. Winter Minimum flows Stressor/Facto r Water Temperatures Water Temperatures. Redds constructed earlier than May 15 would not be protected. Eggs/Fry still in redds after the end date of temperature management ( I 0/3 1, or when 95% alevin have emerged) would also not protected. Flow Conditions MayOctober (May 1 - May 15, and95% WR a levin emergence October 31) Temperatures higher than 53.5°F would result in reduced survival Life Stage (Location) Eggs/Fry (Keswick Dam-CCR gauge) JulyDecember (December) Individua l Response and Rationa le of Effect Juveniles (Upper midSacramento River) Life S tage Timing (Work Window Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Decreased month-to-month flows resulting in stranding caused by a loss of floodplain inundation and 697 P roport ion of Populat ion Expose d Lethal Small to Medium Severity of Stressor/ Level of Benefit Lethal Medium (5- 10% of populati on) Mediu mHigh Magni tude of Effect High High Frequen cy of Exposur e Low (20% of years) Weight of Evidence understandi ng of the effects of seasonal operations on storage and temperatur e. High: Survivaltemperatur e relationship supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. Medium: Supported by select technical publication s specific to the region and Proba ble C h.ange in F itness Reduced survival Decreased survival probabilit y Action Com pone nt Delta Smelt SummerFall Habitat LSNFH Productio n (tier 4 interventi on) Stressor/Facto r Water Temperature Life Stage (Location) Eggs/Fry (Keswick Dam - CCR gauge) Adults (Upper Sacramento River) Individua l Response and Rationale of Effect May October (May 15 - October) Framework programmatic action component. Temperatures higher than 53.5°F would result in reduced survival side-channel habitat. December August (May - August) Life Stage Timing (Work Window Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Increased production at LSNFH. Hatchery effects (minimization for Water Temperatures) Intervention measure to address a lack of suitable spawning and rearing habitat during periods of drought. Adult fish are brought into LSNFH to augment natural production. Covered under 698 Severity of Stressor/ Level of Benefit Lethal Beneficial : High P roport ion of Populat ion Expose d Medium -High High (Uncert ain) Frequen cy of Exposur e Low Low (7% of years) Magni tude of Effect High High Weight of Evidence include species. Quantitativ e results month-tomonth change. High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. High: Multiple scientific and technical publication s covering the influence of hatchery production on wild populations Probable C h.ange in F itness Decreased survival probabilit y Shortterm increased reproducti ve success at the framewor k-level, but also reduced viability due to increased Action Compone nt Small Screen Program (Spawn in g/rearing habitat restoratio n) Temperat ure Modeling Platform Stressor/Facto r Entrainment/1 mpingement at water diversions Water Temperature under Tier management Life Stage (Location) Juveniles (Middle Sacramento River) Eggs/Fry (Kesw ick Dam - CCR gauge) May October (May 15 - October) July December L ife S tage Tim ing (Work W indow I ntersection) the USFWS 2016 HGMP Individua l R esponse and R ationa le of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Framework level action component. Operation of installed fish screens are assumed to comply w ith NMFS and CDFW fish screening guidance. Reduced entrainment into unscreened diversions and minimized potential for injury caused by impingement. Improved modeling should help minimize temperature dependent mortality 699 Severity of Stressor/ Level of Benefit Beneficial :High Beneficial :High P r oport ion of P opulat ion Expose d Medium (Juvenil es <50% passage at RBDD) Large Frequen cy of Exposur e H igh (Operatic ns) Medium Weight of Evidence Proba ble C h.ange in F itness Increased survival probabilit y Magni tude of Effect High Low: (Programm atic action component ) very little information available as to how this action component would be implemente d or its effects when operated. Increased survival probabilit y hatchery influence High High: Supported by multiple scientific and technical publication s that include quantitative Life Stage (Location) Water Temperature Eggs/Fry (Keswick Dam - CCR gauge) Stressor/Facto r Water Temperature Eggs/Fry (Keswick Dam - CCR gauge) May October (May 15 - October) Temperatures higher than 53.5°F would result in reduced survival Individua l Response and Rationale of Effect MayOctober (May 15 - October) Temperatures higher than 53.5°F would result in reduced survival Life Stage Timing (Work Window Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Actions for Year After Two Low Survival Years Division Upper Sacramen to/Shasta Division Drought and Dry Year Actions Action Com pone nt Upper Sacramen to/Shasta Division 700 Severity of Stressor/ Level of Benefit Beneficial :High Beneficial :High P roport ion of Populat ion Expose d Large Large Frequen cy of Exposur e Low Low Magni tude of Effect High High Weight of Evidence models specific to the region and species. High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. Probable C h.ange in F itness Increased survival probabilit y Increased survival probabilit y Stressor/Facto r Life Stage (Location) Life S tage Timing (Work Window I ntersection) Individua l Response and Rationa le of Effect Beneficial :High Severity of Stressor/ Level of Benefit Water Temperature May October (May 15 - October) Beneficial :High Temperatures higher than 53.5°F would result in reduced survival Adults, Juveniles (Middle Sacramento River) Eggs/Fry (Keswick Dam - CCR gauge) Entrainment/[ mpingement at water diversions, Flow Conditions DecemberJuly (MayJuly), JulyDecember (JulyOctober) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Drafting of Temperat ure Managem ent Plan Using Conservat ive Forecasts Action Compone nt Upper Sacramen to/Shasta Division Wilkins Slough intakes (Cold water pool mgmt.) Framework level action component. Operation is assumed to comply with NMFS and CDFW fish screening guidance reducing the potential for entrainment/impi ngement at diversions. 701 P roport ion of Populat ion Expose d Large Low (Adults) , Medium (Juvenil es <50% passage at RBDD) Frequen cy of Exposur e High Magni tude of Effect Weight of Evidence Mediu mHigh High High (Yearly Operatio ns) High: Supported by multiple scientific and technical publication s that include quantitative models specific to the region and species. Low: (uncertain) very little information available as to how this action component would be implemente d or its effects when operated. Proba ble C h.ange in F itness Increased survival probabilit y Increased survival probabilit y Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function Stressor/Facto r Winter Minimum flows Water Temperature Action Compone nt Winter Minimum flows Juveniles (Upper midSacramento River) Life Stage (Location) July December (December) Life S tage Timing (Work Window I ntersection) Individua l Response and Rationa le of Effect Sublethal Severity of Stressor/ Level of Benefit Beneficial :High Reduced growth and potentially increased competition and predation related to decreased habitat carrying capacity (WUA) at lower flows Eggs/Fry (Keswick Dam- CCR gauge) MayOctober (May 15 - October) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Temperatures higher than 53.5°F would result in reduced survival (increase in mean temperature dependent mortality of28 percent [Anderson] and 34 percent [Martin); widest range of 25 and 75 percentiles for 2 different models is 7 to 59 percent) 702 P roport ion of Populat ion Expose d Medium (5- 10% of populati on) Medium (5- 10% of populati on) Low (20% of years) Low (20% of years) Frequen cy of Exposur e Mediu m Mediu m Magni tude of Effect Low: Substantial uncertainty with WUA analyses for the juvenile rearing life stage. Quantitativ e results include WUA analysis. High: Supported by select technical publication s specific to the region and species. Quantitativ e results include month-tomonth change. Weight of Evidence Proba ble C h.ange in F itness Decreased growth rate Increased survival probabilit y Action Com pone nt Fall and Winter Refill and Redd Maintena nee Spring Pulse Flow Stressor/Facto r Water Temperature Life Stage (Location) Life Stage Timing (Work Window Intersection) Individua l Response and Rationale of Effect DecemberJuly (March May 15) May October (May 15 - October) Migrating Adults (Middle, Lower Sacramento River) Eggs/Fry (Keswick Dam - CCR gauge) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Flow Conditions, Loss of Natural River Morphology and Function Passage Impediments/B arners Temperatures higher than 53.5°F would result in reduced survival (increase in mean temperature dependent mortality of28 percent [Anderson] and 34 percent [Martin]; widest range of 25 and 75 percentiles for 2 different models is 7 to 59' percent) Elevated flows may facilitate swimming past barriers, or they may merely serve as a cue for migration. High flows are also correlated with lower temperatures that benefit females migrating upriver by ensuring that eggs are not damaged before spawning. 703 Beneficial :High Severity of Stressor/ Level of Benefit Beneficial :Low P roport ion of Populat ion Expose d Medium (<50% of the populati on) Large Magni tude of Effect Weight of Evidence Increased survival probabilit y Probable C h.ange Frequen cy of Exposur e Mediu m High: Supported by select technical publication s specific to the region and species. Improved reproducti ve success in F itness Low (20% of years) Mediu m Medium (<75% of years) Medium: Correlation of flow and migration supported by multiple scientific and technical publication s but magnitude of benefit uncertain. Action Compone nt Fall and Winter Refill and Redd Maintena nee Spring Mgrnt. of Spawning Locations Stressor/Facto r To build storage for the subsequent year class, fall flows are reduced from the high summer flow. This reduction of flows is likely to influence Flow Conditions, Loss of Riparian Habitat and In stream Cover, Loss of Natural River Morphology and Function. Water Temperature, Spawning Habitat Availability Life Stage (Location) July December (October, November) Life S tage Timing (Work Window I ntersection) December July (April May) Juveniles (Upper Sacramento River) Adults (Upper Sacramento River) Individua l Response and Rationa le of Effect Sublethal Severity of Stressor/ Level of Benefit Low (Uncertain ) Decreased habitat carrying capacity (WUA) at lower flows providing decreased feeding conditions, and potentially increased competition and predation. Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Framework programmatic action component. Proposed research and management to determine the effect of water temperatures on the timing and location of spawning. Warmer temperatures may delay spawning. 704 P roport ion of Populat ion Expose d Medium (<50% of the populati on) Large Magni tude of Effect Weight of Evidence Decreased growth rate, Reduced survival probabilit y Proba ble C h.ange Frequen cy of Exposur e Mediu m Low: Substantial uncertainty with WUA analyses for the juvenile rearing life stage. Quantitativ e results include WUA analysis. Improved reproducti ve success in F itness Low (20% of years) Mediu m (Uncert a in) High (Uncertai n) Low: A number of scientific and technical publication shave suggested a relationship between temperatur e and spawning timing but a direct effect is still Action Compone nt Rice Decompo sition smoothin g (fall ops.) Stressor/Facto r Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function Juveniles (Upper Sacramento River) Life Stage (Location) JulyDecember (October, November) L ife S tage Tim ing (Work W indow I ntersection) Adults, Juveniles (Middle Sacramento River) December July (June July), JulyDecember (JulyOctober) Individua l R esponse and R ationa le of Effect Framework programmatic action component. Construction activities are not described; NMFS assumes that construction would occur during an Proposed coordination may provide more reliable fall flows decreasing the potential for juvenile stranding. Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramen to/Shasta Division Upper Sacramen to/Shasta Division Wilkins Slough intakes (Cold water pool mgmt.) Passage Impediments/B arriers, Flow Conditions, Loss of Riparian Habitat and Instream Cover, Stressors associated with 705 Low (Uncertain ) Severity of Stressor/ Level of Benefit P r oport ion of P opulat ion Expose d Low (20% of years) Frequen cy of Exposur e Low (Uncert ain) Magni tude of Effect Medium (Adults) Uncertain (Construe tion) Uncert ain due to uncerta in frequen cy Medium (<50% of the populati on) Lethal , Medium (Juvenil es <50% passage at RBDD) Weight of Evidence unknown and in need of further understandi ng. Low: (uncertain) little information available as to how this action component would be implemente d or its effects. Low: (uncertain) very little information available as to how this action component would be implemente d Proba ble C h.ange in F itness Uncerta.in. Potential for increased survival probabilit y related to reduced juvenile isolation and fry stranding; and increased storage for following temperatu re managem ent seas "0 PA •• '• •'• ,• .... Mortality Method I • I ro I L.. ' I, I I I Q. ' t . I ' I MartJO I r 0 .25 - Anderson ' I I :::J +"' E cos I ,' 0 OQ I I I I I 0.00 0.25 0.50 0.75 1.00 Fraction of Years Figure 2.8.1-1. Exceedance curves of Upper Sacramento River Winter-run Chinook Salmon TemperatureDependent Egg to Fry Mortality for All Water Year Types (modified from Figure 5.6-21 in the BA). 722 Biological Opinion for the Long-Term Operation of the CVP and SWP 1.00 - , , ,, , , ,, ,, , , , ,, c 0 i3 0.75 «< .... u. ,--- ,.,'.. ..... I ,,, 0 ::lE ..... cQ) ' "0 c , I 8. 0.50 - . I , Scenario .I cos # PA . I i I 53.5°F) Low(7% of years) Frequenc y of Exposure Medium (68% of years) Lethal Large(97% of days >53.5°F) Proportion of Population Exposed Large(76% of days >53.5°F) High High Magnitu de of Effect High benefits, medium magnitude stressors, medium magnitude benefits, low magnitude stressors, low magnitude benefits, uncertain Division Upper Sacrament of Shasta Division Tier2 (Shasta Cold Water Pool Mgmt.) Water Temperature Eggs/Fry (Keswick Dam - BSF gauge) Weight of Evidenc e High: Supporte d by multiple scientific and technical publicati ons High: Supporte dby multiple scientific and technical publicati ons High: Supporte d by multiple scientific and technical publicati ons Reduced survival probability Reduced survival probability Probable Change in Fitness Reduced survival probability Table 2.8.3-2. Summary of proposed action-r elated effects on spring-run Chinook salmon for the Sha sta (Sacramento River), T rinity (Clear Creek), and Delta divisions. Within each division, components are listed top to bott()m in the following order : high magnitude st ressors, high magnitude Upper Sacrament of Shasta Division Tier3 (Shasta Cold Water Pool Mgmt.) stressors/benefits. Upper Sacrament of Shasta Division 756 Action Compone nt Tier4 (Shasta Cold Water Pool Mgmt.) Delta Smelt Summer-Fall Habitat Water Temperature Stressor/Fact or Water Temperature Eggs/Fry (Keswick Darn- BSF gauge) Life Stage (Location) Eggs/Fry (Keswick Darn - BSF gauge) August December (AugustOctober) Life Stage Timing (Work Window Intersecti on) August December (August October) Individual Response a nd Rationale of Effect Temperatures higher than 53.5°F would cause a decrease in egg survival. Lethal Severity of Stresso r/ Level of Benefit Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament o/Shasta Division Framework programmatic action component. Action subcomponents that utilize reservoir releases to achieve additional Delta outflow and increase habitat quantity would reduce cold water pool that would otherwise be available for summer temperature management. Temperatures higher than 53.5°F would result in reduced survival 757 Proportion of Population Exposed Large (99.6%of days >53.5°F) Large Frequenc y of Exposure Low(7% of years) Low Magnitu de of Effect High High Weight of Evidenc e High: Supporte d by multiple scientific and technical publicati ons High: Supporte d by multiple scientific and technical publicati ODS that include quantitati ve models specific to the region and species. Probable Change in Fitness Reduced survival probability Reduced survival probability Action Compone nt Fall and Winter Refill and Redd Maintenance Life Stage (Location) Redds (Upper Sacramento River) Life Stage Timing (Work Window Intersecti on) August December (October, November ) Individual Response a nd Rationale of Effect Decreased month-to-month flows resulting in possible redd dewatering and decreased floodplain inundation and side-channel habitat. Severity of Stresso r/ Level of Benefit Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Stressor/Fact or Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function 758 Proportion of Population Exposed Large Frequenc y of Exposure Low(20% of years) Magnitu de of Effect High Weight of Evidenc e Medium: Supporte d by a limited number of scientific and technical publicati ons specific to the region and species. Quantitat 1ve results monthto-month channel inundatio n(U.S. Fish and Wildlife Service 2006). Probable Change in Fitness Reduced survival probability Action Compone nt Winter Minimum flows Life Stage (Location) Juveniles (Upper midSacramento River) Life Stage Timing (Work Window Intersecti on) November -April (Decembe rFebruary) Severity of Stresso r/ Level of Benefit Sublethal , Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Stressor/Fact or Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function Individual Response a nd Rationale of Effect Decreased habitat carrying capacity (WUA) at lower flows providing decreased feeding conditions, and increased competition and predation. Decreased month-to-month flows resulting in decreased floodplain inundation and side-channel habitat. 759 Proportion of Population Exposed Large (9095%of population) Frequenc y of Exposure High (Yearly) Magnitu de of Effect High Weight of Evidenc e High: Supporte d by multiple scientific and technical publicati ons specific to the region and species. Quantitat ive results include WUA analysis and monthto-month floodplai n inundatio n. Probable Change in Fitness Decreased growth rate, Reduced survival probability Action Compone nt Spring Pulse Flow Temperatme Modeling Platform Water Temperature under Tier management Stressor/Fact or Flow Conditions, Loss of Natural River Morphology and Function Passage Impediments! Barriers Eggs/Fry (Keswick Dam- BSF gauge) Life Stage (Location) Juveniles, Migrating Adults (Middle, Lower Sacramento River) AugustDecember (AugustOctober) Life Stage Timing (Work Window Intersecti on) January May (MarchMay), February August (March May 15) Benefici al: Low Severity of Stresso r/ Level of Benefit Benefici al: High Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament a/Shasta Division Individual Response a nd Rationale of Effect Elevated flows reduce migration times for juveniles, which will in turn reduce predation opportunities. For adults increased flows facilitate upstream migration. High flows are also correlated with lower temperatures that benefit females migrating upriver by ensuring that eggs are not damaged before spawning. Improved modeling should help reduce the uncertainty related to temperature forecasting which could minimize temperature dependent mortality for winter-run 760 Proportion of Population Exposed Large(75% of Juveniles), Large (Adults) Large Frequenc y of Exposure Medium (<75% of years) Medium Magnitu de of Effect High, Medium Medium Weight of Evidenc e High: Multiple scientific and technical publicati ons indicate an associati on between Sacrame nto River or Delta flow and juvenile salmon survival (Michel eta!. 2015, Perry et a!. 20 18). High: Supporte d by multiple scientific and technical publicati ODS that include quantitati ve models Probable Change in Fitness Improved Guvenile) survival probability, Improved reproductive success Increased survival probability Action Compone nt Drought and Dry Year Actions Stressor/Fact or Water Temperature Life Stage (Location) Eggs/Fry (Keswick Dam- BSF gauge) Life Stage Timing (Work Window Intersecti on) AugustDecember (AugustOctober) Individual Response a nd Rationale of Effect Chinook salmon and to a lesser extent the other ESUs or DPSs spawning in the Sacramento River. Benefici al: Low Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament a/Shasta Division Drought and Dry Year Actions have been identified for winter-run Chinook salmon as a way to mitigate for temperatures higher than 53.5°F which result in reduced survival. These actions are expected to benefit other species, ESUs and DPSs in the Sacramento River as well but to a lesser degree. 761 Proportion of Population Exposed Large Frequenc y of Exposure Low Magnitu de of Effect Medium Weight of Evidenc e specific to the region and species. High: Supporte d by multiple scientific and technical publicati ons that include quantitati ve models specific to the region and species. Probable Change in Fitness Increased survival probability Action Compone nt Drafting of TemperatiUfe Management Plan Using Conservative Forecasts Tier I (Shasta Cold Water Pool Mgmt.) Stressor/Fact or Water Temperature Water Temperature Life Stage (Location) Eggs/Fry (Keswick Dam - BSF gauge) Life Stage Timing (Work Window Intersecti on) August December (August October) March October (May IS October) Individual Response a nd Rationale of Effect Using conservative forecasts to inform the development of the Temperature Management Plan is expected to reduce the frequency of there being temperatures higher than 53.5°F during the winter-run Chinook salmon spawning and incubation period. It is expected to provide an indirect benefit to the other species, ESUs, and DPSs that spawn in the Sacramento River as well. Temperatures in excess of 61 °F expected to lead to stress, disease, and bioenergetic depletion. Sublethal Severity of Stresso r/ Level of Benefit Benefici al: Low Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament o/Shasta Division Upper Sacrament of Shasta Division Holding& Spawning Adults (Keswick Dam - BSF gauge) 762 Proportion of Population Exposed Large Small ( 1% of days >6l °F) Frequenc y of Exposure High Medium (45%68%of years) Magnitu de of Effect Medium Low Weight of Evidenc e High: Supporte d by multiple scientific and technical publicati ons that include quantitati ve models specific to the region and species. Medium: Supporte d by multiple scientific and technical publicati ons, however Probable Change in Fitness Increased survival probability Reduced reproductive success Tier3 (Shasta Cold Water Pool Mgmt.) Tier2 (Shasta Cold Water Pool Mgmt.) Action Compone nt Water Temperature Holding& Spawning Adults (Keswick Dam- BSF gauge) Life Stage (Location) Water Temperature Stressor/Fact or March October (May 15 • October) Temperatures in excess of 61 °f expected to lead to stress, disease, and bioenergetic depletion. Individual Response a nd Rationale of Effect MarchOctober (May 15October) Life Stage Timing (Work Window Intersecti on) Sublethal Sublethal Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament of Shasta Division Holding& Spawning Adults (Keswick Dam - BSF gauge) Temperatures in excess of 61 °f expected to lead to stress, disease, and bioenergetic depletion. 763 Low to Medium (17% . 35% of years) Frequenc y of Exposure Small (1% of days >61°f) Low (7%15%of years) Proportion of Population Exposed Medium (13% of days >61°F) Magnitu de of Effect Low Low Weight of Evidenc e not specific to the region and species. Medium: Supporte d by multiple scientific and technical publicati ons, however not specific to the region and species. Medium: Supporte d by multiple scientific and technical publicati ODS, however not specific to the region Probable Change in Fitness Reduced reproductive success Reduced reproductive success Rice Decomp smoothing (fall ops.) Tier4 (Shasta Cold Water Pool Mgmt.) Action Compone nt Holding& Spawning Adults (Keswick Dam- BSF gauge) Life Stage (Location) Water Temperature Redds (Upper Sacramento River) Stressor/Fact or March October (May 15October) Temperatures in excess of 61 °F expected to lead to stress, disease, and bioenergetic depletion. Individual Response a nd Rationale of Effect August December (October, November ) Life Stage Timing (Work Window Intersecti on) Low (5% 7%of years) Frequenc y of Exposure Sublethal Medium (36% of days >6! 0 f) Low Proportion of Population Exposed Benefici a!: Low Medium (33%42%of redds potentially dewatered); Low proportion benefit from storage increase Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament of Shasta Division Flow Conditions, Loss of Riparian Habitat and l nstream Cover, Loss of Natural River Morphology and Function Framework level action component. Proposed coordination may provide more reliable fall flows affecting action component Fall and Winter Refill and Redd Maintenance (2.5.2.3.4.1) 764 Magnitu de of Effect Low Low (Uncerta in) Weight of Evidenc e and species. Medium: Supporte d by multiple scientific and technical publicati ons, however not specific to the region and species. Low: uncertain tyof action compone nt impleme ntation or its effects Probable Change in Fitness reproductive success Increased reproductive success Action Compone nt Wilkins Slough intakes (Cold water pool mgmt.) Stressor/Fact or Construction or instaltation of fish screens on water diversions. Passage Impediments/ Barriers, Flow Conditions, Loss of Riparian Habitat and Instream Cover Adults, Juveniles (Middle Sacramento River) Life Stage (Location) Adults, (Middle Sacramento River) MarchSeptember (JuneSeptember ) November - April (no overlap with proposed constructi on timing), Life Stage Timing (Work Window Intersecti on) March September (June September ) Benefici a!: Low Severity of Stresso r/ Level of Benefit Sublethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament of Shasta Division Small Screen Program (Spawninglr earing habitat restoration) Construction or installation of fish screens on water diversions. Passage Impediments/ Barriers, Flow Conditions, Loss of Riparian Habitat and lnstream Cover Individual Response a nd Rationale of Effect Framework level action component, construction activities are not described. NMFS assumes that construction would occur during an appropriate inwater work window and include BMPs and minimization measures to limit potential effects to species Framework level action component Construction activities are not described but assumed construction effects related to installation of fish screens include: changes in flow, stranding (instaltation of coffer dams), and handling. 765 Proportion of Population Exposed Small Low Frequenc y of Exposure Uncertain (dependin gon Constructi on timing/ext ent) Low: (Uncertain ) Magnitu de of Effect Low Low Weight of Evidenc e Low: (uncertai n) very little informati on available as to how this action compone ntwould be impleme nted (construe tion). Low: (Program matic action compone nt) very little informati on available as to how this action compone nt would be impleme nted Probable Change in Fitness Decreased survival probability Increased survival at diversion (decreased entrainment) Stressor/Fact or Adult rescue (tier 4 intervention) Passage Impediments/ Barriers, Entrainment!I mpingement at water diversions Action Compone nt Adults, Juveniles (Middle Sacramento River) Adults (Middle Sacramento River) Life Stage (Location) MarchSeptember (June September ) November - April (no overlap with proposed constructi March September (Uncertain ) Life Stage Timing (Work Window Intersecti on) Uncertain. Programmatic action component. Increased stress and mortality related to capture and handling. Minimization measure intended to increase relative survival of adult salmon ids entrained in water diversions (e.g. Yolo and Sutter Bypasses). Increased habitat quality and quantity. Framework level action component. Individual Response a nd Rationale of Effect Benefici a!: Medium Benefici al: Low Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament of Shasta Division SideChannel habitat (Spawning!r earing habitat restoration) Riparian vegetation, Loss of Riparian Habitat and lnstream Cover, Physical Habitat Alteration 766 Uncertain, Low (tier 4 years = 5 -7% of all years) Frequenc y of Exposure Uncertain High (Permanen t) Proportion of Population Exposed Low/Mediu m Magnitu de of Effect Low (Uncerta in) Low Weight of Evidenc e (construe tion). Low: (Program matic action compone nt) very little informati on available as to how this action compone ntwould be impleme nted or as to its effects. Medium: (previous Program matic Opinion evaluate d) Probable Change in Fitness Increased reproductive success, Increased survival probability Continued Increased growth rate, increased productionls pawning success Stressor/Fact or Life Stage (Location) Adults, Juveniles (Middle Sacramento River) Juveniles (Middle Sacramento River) November -April (no overlap with proposed constructi on timing), AugustOctober November - April Life Stage Timing (Work Window Intersecti on) on timing), Framework level action component, operation is assumed to comply with NMFSand CDFW fish screening guidance. Increased habitat quaLity and quantity. Framework level action component. Individual Response a nd Rationale of Effect Benefici al: Low Benefiel a!: Low Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Spawning Gravel Injection (Spawninglr earing habitat restoration) Action Compone nt Upper Sacrament of Shasta Division Wilkins Slough intakes (Cold water pool mgmt.) Divisio n Upper Sacrament of Shasta Division Spawning Habitat Availabi lity, Loss of Riparian Habitat and Instream Cover, Physical Habitat Alteration Operation of new or repaired fish screens on water diversions. Entrainment/1 rnpingement at water diversions 767 Proportion of Population Exposed Uncertain Large Magnitu de of Effect Increased growth rate, Increased lifetime reproductive success Probable Change in Fitness Frequenc y of Exposure Low Medium: (Previou s program matic Opinion evaluate d) Increased survival probability, Weight of Evidenc e High (Permanen t) Uncertai n, High High (Permanen t) Low: (uncertai n) very little informati on available as to how this action compone ntwould be impleme nted or its effects when operated. Action Compone nt Small Screen Program (Spawning/r earing habitat restoration) Juvenile Trap and Haul (tier 4 intervention) Stressor/Fact or Operation of new or repaired fish screens on water diversions. Entrainment/1 mpingement at water diversions Life Stage (Location) Juveniles (Middle Sacramento River) Juveniles (Upper Sacramento River) Life Stage Timing (Work Window Intersecti on) November -April (Uncertain ), November -April (Uncertain ), Individual Response a nd Rationale of Effect Framework level action component. Programmatic action component. Construction activities are not described but operation is assumed to comply with NMFSand CDFW fish screening guidance. Benefici al: Uncertai n Severity of Stresso r/ Level of Benefit Benefici al: High Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Upper Sacrament of Shasta Division Monitoring, Maintenance, Research Studies, etc. (minimization for Water Temperatures) Frameworklevel Programmatic action component. Increased survival -small proportion stress and mortality related to capture and handling. Minimization measure 768 Proportion of Population Exposed Uncertain Uncertain Frequenc y of Exposure High (Permanen t) Low(7% of years) Magnitu de of Effect Uncertai n, High Uncertai n Weight of Evidenc e Low: (Program matic action compone nt) very little informati on available as to how this action compone ntwould be impleme nted (construe tion) or its effects when operated. Low: (Program matic action compone nt) very little informati on available as to how this action compone Probable Change in Fitness Increased survival probability (NMFS/CD FW fish screening criteria 5% Joss), Increased survival Operation of a Shasta Dam Raise Action Compone nt NA Stressor/Fact or NA Life Stage (Location) NA Life Stage Timing (Work Window Intersecti on) NA Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Individual Response a nd Rationale of Effect intended to increase relative survival of Juvenile winterrun during Tier 4 water temperature operations. Depending on timing and location of trap and haul operations, juvenile springrun could be collected and returned to the nver or relocated. None. Reclamation has committed to no change in operations with the inclusion of a Shasta Dam raise such that there will be no change in the frequency of meeting management criteria nor will there be any change in the timing and volume of releases. 769 Proportion of Population Exposed NA Frequenc y of Exposure NA Magnitu de of Effect NA Weight of Evidenc e ntwould be impleme nted or as to its effects. NA Probable Change in Fitness None Action Compone nt Shasta TCD improvemen ts (Cold water pool mgmt.) Stressor/Fact or Water Temperature Life Stage (Location) all Life Stage Timing (Work Window Intersecti on) Warmer months Sept-Oct Adults are exposed to >60°F, which may cause streS-S; disease, reduced fecundity, and prespawn mortality. Flow decreases cause isolation and stranding. Ramping rates will reduce the magnitude. Increased flows create migration cues by increasing turbidity, decreasing water temperatures, and improving Individual Response a nd Rationale of Effect Framework level action component. Unknown changes/modi tic ations to existing Reddsare exposed to water temperatures >56°F, resulting in temperature dependent mortality. Medium Proportion of Population Exposed NA Medium Frequenc y of Exposure NA HighMedium Magnitu de of Effect NA High (annual) Medium Medium Small High (annual) Medium Sublethal -Lethal High Medium Benefici at: LowMedium Low Medium, given the limited success of this action in the past Sublethal Lethal and Sublethal Severity of Stresso r/ Level of Benefit NA Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Upper Sacrament of Shasta Division Trinity (Clear Creek) Water Temperature, Spawning Habitat Availabi lity. May-Jun Jun-mid Sept Juveniles: creek-wide May-Jun Water temperatu-re management :Fall Water Temperature Flow Conditions Water temperature management :Summer Spring attraction pulse flows Trinity (Clear Creek) Trinity (Clear Creek) Spring attraction pulse flows Adults migrating/h olding:creek -wide Eggs/ alevins upstream and downstream of compliance point. Adults holding downstream of compliance point. Trinity (Clear Creek) Flow Conditions; Loss of Natural River Morphology and Function; Passage 770 Probable Change in F itness Increased survival Reduced survival and reduced reproductive success. Reduced survival. Reduced reproductive success. Medium Weight of Evidenc e Low: (uncertai nty regardin g effective ness) t High: supporte d by water tempera! ure and monitori ng data. Medium: supporte dby water temperat ure and monitori ng data .. Medium Increased survival. Increased reproductive success Adults migrating creek-wide Life Stage Timing (Work Window Intersecti on) Jun-Sept Jun-Sept Jun-Aug reaches for holding. Implementation of this action in the past has helped attract spring-run into Clear Creek, but has had limited success attracting them to upstream holding habitats. Low flow barriers at riffles and cascades may inhibit access to holding locations. Temperatures may be above optimal growth and survival >65°F. Increased stress, risk of predation and disease. Warm water temperatures >65°Fmay block or inhibit upstream Individual Response a nd Rationale of Effect passage of physical barriers to the most Minor Minor Minor Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Flow Conditions; Passage Impediments Juveniles: creek-wide Life Stage (Location) Minimum in stream base flows Water Temperature Action Compone nt Trinity (Clear Creek) Water temperature management :Summer Water Temperature Adults migrating creek-wide Divisio n Trinity (Clear Creek) Water temperatu·re management :Summer Stressor/Fact or Impediments/ Barriers Trinity (Clear Creek) 771 Proportion of Population Exposed Medium Small Small Frequenc y of Exposure Medium Magnitu de of Effect (see Res pons e column) Low Low High High High Low Reduced survival and reprod.uctive success Probable Change in Fitness Medium Reduced growth and survival. Weight of Evidenc e Medium Reduced survival and reproductive success Life Stage Timing (Work Window Intersecti on) Individual Response a nd Rationale of Effect upstream migration Base flow reductions in Critical water year types, and/or after the fall water temperature management period will dewater redds. Eggs and a Ievins will be exposed to effects of dewatering and reduced hyporheic flow. Flow decreases cause isolation and strandi ng. Ramping rates will reduce the magnitude. Increased flows create migration cues and improve downstream passage by decreasing water temperatures, increasing turbidity. Sublethal Severity of Stressor/ Level of Benefit Medium Medium Proportion of Population Exposed High (annual) Medium (30-60% of years) Low Frequenc y of Exposure Low Low Low Magnitu de of Effect Medium Medium Medium Weight of Evidenc e Reduced survival. Reduced survival. Probable Change in Fitness Sublethal Low Benefici a!: Low Increased growth. Improved survival. Increased life history diversity. Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage (Location) Nov-Jan Stressor/Fact or Eggs/ alevins: upstream of segregation weir Jan-Apr Action Compone nt Flow conditions Juveniles/ smolts: creek-wide Divisio n Flow Conditions Minimum instream base flows. Channel maintenance pulse flows Trinity (Clear Creek) Trinity (Clear Creek) May-Jun Spring attraction pulse flows Juveniles/ smolts: creek-wide Trinity (Clear Creek) Flow Conditions; Loss of Natural River Morphology and Function; Passage Impediments/ Barriers 772 Divisio n Channel maintenance pulse flows Action Compone nt Stressor/Fact or Juveniles/ smolts: creek-wide Life Stage (Location) Mar-Apr Jan-Apr Life Stage Timing (Work Window Intersecti on) Benefici a!: Low Benefici a!: Low Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Trin ity (Clear Creek) Flow Conditions, Loss of Natural River Morphology and Function, Passage Impediments! Barriers Adults migrating: creek-wide Channel maintenance pulse flows Trinity (Clear Creek) Flow Conditions, Loss of Natural R iver Morphology and Function, Passage Impediments! Barriers Individual Response a nd Rationale of Effect Provide temporary access to additional rearing habitat. Increased flows create migration cues and improve downstream passage: decreasing water temperatures, increasing turbidity and reducing predation risk. Provide temporary access to additional rearing habitat. Increased flows create migration cues by increasing turbidity, decreasing water temperatures, and improving passage of physical barriers to the most upstream reaches for holding. 773 Proportion of Population Exposed Medium Low Frequenc y of Exposure Magnitu de of Effect Weight of Evidenc e Probable Change in F itness Increased growth. Improved survival. Increased life history diversity. Medium Medium Low Low Medium (30-60% of years) Medium (30-60% of years) Increased survival. Increased reproductive success Life Stage (Location) Juveniles Sacramento River -Delta Life Stage Timing (Work Window Intersecti on) Juvenile migration and rearingDec - May Severity of Stresso r/ Level of Benefit Minor to Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Action Compone nt DCC Gate operations - Stressor/Fact or Altered Hydrodynami cs downstream of DCC location Individual Response a nd Rationale of Effect Increased mortality when gates are open due to changes in routing or transit time through interactions with changes in river flow and tidal influence downstream of DCC location and gate operations 774 Proportion of Population Exposed Medium opening of gates reduces the proportion of riverine reaches adjacent to the DCC location; closing of gates extends the riverine reaches farther downstrea m. All fish emigrating in Oct and Nov have the potentia l to see open gates, fish emigrating rna drought year may see up to 10 days in Dec and January with the gates in the open position, although Frequenc y of Exposure High Magnitu de of Effect High Weight of Evidenc e HighThere are a number of publicati ons regard in g the relative survival in various North Delta and Central Delta migrator y routes; conclusi ons supporte d by modellin g results. Probable Change in Fitness reduced fitness and/or survival when gates are open; lesser effect in final PA due to revised DCC operations in DecemberJanuary Action Compone nt C02 injections Stressor/Fact or JuvenilesSacramento River -Delta Life Stage (Location) Life Stage Timing (Work Window Intersecti on) Individual Response a nd Rationale of Effect Benefici a!: High Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta CVP Improvemen ts Juvenile migration and rearing Dec- May Removal of predators from secondary channel at the Tracy Fish Collection Facility 775 Proportion of Population Exposed the joint probability of occurrence is I in 10 years. Medium High Frequenc y of Exposure High Magnitu de of Effect Weight of Evidenc e Medium - several studies have looked at predation impacts in the salvage process, long term effective ness of this method is not certain Probable Change in Fitness Increased survival Action Compone nt DCC Gate operations - Stressor/Fact or Routing Life Stage (Location) Juveniles Sacramento River Delta JuvenilesSacramento River -Delta Juvenile migration and rearing Dec- May Life Stage Timing (Work Window Intersecti on) Juvenile migration and rearingDec - May Individual Response a nd Rationale of Effect increased mortality due to routing into the delta interior with lower survival rates Sublethal to Lethal Severity of Stresso r/ Level of Benefit Sublethal -Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta CVP/SWP South Delta Exports Altered hydrodynamic s in south Delta/ routing Mortality or decreases in condition due to migratory delays in response to altered hydrodynamics in channels of the south Delta. Loss of appropriate migratory cues. Delays increase 776 Proportion of Population Exposed Medium gates open from Oct I through Nov 30, typically closed Dec 1 through Jan 31. Closed Feb 1 through May20. Estimated 5%of juvenile SR population emigrates by the end of January. Higher risk to yearling SR than young of year. Medium- Frequenc y of Exposure Low. DCC gates infrequent! y operated in December and January Highcontinual exports Magnitu de of Effect MediumHigh Medium to High Weight of Evidenc e HighThere are a number of publicati ons regard in g the relative survival in various North Delta and Central Delta migrator y routes; conclusi ons supporte d by modellin g results. Medium to High effects of hydrody namics well studied and modelled . Effects of hydrody namics Probable Change in Fitness Reduced survival; lesser effect in final PA due to revised DCC operations in DecemberJanuary Reduced survival, reduced growth; I ikely lesser effect in final PA due to revised loss thresholds, though no Joss threshold Action Compone nt Stressor/Fact or Life Stage (Location) JuvenilesDelta Life Stage Timing (Work Window Intersecti on) Juvenile migration and rearingDec- May Loss is approximately 35% at the CVP and 84% at the SWP fish salvage facilities Individual Response a nd Rationale of Effect transit time and exposure to predators, poor water quality, and contaminants. Sublethal to Lethal Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta CVP/SWP South Delta Exports Entrainment and loss at the south Delta export facilities 777 Proportion of Population Exposed Small Frequenc y of Exposure High Magnitu de of Effect Medium to Highsustained high frequenc y exposure on small proportio n of populati on Weight of Evidenc e on salmonid migratio ns in south Delta less certain. HighNumerou s studies have evaluate d the efficienc y of the screen in g facilities, predation , as well as survival through the facilities Probable Change in Fitness specific to spring-run. reduced survival; likely lesser effect in final PA due to revised loss thresholds, though no loss threshold specific to spring-run. Action Compone nt DCC Gate operations - Stressor/Fact or Transit times Shift in Operations Life Stage (Location) Juveniles Sacramento River -Delta JuvenilesSacramento River -Delta Life Stage Timing (Work Window Intersecti on) Juvenile migration and rearingDec - May Individual Response a nd Rationale of Effect Increased mortality due to increased migration times with concurrent increased exposure to predators Benefici al: High Severity of Stresso r/ Level of Benefit Sublethal to Lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta CVP/SWP exports Juvenile migration and rearing Dec- May Shift in exports toCVP from SWP to reduce impacts of predation from the CCFwhen capacity at CVP exists 778 Proportion of Population Exposed Medium gates open from Oct I through Nov 30, typically closed Dec I through Jan 31. Closed Feb 1 through May20. Estimated 5 %of juvenile SR population emigrates by the end of January Small Frequenc y of Exposure Low. DCC gates infrequent! y operated in December and January Medium Magnitu de of Effect Medium to High Medium Weight of Evidenc e HighThere are a number of publicati ons regard in g the relative survival in various North Delta and Central Delta migrator y routes; conclusi ons supporte d by modellin g results. Medium - Several studies show lower losses at the CVP for salvaged fish availabili ty of capacity Probable Change in Fitness Reduced survival; lesser effect in final PA due to revised DCC operations in DecemberJanuary Increased survival DCC Gate operations - Action Compone nt Routing Stressor/Fact or JuvenilesSacramento River -Delta AdultsSacramento RiverDelta Life Stage (Location) Jan- June Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Increased straying into t he Mokelumne River system when gates are opened, followed by migratory delays when gates are closed for water quality concerns Individual Response a nd Rationale of Effect Juvenile migration and rearing Dec- May Life Stage Timing (Work Window Intersecti on) Sublethal to Lethal Minor Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta DCC Gate operations - Increased entrainment and loss at the South Delta E xports facilities 779 Proportion of Population Exposed Low- gates opened infrequent! y in January, c losed February I -May 20 Small to Medium Frequenc y of Exposure Medium High Medium -tagging studies related to straying of Chinook through the DCC when open. Magnitu de of Effect Low Highnumerou s studies have evaluate d the potential risk to salmonid s entering the Delta interior and becomin g Weight of Evidenc e at the CVP is uncertain Lowsustained populati on effects on a small to medium proportio n of the populati on present in the Delta Probable Change in Fitness Delayed migration, possible reduction of spawn·ing success; lesser effect in final PA due to revised DCC operations in DecemberJanuary reduced survival; lesser effect in final PA due to revised DCC operations in DecemberJanuary Action Compone nt Routing Stressor/Fact or JuvenilesSacramento River -Delta Life Stage (Location) Juveniles Sacramento River -Delta North Bay Aqueduct Juvenile migration and rearingDec- May Increased mortality due to routing into the channels of the Lindsey Slough/ Barker Slough region Minor Minor Severity of Stresso r/ Level of Benefit Small Small Proportion of Population Exposed High exports occur on annual basis High Frequenc y of Exposure Magnitu de of Effect Individual Response a nd Rationale of Effect Juvenile migration and rearingDec - May Lowvery small proportio n of populati on will be present in Barker Slough, low impacts of diversion volumes on hydrody namics Low screens are designed for delta smelt criteria, few salmonid s expected to be Life Stage Timing (Work Window Intersecti on) Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta North Bay Aqueduct Entrainment and impingement onto fish screens Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. 780 Weight of Evidenc e vulnerabl e to entrainm ent at the fish salvage facilities. Medium -few Chinook salmon observed in regional monitori ng efforts in the past. No fish observed behind screens in monitori ng efforts. Highmonitori ng has few observati ons of Chinook salmon at this location, multiple studies Probable Change in Fitness reduced survival Minimal change in fitness North Bay Aqueduct North Bay Aqueduct Action Compone nt routing Impingement/ capture during aquatic weed cleaning Entrainment during sediment cleaning Stressor/Fact or Inj ury or death due to entrainment into dredge or impingement onto fish screens Individual Response a nd Rationale of Effect JuvenilesSacramento River -Delta Juvenile migration and rearingDec- May Life Stage Timing (Work Window Intersecti on) JuvenilesSacramento River -Delta Juvenile migration and rearingDec- May Juveniles Sacramento River -Delta Injury or death due to impingement, capture by grappling hooks during weed removal Life Stage (Location) Sublethal to Lethal Sublethal to Lethal Sublethal to Lethal Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta Delta CCWD Rock Slough water diversions Juvenile migration and rearingDec - May Delayed migration and increased transit times with potential for increased mortality due to routing into the channel of Rock Slough where predation is likely to be elevated 781 small Small Low. Aquatic weeds removed infrequent! y Low. Sediment removed infrequent! y Frequenc y of Exposure Magnitu de of Effect present at screen location Proportion of Population Exposed Small High pumping through the Rock Slough d iversion occurs every year Lowfish unlikely to be in area of screens during cleaning Lowfish unlikely to be in area of screens during cleaning Lowmedium - small numbers of fish are likely to be in the vicinity of the fish screens and intake Probable Change in Fitness minimal change in fitness Minimal change in fitness Low. No reports or studies available reduced fitness due to delay in migration or increased predation. Weight of Evidenc e regard in g efficienc yof positive barrier fish screens Low. No reports or studies available Medium -annual monitori ng reports indicate that no fish are entrained through the screens, however some Action Compone nt Stressor/Fact or Life Stage (Location) Juveniles Sacramento River -Delta AdultsDelta Transit times capture in sampling gear capture in sampling gear JuvenilesSacramento River -Delta Predator removal studies Water Transfers Life Stage Timing (Work Window Intersecti on) Juvenile migration and rearingOct- Nov -(yearling SR) Adult migration - Jan June Individual Response a nd Rationale of Effect Elevated river flows may reduce transit times through riverine reaches of the Delta Increased vulnerability to injury and mortality due to entanglement/en trapment in sampling gear Severity of Stresso r/ Level of Benefit Proportion of Population Exposed Frequenc y of Exposure Low Magnitu de of Effect Low Lowinfreque nt sampling over two to three years of study Low Small Small Low Small Sublethal to Lethal Sublethal to Lethal Low inireque nt sampling over two to three minor Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta Delta Predator removal studies Juvenile migration and rearing Dec - May Increased vulnerability to injury and predation due to entanglement/en trapment in sampling gear 782 Weight of Evidenc e fish are observed in front of the screens, and have been observed in historical monitori ng. Low. No reports or studies available Medium -Several reports from previous predator removal studies, literature on sampling methods. Medium -Several reports from previous predator removal Probable Change in Fitness increased fitness reduced survival reduced survival CVP Improvemen ts Action Compone nt Temporary change in water flow/water quality (20 days Oct-May, 60 days JuneSept) C02 Injections Stressor/Fact or JuvenilesSacramento River -Delta Life Stage (Location) Frequenc y of Exposure Low Proportion of Population Exposed High Low Severity of Stresso r/ Level of Benefit Small Low Individual Response a nd Rationale of Effect Sublethal to Lethal Low Magnitu de of Effect years of study Juvenile migration and rearing Dec- May Small increase in morbidity and mortality due to C02 exposure during predator clean outs of secondary channel Minor June)Juve nile migration and rearingDec - May (Jan - Adult migration Life Stage Timing (Work Window Intersecti on) Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Delta Suisun Marsh Roaring River Distribution System Food Subsidy Studies Adults and juveniles may migrate through the area on their way to spawning grounds or as outmigratin g juveniles. During the annual 20 days of periodic operation Oct May, individual adult spring-run may be delayed in their spawning migration from a few hours to several days. Juveniles may be delayed on 783 Weight of Evidenc e studies, literature on sampling methods. Medium -several studies show effective ness of C02 in removal of predators and sensitivit yof smaller fish to C02 exposure Mediumdata on Chinook salmon migratio nand rearing in Suisun Marsh is medium, based on a few studies of the Probable Change in Fitness Reduced fitness Minimal Action Compone nt Altered hydrodynamic sand migration routing in the Ship Channel Stressor/Fact or Adults and Juveniles Life Stage (Location) (Jan - Adult migration Life Stage Timing (Work Window Intersecti on) Sublethal to Lethal Severity of Stresso r/ Level of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Divisio n Delta Sacramento Deep Water Ship Channel Food Study June)Juve nile migration and rearingDec- May Individual Response a nd Rationale of Effect their downstream movements by closed gates for several hours while gates are closed on flood tides. Potential delays and false attraction to the opening and closing of the boat locks, potential diversion from Sacramento River into Deepwater ship channel when boat locks are open, exposure to reduced water quality in Port of Sacramento and Deepwater ship channel, increased exposure to angling and poaching, predation for juvenile fish 784 Proportion of Population Exp osed Low Frequenc y of Exposure Low Magnitu de of Effect Low Weight of Evidenc e Salinity gate operation s Low little informati on on springrun migratio n behavior and use within the Sacrame nto Deepwat ership channel, and Port of Sacrame nto Probable Change in F itness Reduced fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Overall for the Sacramento River basin and Delta ( Table 2.8.3-2), under the PA, there are 35 action components expected to create stressors for varioll!S life stages and 13 action components that benefit various life stages. (Table 2.8.3-3). Table 2.8.3-3. Summary of the number of PA components expected to create stressors or benefits of varying levels of magnitude to listed species as identified in Table 2.8.3-2. Magnitude Level Actions Creating Stressors Under the PA Actions C reating Benefits Under the PA High1 11 2 Medium 4 5 Low 20 6 TotaJ2 35 13 1 If the magnitude was a range that included "High" then that stressor or benefit was counted in the "High" category, and not recounted in the " Medium" or "Low" categories. 2 If the magnitude was identified as "Uncertain" or "NA", then that stressor or benefit was not counted. The Sacramento River water temperature stressor was only counted once for its impact on eggs and once for its impact on adults even though there are eight "High" magnitude stressor rows for those stressor-life stage combinations, because each row per life stage corresponds to a different tier and not an additional stressor. Similarly, the "Medium" magnitude beneficial actions related to the single issue of Sacramento River water temperature planning were counted once. While the entire suit,e of adverse and beneficial effects associated with the PA are described in Section 2.5 and summarized above in Table 2.8.3-2 and Table 2.8.3-3, water temperature management, low Sacramento River base flows, DCC gate operations, and CVP/SWP south Delta export operations warrant further exploration as the most significant PA-related factors affecting CV spring-run Chinook salmon. Each of those factors has a high weight of evidence suggesting there will be a high magnitude of effect on at least one life stage for at least one individual spring-run population. First, water temperature under the PA is expected to be a high magnitude stressor for CV springrun Chinook salmon in the Sacramento River and Clear Creek. It should be noted that CV spring-run Chinook salmon spawning in the Sacramento River are part of a small dependent population and are introgressed with fall-run Chinook salmon due to environmental baseline factors (large darns) as well as CVP/SWP-related impacts. Clear Creek is considered a Core 1 population in the NMFS salmonid recovery plan, though the population is currently small in most years. The PA's tiered cold water pool management approach for the Sacramento River, is expected to result in water temperature-dependent egg mortality every year given the water temperature-egg survival relationship and the available information on what water temperatures under the PA are likely to be. Mortality of Chinook salmon eggs in the river is expected to increase quickly as temperatures become warmer than 53.5°F (Swart 2016, Martinet al. 2017). Based on the water temperature modeling results from the ROC on LTO BA, Sacramento River water temperatures at CCR under the PA during CV spring-run Chinook salmon spawning and egg incubation in 785 Biological Opinion for the Long-Term Operation of the CVP and SWP August through October are expected to exceed 53.5°F for 76 percent of the days under tier 1, 80 percent of the days under tier 2, 97 percent of the days under tier 3, and 100 percent of the days under tier 4. Revisions to the Cold Water Pool Management section of the final PA include the addition of Section 4.10.1.3.3 Upper Sacramento Performance Metrics. The objective of these performance metrics is to ensure that the performance of the PA operations for temperature management falls within the modeled range, and shows a tendency towards performing at least as well as the distribution produced by the simulation modeling of winter-run Chinook salmon temperature dependent mortality. This revision affects the CV spring-run Chinook salmon analysis by increasing the certainty that the analysis more accurately characterizes exposure and risk to CV spring-run Chinook salmon due to the PA operations. With this change, we consider our previous analysis of the modeled outcomes of temperature management- which is based on the central tendency to capture the most likely conditions - to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management do not change quantitatively due to the revisions included in the final PA, as this commitment to assess cold water management does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected long-term proportion of years in each Tier type. Given that the modeling results are likely merely a coarse predictor of actual water temperatures that would occur under the P A, the examination of observed data provides another source of information to frame Sacramento R iver temperatures under PA implementation. The assumption that observed data on Sacramento River water temperature during August through October is a reasonable indicator of water temperatures that could occur with P A implementation is supported by the facts that: (I) the observed data reflect implementation of current operations; and (2) the modeling results show there is very little difference between the PA and COS water temperatures during those months. Therefore, recent observed data can serve as an indicator for expected water temperatures under the P A for months where the modeled P A and COS water temperatures are similar. In the ROC on LTO BA, Figure 6-1 shows that modeled Sacramento River water temperatures at CCR for the two scenarios are within 1°F of each other, with slightly warmer levels under the PA in September and slightly cooler levels in October, relative to the COS. Based on observed Sacramento River water temperatures at CCR from 2009 through 2018 during August through October, CV spring-run Chinook salmon have been exposed to water temperatures warmer than 53.5°F every year except for 2017. The range varies greatly, between less than 10 or more than 95 of percent of days with August through October water temperatures over 53.5°F in a given year from 2009 through 2017; 45 percent of the days in 2018 were over 53.5°F. The modeled PA water temperature projections at CCR indicate 76 to 100 percent of the days during the CV spring-run Chinook salmon egg incubation months of August through October are expected to be over 53.5°F every year. Observed data from 2009 through 2018 ranged greatly from 0 to 100 percent, which indicates thermal impacts on CV spring-run Chinook salmon eggs would be worse under the PA than they are in the baseline condition. The PA proposes a water temperature management approach to protect winter run Chinook salmon egg incubation, which may result in warmer temperatures for CV spring-run Chinook salmon egg incubation. The PA proposes to cease providing 53.5°F at CCR when the monitoring working group determines based on real-time monitoring that 95 percent of winter-run Chinook salmon eggs have hatched, 786 Biological Opinion for the Long-Term Operation of the CVP and SWP and alevin have emerged, or on October 31, whichever is earlier. Based on both modeling results and observed data from 2009 through 2018, the PAis expected to expose a large proportion of the Sacramento River population of CV spring-run Chinook salmon eggs to water temperatures warmer than 53.5°F as the end of October and November are key periods for egg incubation, resulting in water temperature-dependent egg mortality every year, and likely deepens the harm to this population, relative to baseline conditions. We do consider the proj ect components that are intended to offer as much protection as practicable in drought or extreme conditions, including the process for development of an annual temperature management plan, the use of conservative forecasts, protection of the third cohort of winter-run Chinook salmon after two consecutive years of poor survival, and specific "at the ready" actions for drought and dry years. The temperature management plan may reduce the likelihood of exceeding the temperature target, which is used in the characterization of exposure to increased temperatures in the analysis. The conservation measures intended to protect the third cohort of winter-run Chinook salmon after two consecutive years of poor survival may allow opportunities for ac6ons to be implemented to reduce temperature-related effects on spring-run Chinook salmon despite the probability of year types that may occur. Finally, NMFS expects a reduction in extreme effects on the species throughout extended drought due to the Drought and Dry Year Actions. We note that potential benefit of a toolkit of actions to be taken in drought conditions, and the process by which early warnings of drought conditions may allow for clear and swift development of a drought contingency plan. We also note that the action to reintroduce spring-run Chinook salmon to their historic habitat upstream of Shasta Reservoir included in the NMFS 2009 Opinion RP A that is not being carried forward as part of this PA would be an important addition to the tool kit to help the species withstand droughts. Water temperature and biological monitoring in Clear Creek indicate that CV spring-run Chinook salmon eggs are annually exposed to lethal water temperatures considering that the September 15th through October requirement for a daily average of 56°F at Igo has been exceeded almost every year since the requirement was established in the NMFS 2009 Opinion, about half of the CV spring-run Chinook salmon redds occur downstream from the Igo gauge, where they would be exposed to temperatures warmer than 56°F, and based on redd observations dates from 2003 through 2018, an average of 8 percent of CV spring-run Chinook salmon spawning occurs prior to September 15 (Provins 2019a). Additionally, the established 56°F requirement at Igo may not be as protective as intended, based on recent science indjcating that Chinook salmon egg mortality increases rapidly at water temperatures warmer than 53.5°F (Swart 2016, Martin et al. 20 17). As there is virtually no difference between the modeled PA and COS, this frequent lethality to a large proportion ofCV spring-run Chinook salmon eggs in Clear Creek currently occurring, is assumed to represent impacts expected under the PA (Figure 2). The next key stressor to spring-run Chinook salmon that will result from PA implementation is reduced Sacramento River base flows in the spring, which will limit access to food rich floodplain habitat and reduce juvenile survival. As the pre-dam hydrograph in Figure 2.5.2 2 shows, the median monthly flows for February through April would naturally have been at nearly double the flowrate currently managed to flow into the upper Sacramento in more recent decades. Under the PA minimum winter releases (described in Section 2.5.2.3.1.1 Winter Minimum Flows) will be maintained into the spring and until "flows are needed to support instream demands on the mainstem Sacramento River and Delta Outflow requirements" (U.S. Bureau of Reclamation 2019). Modeling confirms that for both the PA and the COS, early spring 787 Biological Opinion for the Long-Term Operation of the CVP and SWP (February -April) flows are maintained at minimum levels to build storage. Keeping flows at Keswick Dam artificially low restricts the river's "natural" physical, biochemical, and ecosystem functions such as floodplain connectivity (Yameli et al. 2015, Mount et al. 20 17), and limits juvenile salmon survival given that flow has repeatedly been the most important factor affecting overall survival of Chinook salmon in the Central Valley (Kjelson and Brandes 1989, Zeug et al. 2014, Michel et al. 2015, Iglesias et al. 20 17) In the Sacramento River, the dynamic natural flows that would result from unregulated tributary contributions have been replaced by a spring base flow - a single minimum instream flow intended to be sufficient to maintain aquatic species during crucial low-flow periods. This is in contrast to the tributaries of the upper Sacramento River, which mostly have unmodified hydrographs subject to a seasonal flow regime. This contrast, between the unmodified flows of the tributaries and the minimum flows in the mainstem, creates a hydrologic disconnect for juveniles migrating out of the tributaries. Juvenile CV spring-run Chinook salmon migration out of Mill and Deer creeks begins in mid-to-late April, extends through May, and is triggered by spring storm events or warming air temperatures causing rapid snowmelt. Peak migration out of these tributaries typically occurs early to mid-May according to 15 years of rotary screw trap data (1995-2010). And while CalSimii modeling ofthe PA and COS shows Keswick releases increasing in May for the PA, this increase is made in part to satisfy agricultural deliveries which then reduce flows downstream of the point of diversion (i.e., at Wilkins Slough). These diminishing flows are also described in the modeling for both the PA and the COS where average flows at Wilkins Slough in May are approximately 6,500-7,000 cfs, which is 1,2001,300 cfs lower than flows below Keswick Dam. For those fish originating from Battle, Cottonwood, and Clear creeks, as well as from the mainstem Sacramento River, juvenile migration past RBDD occurs November to May (University of Washington Columbia Basin Research 2019). These fish are therefore subject to the drastically reduced managed winter and spring flow hydrograph and the resulting low flow habitat conditions created by the winter and spring base flows. The spring pulse flow should help offset the otherwise low flow conditions by improving survival, but benefits associated with consistently higher base flows accompanied by floodplain inundation flows will be restricted under the PA. Under the PA, the DCC gates are expected to be opened more during October and November, and could be opened up to 10 days more during December through January for water quality concerns (compared to up to 3 days for water quality concerns, and some possible openings for experiments, under the COS). However, revisions to the PA not captured in the modeling include (a) the potential for increased fall flows in Above Normal and Wet years for the Fall Delta Smelt Habitat Action, which might reduce the DCC openings under the PAin October and November, and (b) clarifications that these additional DCC gate openings in December and January will only occur when drought conditions are observed (defined in the final, June 14, 2019, PA as "fall inflow conditions are less than 90 percent of historic flows") and modeling shows that DCC opening will avoid exceedance of a water quality concern level. This joint condition is expected to occur in less than 1 in 10 years, and Reclamation and DWR will coordinate with U SFWS, NMFS and the SWRCB on how to balance D-1641 water quality and ESA-listed fish requirements. The revised PA also included a new commitment to reduce combined CVP/SWP exports to health and safety levels (1,500 cfs) during any DCC gate opening in December or January. The revisions to DCC operations in the final PA lessens the resulting impacts from the expected impacts of the PA as first communicated by Reclamation to NMFS. During the months 788 Biological Opinion for the Long-Term Operation of the CVP and SWP of operation (gates open), approximately 5 percent of juvenile CV spring-run Chinook salmon may be subjected to entrainment where survival is reduced compared il:o remaining in the Sacramento River migratory route. In particular, yearling CV spring-run Chinook salmon from Mill, Deer, and Butte creeks, and other Sacramento River tributaries supporting the yearling life history strategy that are emigrating during the fall would be exposed to an open DCC gate more frequently under the PA than under the COS. These fish emigrate at larger sizes than juvenile YOY CV spring-run Chinook salmon, and are thus less likely to be observed in the trawls and other monitoring actions due to their ability to avoid them. Yearling spring-run Chinook salmon are expected to enter the Delta after precipitation events in the upper Sacramento River basin increase flows in the tributaries and the mainstem Sacramento River and stimulate the yearling CV spring-run to start emigrating downstream. This may occur as early as October and extends through January and February. These fish would likely encounter the open DCC gates prior to December 1, and anytime the gates are opened from December 1 through January 31 for water quality issues. The PA also extends the number of days transfers can occur (transfer window) for project and non-project water supplies through CVP and SWP. This PA component potentially affects all life stages of CV spring-run Chinook salmon, and increases the risk of entrainment, particularly juveniles, into the export faci lities, increasing the risk of mortality to exposed fish. Modeled OMR flows under the original PA will be approximately 3,500 to 4,000 cfs more negative during April and May in wetter water year types with the elimination of the San Joaquin inflow-to-export ntio under RPA 70° F delay migration timing, and >65• F increase stress and susceptibility to disease, leading to reduced fecundity, and increased prespawn mortality. Suboptimal temperatures >60° F cause stress and reduced growth, and susceptibility to disease and predation, and mortality. 822 Flow Conditions Stressor Eggs/ alevins: creekwide. Juveniles /smolts: creekwide Life Stage (Locatio n) Jan-Apr MayJune Life Stage (Timing) Flow decreases following pulse flows cause isolation and stranding. Down-ramping rates will reduce magnitude. Pulse flows transport sediment that can expose redds to scour and infiltration of fme sediment. Individual Response and Rationale of Effect Jan-Apr Jan-Apr stranding, Flow decreases following pulse flows cause isolation and Flow Conditions; Loss of Natural River Morphology and Function Flow Conditions Juveniles /smolts: creekwide Juveniles /smolts: creekwide Frequenc y of Exposure Magnitud e of Effect Medium Weight of Evidence Reduced sun ivai. Severity of Stressor/Lev el of Benefit Low Low Reduced sun•ival. of years) of years) (30-60% Probabl e C hange in Fitness Reduced sun•ival. High (annually) Medium Medium. Proportio n of Populatio n Exposed Medium Medium Medium Medium Sub-lethal High (annually) Medium Large Medium Medium Sub-lethal Sub-lethal Medium (30-60% Beneficial: medium Increase d growth. Improve d sun•ival. Increase d life history diversity. Biological Opinion for the Long-Term Operation of the CVP and SWP Division Spring attraction pulse flows Action Component Trinity (Clear Creek) Channel maintenance pulse flows Channel maintenance pulse flows Channel maintenance pulse flows Trinity (Clear Creek) Trinity (Clear Creek) Trinity (Clear Creek) Flow Conditions; Loss of Natural River Morphology and Function resulting in mortality. Down-ramping rates will reduce magnitude. Pulse flows improve downstream passage by creating migration cues, increasing turbidity, and increasing passage routes. High flows provide temporary 823 Fall and Winter Refill and Redd Maintenance Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function Stressor Migratin g, Spawn in gAdults (Upper Sacramen to River) Life Stage (Locatio n) Action Component Winter M inimum flows Life Stage (Timing) August Decembe r (October ' Novemb er) - January · June (January February ) Individual Response and Ra tion ale of Effect access to rearing habitat. Decreased month to month flows resulting in possible dewatering and stranding as decreased floodplain inundation and side-channel habitat isolated by reduced flows. Decreased month to month flows resulting in decreased floodplain inundation and a temporary loss of spawning habitat leading to steelhead redds being dewatered. Lethal Lethal Severity of Str essor/L ev el of Benefit Large Medium (33% 42%of redds potentially dewatered ) P r oportio n of Populatio n Exposed Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Redds, (Upper midSacramen to River) Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function 824 Frequenc y of Exposur e Low (20% of years) Low (20% of years) Magnitud e of Effect High High W eight of Evidence Reduced survival probabili ty P robabl e C ha nge in Fitness Reduced survival probabili ty Medium: Supported by select technical publicatio ns specific to the region and species. Quantitati ve results include average spawning flows to proposed minimum flows. Medium: Supported by a limited number of scientific and technical publicatio ns specific to the region and species. Quantitati ve results month-tomonth channel inundation Action Component Small Screen Program (Spawning/rea ring habitat restoration) Drought and Dry Year Actions Stressor Operation of new or repaired fish screens on water diversions. Entrainment/ Impingemen tat water diversions, Water Temperature Juveniles (Keswick DamRBDD) Juveniles (Middle Sacramen to River) Life Stage (Locatio n) April October (Uncertai n) Framework level action component. Programmatic action component. Construction activities are not described but operation is assumed to comply with NMFSand CDFW fish screening guidance. Life Stage (Timing) JanuaryJuly (May 15 - July) Individual Response and Rationale of Effect Beneficial: Low Beneficial: High Severity of Str essor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Drought and Dry Year Actions have been identified for winter-run Chinook salmon as a way to mitigate for temperatures higher than 53.5°F which result in reduced egg survival. 825 Proportio n of Populatio n Exposed Uncertain Medium Frequenc y of Exposure High (Permane nt) Low Magnitud e of Effect High, uncertain Medium Weight of Evidence 2006) (U.S. Fish and Wildlife Service 0 Low: (Program matic action componen t) very little informatio available as to how this action componen t would be implement ed (constructi on) or its effects when operated. High: Supported by multiple scientific and technical publicatio ns that include quantitativ e models specific to Probabl e C hange in Fitness Increase d survival probabili ty (NIMFS/ CDFW reduced fish screen in g criteria 5% loss) Increase d survival probabili ty Action Component Stressor Water Temperature Juveniles (Keswick Dam RBDD) Life Stage (Locatio n) Life Stage (Timing) JanuaryJuly (May IS -July) Individual Response and Rationale of Effect Beneficial: Low Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Drafting of Temperature Management Plan Usrng Conservative Forecasts These actions are expected to benefit steelhead that spawn in the Sacramento River as well, but to a lesser degree. Using conservative forecasts to inform the development of the Temperature Management Plan is expected to reduce the frequency of there being temperatures higher than 53.SOF during the winter-run Chinook salmon spawning and incubation period. It is expected to provide an indirect benefit to the other species, including steelhead, that spawn in the Sacramento River as well. 826 Proportio n of Populatio n Exposed Medium Frequenc y of Exposure High Magnitud e of Effect Medium Weight of Evidence the region and species. High: Supported by multiple scientific and technical publicatio ns that include quantitativ e models specific to the region and species. Probabl e C hange in Fitness Increase d survival probabili ty Action Component Tier I (Shasta Cold Water Pool Mgmt.) Winter Minimum flows Water Temperarure St ressor Juveniles (Keswick DamRBDD) Life Stage (Loca tio n) JanuaryJuly (May 15 - July) Life St age (Timing) Individual Response a nd Rationale of Effect Sub-lethal Severity of Stressor/L ev el of Benefit Beneficial: medium Temperatures in excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. ) Decembe r- April (Decemb erFebruary Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Spawn in g Adults, (Upper midSac ramen to River) Increased habitat carrying capacity (WUA) at lower flows providing improved spawning conditions. Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function 827 Proportio n of Populatio n Exposed Medium ( 12% of days >6J OF) Large Frequenc y of Exposure Medium Magn itud e of E ffect Weight of Evid ence Medium Medium (45 - 68% of years) Low (20% of years) Medium: Supported by multiple scientific and technical publicatio ns, however not specific to the region and species. High: Supported by multiple scientific and technical publicatio ns specific to the region and species. Quantitati ve results include WUA analysis. Probabl e Change in Fitness Reduced growth rate and survival probabili ty Increase d spawn in g success Action Component Tier 2 (Shasta Cold Water Pool Mgmt.) Tier 3 (Shasta Cold Water Pool Mgmt.) Tier 3 (Shasta Cold Water Pool Mgmt.) Water Temperature Stressor Life Stage (Locatio n) January July (May 15 - July) Life Stage (Timing) Individual Response and Rationale of Effect Sub-lethal Severity of Str essor/Lev el of Benefit Proportio n of Populatio n Exposed Medium (20% of days >61°F) Frequenc y of Exposure Low Medium Magnitud e of Effect Weight of Evidence Low Low Low Medium (17- 35% of years) Low (715%of years) Juveniles (Keswick DamRBDD) Sub-lethal Medium (44% of days >61°F) Temperatures in excess of 61 op can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Water Temperature Sub-lethal Low (715%of years) JanuaryJuly (May 15 -July) Juveni les (Keswick DamRBDD) October) Medium: Supported by multiple scientific and technical publicatio ns, however not specific to the region and species. Medium: Supported by multiple scientific and technical publicatio ns, however not specific to the region and species. Medium: Supported by multiple scientific and technical publicatio ns, Small (1% of days >68°F) Temperatures in excess of 6 1op can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Water Temperature Migratin g Adults (Keswick DamRBDD) - AugustDecembe r (August Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Temperatures higher than 68°F would cause increased disease and decreased swimming performance in adults, and 828 Probabl e C hange in Fitness Reduced growth rate, reduced survival Reduced growth rate Reduced growth, decrease d survival Action Component Tier 4 (Shasta Cold Water Pool Mgmt.) Tier 4 (Shasta Cold Water Pool Mgmt.) Stressor Water Temperature Water Temperature Juveniles (Keswick DamRBDD) Life Stage (Locatio n) Life Stage (Timing) JanuaryJuly (May 15 -July) - August Decembe r (August October) increased disease, impaired smoltification, reduced growth, and increased predation for late emigrating juveniles. Temperatures in excess of61°F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Individual Response and Rationale of Effect Low (57%of years) Frequenc y of Exposure Sub-lethal Medium (59% of days >6JOF) Low (5 7% of years) Proportio n of Populatio n Exposed Sub-lethal Medium (15% of days >68°F) Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Migratin g Adults (Keswick Dam RBDD) Temperatures higher than 68°F would cause increased disease and decreased swimming performance in adults, and increased disease, impaired smoltification, reduced growth, and increased 829 Magnitud e of Effect Low Low Weight of Evidence however not specific to the region and species. Medium: Supported by multiple scientific and technical publicatio ns, however not specific to the region and species. Medium: Supported by multiple scientific and technical publicatio ns, however not specific to the region and species. Probabl e C hange in Fitness Reduced growth rate Reduced reproduc tive success Construction or installation offish screens on water diversions. Passage Impediments I Barriers, Flow Conditions, Loss of Riparian Habitat and Instream Cover Stressor Small Screen Program (Spawning/rea ring habitat restoration) Water Temperature Action Component Delta Smelt Summer-Fall Habitat Life Stage (Locatio n) Adults, Juveniles (Middle Sacramen to River) Juveniles (Keswick DamRBDD) Life Stage (Timing) July Decembe r (Uncertai n), April - October (Uncertai n) JanuaryJuly (May IS -July) Individual Response and Rationale of Effect predation for late emigrating juveniles. Severity of Stressor/Lev el of Benefit Low Proportio n of Populatio n Exposed Low: (Uncertain ) Frequenc y of Exposure Sub-lethal Low Sublethal Low Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Framework programmatic action component. Construction activities are not described but assumed construction effects related to installation of fish screens include: changes in flow, stranding (installation of coffer dams), and handling. Temperatures in excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. 830 Magnitud e of Effect Low Low Weight of Evidence Low: (Program matic action componen t) very little informatio n available as to how this action componen t would be implement ed (constructi on). Low Probabl e C hange in Fitness Reduced survival probabili ty Decrease d survival probabili ty Action Component Juvenile Trap and Haul (tier 4 intervention) St ressor Juveniles (Upper Sacramen to River) Life Stage (Loca tio n) January July (Uncertai n) Life St age (Timing) Individual Response a nd Rationale of Effect Sub-Lethal Severity of Stressor/L ev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Monitoring, Maintenance , Research Srudies, etc. (minimizatio n for Water Temperarure s) timing and Uncertain. Programmatic action component. Increased stress and mortality related to capture and handling. Minimization measure intended to increase relative survival of Juvenile winterrun during Tier 4 water temperature operations. Depending on location of trap and haul operations, juvenile steelhead could be collected and returned to the river or relocated. 83 1 Proportio n of Populatio n Exposed Uncertain Low (5 7%of years) Frequenc y of Exposure Low Magn itud e of E ffect Low: (Program matic action componen t) very little informatio n available as to how this action componen t would be implement ed or as to its effects. Weight of Evid ence Probabl e Change in Fitness Decrease d growth rate, Decrease d survival probabili ty Wilkins Slough intakes (Cold water pool mgmt.) Construction or installation of fish screens on water diversions. Passage Impediments I Barriers, Flow Conditions, Loss of Riparian Habitat and Instream Cover Stressor Action Component Wilkins Slough intakes (Cold water pool mgrnt.) Adults, Juveniles (Middle Sacramen to River) Life Stage (Locatio n) Life Stage (Timing) Individual Response and Rationale of Effect , AprilOctober (JuneOctober) , July Decembe r (July October) AprilOctober (JuneOctober) Juveniles (Middle Sacramen to River) Framework programmatic action component, construction activities are not described. NMFS assumes that construction would occur during an appropriate inwater work window and include BMPs and minimization measures to limit potential effects to species Framework programmatic action component, operation is assumed to comply with NMFSand CDFW fish screening guidance. Beneficial: Low Sub-lethal Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Operation of new or repa ired tish screens on water diversions. Entrainment/ lmpingemen tat water diversions 832 Proportio n of Populatio n Exposed Small Small Uncertain (Construct ion) Frequenc y of Exposure Low Low Magnitud e of Effect Low: (uncertain ) very little informatio n available as to how this action componen t would be implement ed (constructi on). Weight of Evidence High (Perrnane nt) Low: (uncertain ) very little informatio n available as to how this action componen t would be implement ed or its effects when operated. Probabl e C hange in Fitness Decrease d survival probabili ty Increase d survival probabili ty Action Component Adult rescue (tier 4 intervention) Stressor Life Stage (Locatio n) July Decembe r (Uncertai n) Life Stage (Timing) Individual Response and Rationale of Effect October (Uncertai n) - JulyDecembe r (Uncertai n), April Adults (Middle Sacramen to River) Adults, Juveniles (Middle Sacramen to River) Passage Impediments I Barriers, Entrainment/ Impingemen tat water divers ions Low Beneficial: Beneficial: Low Severity of Str essor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Side-Channel habitat (Spawning/rea ring habitat restoration) Uncertain. Programmatic action component. Increased stress and mortality related to capture and handling. Minimization measure intended to increase relative survival of adult salmon ids entrained in water diversions (e.g. Yolo and Sutter Bypasses). Increased habitat quality and quantity. Framework programmatic action component, no description of timing, location or extent of effects. Riparian vegetation, Loss of Riparian Habitat and Instream Cover, Physical Habitat Alteration 833 Proportio n of Populatio n Exposed Small (Interventi on measure may not apply to steelhead) Uncertain Low (tier 4 years = 5-7% of all years) Frequenc y of Exposure Low Low Magnitud e of Effect Low: (Program matic action componen t) very little informatio n available as to how this action componen t would be implement ed or as to its effects. Weight of Evidence High (Permane nt) Low: (Program matic action componen t) very little informatio n available as to how or where this action componen t would be implement ed or the extent of its effects. Probabl e C hange in Fitness Increase d reproduc tive success, Increase d survival probabili ty Increase d growth rate Action Component Spawning Gravel Injection (Spawning/rea ring habitat restoration) Rice Decomp smoothing (fall ops.) St ressor Spawning Habitat Availability, Loss of Riparian Habitat and lnstream Cover, Physical Habitat Alteration Life St age (Timing) Increased habitat quality and quantity. Framework programmatic action component, no description of timing, location or extent of effects. Individual Response a nd Rationale of Effect Beneficial: Low Severity of Stressor/L ev el of Benefit n) Adults, Juveniles (Middle Sacramen to River) July Decembe r (Uncertai n, typical in-water work windows don't apply), April October (Uncertai n) Novemb er) (Uncertain) Low Beneficial: Migratin g, Spawn in gAdults (Upper Sacramen to River) . AugustDecembe r (October Life Stage (Loca tio Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function Framework programmatic action component. Proposed coordination may provide more reliable faU flows affecting action component Fall and Winter Refill and Redd Ma intenance (2.5.2.3.4.1) 834 Proportio n of Populatio n Exposed Uncertain Medium (33% 42%of redds potentially dewatered ) High (Permane nt) Frequenc y of Exposure Low Magn itud e of E ffect Weight of Evid ence Low Low (Uncertain ) Low: (Program matic action componen t) very little informatio n available as to how or where this action componen t would be implement ed or the extent of its effects. Low: (uncertain ) very little informatio n available as to how this action componen t would be implement ed or its effects. Probabl e C h ange in Fitness Increase d growth rate, Increase d lifetime reproduc tive success Increase d reproduc rive success Action Component Shasta TCD improvements (Cold water pool mgmt.) Operation of a Shasta Dam Raise Battle Creek Restoration (Cold water pool mgmt.) Frequenc y of Exposur e Magnitud e of Effect W eight of Evidence Stressor Severity of Str essor/L ev el of Benefit NA Low: (uncertain ) very little informatio n available as to how this action componen t would be implement ed or its effects. NA Individual Response and Ra tion ale of Effect NA NA Life Stage (Timing) P r oportio n of Populatio n Exposed NA NA Life Stage (Locatio n) NA NA NA NA NA NA NA NA None. Reclamation has committed to no change in operations with the inclusion of NA raise such that there will be no change in the frequency of meeting management criteria nor will there be any change in the timing and volume of releases. Covered under 2005 NMFS/USFWS Biological Opinions a Shasta Dam NA Water Temperature NA NA NA Framework programmatic action component. Unknown changes/moditic ations to existing TCD dependent on type/extent of Shasta Dam raise. Unknown effect. NA NA NA Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division Upper Sacramento /Shasta Division 835 P robabl e C ha nge in Fitness None None None (included in the baseline) Severity of Stressor/Lev el of Benefit Frequenc y of Exposure Magnitud e of Effect Weight of Evidence Stressor Action Component Individual Response and Rationale of Effect Life Stage (Timing) NA Life Stage (Locatio n) NA Probabl e C hange in Fitness NA Reduced sun•ival, reduced reproduc tive success NA NA high Proportio n of Populatio n Exposed NA NA high high NA NA high high NA Spring Mgmt. of Spawning Locations small high LateDec. early Apr sublethal high Reduced genetic integrity high Spawn in g Primarily upstream of Watt Ave. area LateDec.early Apr. medium American River Folsom!Nim bus releases - flow fluctuations Spawnin g Primarily upstream of Watt Ave. area sublethal medium small American River Nimbus Hatcheryhatchery 0. mykiss spawning with naturalorigin steelhead Yearround Reduced growth; Reduced sun•ival lethal American River Juvenile rearing Primarily upstream of Watt Ave. area Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento /Shasta Division American River American River American River Water temperatures warmer than life stage requirements , particularly occurring upstream of Watt Ave. through September during June Redd dewatering and isolation prohibiting successful completion of spawning Reduced genetic diversity. Garza et a!. (2008) showed that genetic samples from the population spawning in the river and the hatchery population were "extremely similar". Physiological effects increased susceptibility to disease (e.g., anal vent inflammation) and predation. Visible symptoms of thermal stress in juvenile steelhead are associated with exposure to 836 Stressor Life Stage (Timing) Individual Response and Rationale of Effect Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Action Component Life Stage (Locatio n) daily mean water temperatures above 65°F (Water Forum 2005a). From August through September in years 1999 through 2018, daily mean water temperatures were warmer than 65°F at Watt Avenue for 57 percent of days and warmer than 68°F for20 percent of days (Table 2.5.4-2 in section 2.5.4 American River Division). Modeled longterm average water temperatures at Watt Avenue from June through September under the proposed Project (including 2025 climate change simulation) range from 837 Proportio n of Populatio n Exposed Frequenc y of Exposure Magnitud e of Effect Weight of Evidence Probabl e C hange in Fitness Embryo incubatio n Primarily upstream of Watt Ave. area Stressor American River Water temperatures wanner than life stage requirements , particularly occurring upstream of Watt Ave. in April and May Action Component American River Folsom/Nim bus releases - flow fluctuations Life Stage (Locatio n) American River Embryo incubatio n Primarily upstream of Watt Ave. area Juvenile rearing Primarily upstream of Watt Ave. area Late-Dec -May Life Stage (Timing) LateDec.May Yearround Individual Response and Rationale of Effect approximately 66°F to 70°F (ROCLTO BA). Sub-lethal effects - reduced early life stage viability; direct mortality; restriction of life history diversity (i.e., directional selection against eggs deposited in Mar. and Apr.) Redd dewatering and isolation. Fry stranding and juvenile iso lation; low flows limiting the availability of quality rearing habitat including predator refuge habitat sublethal and lethal Severity of Stressor/Lev el of Benefit small small Proportio n of Populatio n Exposed medium medium high medium medium medium low high high Weight of Evidence Reduced survival Reduced survival Reduced sun•ival Probabl e C hange in Fitness Magnitud e of Effect lethal small Frequenc y of Exposure lethal Biological Opinion for the Long-Term Operation of the CVP and SWP Division American River American River American River Folsom/Nim bus releases - flow fluctuations; low flows, particularly during late summer and early fall 838 Action Component American River DCC Gate operations Stressor Life Stage (Timing) Individual Response and Rationale of Effect Severity of Stressor/Lev el of Benefit Life Stage (Locatio n) Jan.Jun. sublethal Smolt emigratio n Througho ut entire river sublethal to lethal sublethal lethal increased mortality due to routing into the delta interior with lower survival rates Increased mortality due to increased Physiological effects reduced ability to successfully complete the smoltification process, increased susceptibility to predation - Juveniles Sacramen to RiverDelta Juveniles - Sacramen Juvenile migratio nand Water temperatures warmer than life stage requirements , particularly occurring downstream of Watt Ave. during March through June Routing Transit times Juvenile migratio nand rearing Nov June Biological Opinion for the Long-Term Operation of the CVP and SWP Division American River Delta Delta DCC gate operations 839 Proportio n of Populatio n Exposed small mediumgates open from Oct I through Nov 30, typically closed Dec I through Jan 31. Closed Feb I through May20. Estimated 25%to 50% of juvenile SH population emigrates by the end of January. medium gates open from Oct Frequenc y of Exposure Magnitud e of Effect high Weight of Evidence Reduced survival; lesser effect in final PA due to revised DCC operation s in Decembe r-January medium High HighThere are a number of publicatio ns regarding the relative survival in variOus North Delta and Central Delta migratory routes; conclusio ns supported by modelling results. Reduced survival; lesser Probabl e C hange in Fitness Reduced growth; Reduced sun·ival High Medium to HighThere are medium low. DCC gates infrequent ly operated in December and January low. DCC gates infrequent Action Component DCC gate operations Stressor to River Delta Life Stage (Locatio n) rearing Nov June Life Stage (Timing) Individual Response and Rationale of Effect Juvenile migratio nand rearingNov June migration times with concurrent increased exposure to predators - Juveniles Sacramen to RiverDelta Minor to lethal Severity of Stressor/Lev el of Benefit Medium opening of gates reduces the proportion of riverine reaches adjacent to the Proportio n of Populatio n Exposed I through Nov30, typically closed Dec I through Jan 3 J. Closed Feb I through May20. Estimated 25% to 50% of juvenile SH population emigrates by the end of January. Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Altered Hydrodyna mics downstream of DCC location Increased mortality when gates are open due to changes in routing or transit time through interactions with changes in river flow and tidal 840 Frequenc y of Exposure ly operated in December and January High Magnitud e of Effect High Weight of Evidence a number of publicatio ns regarding the relative survival of Chinook salmon in various North Delta and Central Delta migratory routes but not steelhead; routing and transit time conclusio ns supported by modelling results. High There are a number of publicatio ns regarding the relative survival Probabl e C hange in Fitness effect in final PA due to revised DCC operation s in Decembe r-January reduced fitness and!or survival when gates are open; Jesser effect in final PA Stressor Life Stage (Timing) Individual Response a nd Rationa le of Effect Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Action Component Life Stage (Locatio n) influence downstream of DCC location and gate operations 84 1 Proportio n of Popula tio n Exoosed DCC location, closing of gates extends the riverine reaches farther downstrea m. All fish emigratin gin Oct and Nov have the potential to encounter open gates, fish emigratin gin drought year may encounter up to 10 days in Dec and January with gate in open position Frequenc y of Exposure Magnitud e of Effect Weight of Evidence of Chinook salmon, but not steel head in various North Delta and Central Delta migratory routes; hydrodyna mic conclusio ns supported by modelling and physical testing results. Probabl e C hange in Fitness due to revised DCC operation s in Decembe r-January Action Component CVP Improvements DCC Gate operations Stressor C02 injections Routing Juveniles Life Stage (Locatio n) Life Stage (Timing) Removal of predators from secondary channel at the Tracy Fish Collection Facility Individual Response a nd Rationa le of Effect Beneficial: High Severity of Stressor/Lev el of Benefit Adults Delta Sac ramen to River Delta - Juvenile migratio nand rearing OctApril Minor Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Adult migratio n JulyMay Increased straying into the Mokelumne River system when gates are opened, followed by migratory delays when gates are closed. Gate operations for water quality concerns 842 Proportio n of Popula tio n Exoosed medium Highgates opened over summer and into fall while adults are migrating. Potential for closures Nov- Jan. Frequenc y of Exposure high Magnitud e of Effect Weight of Evidence Medium high Highopened and closed annually Medium several studies have looked at predation impacts in the salvage process, long term effectiven ess of this method is not certain mediumtagging studies related to straying of Chinook through the DCC when open. Should apply to steel head Probabl e C hange in Fitness Increase d survival Delayed migratio n, possible reduction of spawnin g success; lesser effect in final PA due to revised DCC operation sin Decembe r-January Action Component CVP/SWP South Delta Exports Stressor Altered hydrodynam ics in south Delta/ routi ng Juveniles Life Stage (Locatio n) Life Stage (Timing) Individual Response a nd Rationale of Effect Sac ramen to RiverDelta Juveniles - Delta Juvenile migratio nand rearing NovJune Juvenile migratio nand rearing Nov June Sublethal to let hal Sublethal to let hal Severity of Stressor/ Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta CVP/SWP South Delta Exports Entrainment and loss at the south Delta export facilities Mortality or decreases in condition due to migratory delays in response to altered hydrodynamics in channels of the south Delta. Loss of appropriate migratory cues. De lays increase transit time and exposure to predators, poor water qual ity, and contaminants. Loss ranges from approximately 1-8 percent of Delta juvenile fish population at salvage facilities. See 2.8.5.2.5 Population Context below 843 Proportio n of Populatio n Exoosed Medium - small (overall CCV population ), medium to large for SJR baisn steelhead) Highcontinual exports Frequenc y of Exposure Medium Magnitud e of Effect Medium to Higheffects of hydrodyna micswell studied and modelled. Effects of hydrodyna mics on salmonid migrations in south Delta less certain. Weight of Evidence high Mediumsustained high frequency exposure on small proportion of population HighNumerous studies have evaluated the efficiency of the screening facilities, predation, as well as survival through the facilities Probabl e C hange in Fitness Reduced survival, reduced growth; likely lesser effect in fi nal PA due to revised loss threshold s. reduced survival; lesser effect in final PA due to revised loss threshold s. Action Component South Delta Agricultural Barriers Stressor Juveniles Life Stage (Locatio n) Life Stage (Timing) Sacramen to River Delta - transit times Juvenile migratio nand rearing NovJune transit times Adults Delta Individual Response and Rationale of Effect Sublethal to lethal Severity of Stressor/Lev el of Benefit Sublethal to lethal Delayed migration and increased transit times with potential for increased mortality due to increased exposure to predators Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta South Delta Agricultural Barriers Adult migratio n - July January (south DeltaSJ River populatio n) Delayed migration and increased transit times with potential for increased mortality due to increased exposure to warmer water conditions while 844 Proportio n of Populatio n Exposed medium includes SJR population Low- only SJ River population high high Frequenc y of Exposure Medium installatio n of barriers occurs during adult SH migratory period, exposure to the barriers is Medium installatio n of barriers occurs during Steethead migratory period, exposure to the barriers is expected to be low for Sacrament o River basin SH, high for SJR basin population SH. Magnitud e of Effect Medium several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of spring-run in the south Delta channels is well document ed by salvage records. Medium several studies have indicated that the barriers increase transit time through the south Weight of Evidence Probabl e C hange in Fitness Reduced sun•ival Reduced survival Action Component CVP/SWP exports DCC gate operations Stressor Shift in Operations - Sacramen to River Delta Juveniles Sacramen to RiverDelta - Juveniles Life Stage (Locatio n) Shift in exports to CVP from SWP to reduce impacts of predation from the CCF when capacity at CVP exists Sublethal to lethal Beneficial: High Severity of Stressor/Lev el of Benefit Juvenile migratio nand rearingOctApril Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Life Stage (Timing) Juvenile migratio n and rearing NovJune moving upriver over barriers Individual Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Increased entrainment and loss at the South Delta Exports facilities 845 Proportio n of Populatio n Exposed small Small to medium Frequenc y of Exposure medium High Magnitud e of Effect expected to be high for SJR basin population SH. medium Low sustained population effects on a small to medium proportion of the Weight of Evidence Delta and increase predation risks. Timing of spring-run in the south Delta channels is well document ed by salvage records. MediumSeveral studies show lower losses at theCVP for salvaged fish availabilit y of capacity at the CVP is uncertain High numerous studies have evaluated the potential risk to Probabl e C hange in Fitness Increase d survival Reduced survival; lesser effect in final PA due to revised DCC Action Component North Bay Aqueduct Stressor Routing - Juveniles Sacramen to River Delta - Sacramen to R iverDelta Juveniles Life Stage (Locatio n) small high Frequenc y of Exposur e Minor Severity of Str essor/L ev el of Benefit Increased mortality due to routing into the channels of the Lindsey Slough/ Barker Slough region Small Life Stage (Timing) Juvenile migratio nand rearingNovJune Minor high exports occur on annual basis P r oportio n of Populatio n Exposed Juvenile migratio nand rearingNovJune Individual Response and Ra tion ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta North Bay Aqueduct Entrainment and impingemen tonto fish screens Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough 846 population present in the Delta Magnitud e of Effect salmonids entering the Delta interior and becoming vulnerable to entrainme nt at the fish salvage facilities mediumfew salmonids observed in regional monitorin g efforts in the past. No fish observed behind screens in monitorin g efforts. High monitorin g has few observatio ns of salmonids at this location, multip le studies W eight of Evidence low- very small proportion of population will be present in Barker Slough, low impacts of diversion volumes on hydrodyna mics low screens are designed for delta smelt criteria, few salmon ids expected P robabl e C ha nge in Fitness operatoin sand revised Joss threshold s. reduced survival minimal change in fitness Action Component North Bay Aqueduct Stressor Impingemen tl capture during aquatic weed cleaning Entrainment during sediment cleaning North Bay Aqueduct routing Juverules - Juverules Sacramen to RiverDelta - Sacramen to RiverDelta - Juveni les Life Stage (Locatio n) Injury or death due to entrainment into dredge or impingement onto fish screens Life Stage (Timing) Juvenile migratio nand rearingNov June Juvenile migratio nand rearingNovJune Juvenile migratio nand rearingNovJune Pumping Plant intake. Individual Response and Ra tionale of Effect sublethal to lethal sublethal to lethal sublethal to lethal Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Delta CCWD!Rock Slough water diversions Sacramen to River Delta Injury or death due to impingement, capture by grappling hooks during weed removal De layed migration and increased transit times with potential for increased mortality due to routing into the channel of Rock Slough where predation is likely to be elevated 847 Small low. Sediment removed infrequent ly Frequenc y of Exposure Small low. Aquatic weeds removed infrequent ly P roportio n of Populatio n Exposed Small high pumping through the Rock Slough diversion occurs every year Magnitud e of Effect to be present at screen location low- fish unlikely to be in area of screens during cleaning low- fish unlikely to be in area of screens during cleaning low small numbers offish are likely to be in the vicinity of the fish screens and intake Weight of Evidence P robabl e C ha nge in Fitness minimal change in fitness minimal change in fitness regarding efficiency of positive barrier fish screens low. No reports or studies available low. No reports or studies available reduced fitness due to delay in migratio nor increased predation are Medium annual monitorin g reports indicate that no fish are entrained through the screens, however some fish observed in front of the screens, and have Action Component Predator removal studies Predator removal studies CVP Improvements Stressor capture in sampling gear capture in sampling gear C02 Injections Juveniles - Juveniles Sacramen to RiverDelta - AdultsDelta Life Stage (Locatio n) Increased vulnerability to injury and mortality due to entanglement/en trapment in sampling gear Life Stage (Timing) Adult migratio n JulyMay Increased vulnerability to injury and predation due to entanglement/en trapment in sampling gear Juvenile migratio nand rearingOct April Juvenile migratio nand rearingNov June Individual Response and Rationale of Effect Sub-lethal to lethal Sublethal to lethal Sublethal to lethal Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Delta Sacramen to RiverDelta Small increase in morbidity and mortality due to C02 exposure during predator clean outs of secondary channel 848 Proportio n of Populatio n Exposed Small small (overall CCV population ), medium to large for SJR baisn steelhead) small low Lowinfrequent sampling over two to three years of study Lowinfrequent sampling over two to three years of study Magnitud e of Effect low low Frequenc y of Exposure high Weight of Evidence been observed m historical monitorin g. MediumSeveral reports from previous predator removal studies, literature on sampling methods. MediumSeveral reports from previous predator removal studies, literature on sampling methods. Medium several studies show effectiven ess of C02 in removal of Probabl e C hange in Fitness reduced survival reduced survival Reduced fitness Action Component Suisun Marsh Roaring River Distribution System Food Subsidy Studies Water Transfers low flows Temporary change in water flow/ water quality (20 days OctMay, 60 days JuneSept) Stressor AdultsDelta Adults and juveniles may migrate through the area on their way to spawning grounds or as outmigrat ing juveniles. Life Stage (Locatio n) Adult migratio n (July May) and juvenile ernigrati on (Nov - June). Life Stage (Timing) Individual Response and Rationale of Effect Severity of Stressor/Lev el of Benefit Proportio n of Populatio n Exposed Large low Beneficial: low minor Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Adult migratio n JulyMay During the annual 70 to 80 days of periodic operation, individual adult steelhead may be delayed in their spawning migration from a few hours to several days. Juveniles may be delayed on their downstream movements by closed gates for several hours while gates are closed on flood tides. Elevated river flows may reduce straying by providing stronger homing cues to adult steelhead migrants in the lower reaches of the Delta 849 Frequenc y of Exposure Low low Magnitud e of Effect low low Weight of Evidence predators and sensitivity of smaller fish to C02 exposure Low- data on steelhead migration and rearing in Suisun Marsh is low low. No reports or studies available Probabl e C hange in Fitness minimal increased fitness Action Component Water Transfers Fall Delta Smelt Habitat Operatio ns Stressor Juveniles Life Stage (Locatio n) Life Stage (Timing) Adults and Juveniles AdultsDelta Sacramen to River Delta - Transit times Temporary change in water flow/water quality Juvenile migratio nand rearing Nov June Adult upstream migratio n (July May) Individual Response and Rationale of Effect Sublethal to Lethal Minor benefit Beneficial: low Severity of Str essor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Delta Sacramento Deep Water Ship Channel Food Study Altered hydrodynam ics and migration routing in the Ship Channel Adult migratio n (July May) and juvenile emigrati on (Nov - June). Elevated river flows may reduce transit times through riverine reaches of the Delta Potential changes in Delta hydrodynamics due to export reductions and increased Delta inflow from upstream may create better flow attractions for upstream migrations of adult steelhead Potential delays and false attraction to the opening and closing of the boat locks, potential diversion from Sacramento River into Deepwater ship channel when boat locks are open, exposure to reduced water quality in Port of Sacramento and Deepwater ship channel, increased 850 high low Medium (Septembe rand October of above normal and wet water year types) low Frequenc y of Exposure low Low adult steel head already migrate upstream during this period low Magnitud e of Effect Low little informatio n available on adult migration cues in the Delta low. No reports or studies available Weight of Evidence Proportio n of Populatio n Exposed Small low 0 Lowlittle informatio non steelhead migration behavior and use withln the Sacrament 0 Deepwate rship channel, and Port of Sacrament Minimal benefit Probabl e C hange in Fitness increased fitness Reduced fitness Action Component Stressor Floodplain Habitat PA Conditions Lack of overbank flow to inundate rearing habitat Conservation Measure Lower San Joaquin River Habitat PA Conditions Life Stage (Locatio n) Juvenile rearing and migration Juvenile rearing Confluen ce of Stanislau Mossdale s to Juvenile rearing Confluen ce of Stanislau s to Mossdale Severity of Stressor/Lev el of Benefit Life Stage (Timing) Proportio n of Populatio n Exposed Individual Response and Rationale of Effect Beneficial: High Medium (likely medium exposure once completed c juvenile fish exposure to angling and poaching, predation for Dec-May for rearing; Feb-June for migratio Sublethal and indirectly lethal via predation Medium Medium depending on project design) , Dec-May Dec-May Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller Sublethal and indirectly lethal via predation n Biological Opinion for the Long-Term Operation of the CVP and SWP Division San Joaquin River San Joaquin River San Joaquin River Reduction in rearing habitat complexity due to reduction in channel forming flows 851 Frequenc y of Exposure Medium (likely medium frequency of exposure once completed , depending on project design) High High Magnitud e of Effect High (applicabl e once project completed ) Medium to High Medium to High Weight of Evidence High (for beneficial effects of floodplain habitat); Low (for likelihood will be completed by 2030 given complexit y of project) Medium Medium Probabl e C hange in Fitness Increase d survival, increased growth Reduced growth rates; Reduced survival Reduced growth rates; Reduced survival Action Component PA Conditions PA Conditions PA Conditions Stressor Springtime water temperatures warmer than life history stage requirements , primarily March-May Suboptimal flow Life Stage (Locatio n) Juvenile migration Confluen ce of Stanislau s to Mossdale Juvenile outmigration Confluen ce of Stanislau s to Mossdale Juvenile outmigration Confluen ce of Stanislau s to Moss dale Severity of Stressor/Lev el of Benefit P roportio n of Populatio n Exposed Life Stage (Timing) Medium Individual Response and Ra tionale of Effect Sublethal and indirectly lethal via predation size at time of emigration; Dec-May Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Medium Medium FebJun Sublethal Sublethal and indirectly lethal via predation Feb Jun Fish do not leave reach of river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased res idence time and higher risk of predation Fish do not leave reach of river before temperatures rise at lower river reaches and in Delta; thermal stress; Biological Opinion for the Long-Term Operation of the CVP and SWP Division San Joaquin River San Joaquin River San Joaquin River Water temperatures warmer than life history stage requirements , primarily in May and June 852 Frequenc y of Exposure Medium High High Magnitud e of Effect Medium to High Medium to High Medium Medium Medium to High Weight of Evidence Reduced growth rates; Reduced survival P robabl e C ha nge in Fitness outmigra lion timing ill Reduced sun•ival; Reduced diversity Medium lD Reduced survival; Reduced diversity outmigra tion timing Action Component Seasonal operations and Stepped Release Plan Seasonal operations and Stepped Release Plan Excessive fmes in spawning gravel resulting from lack of overbank flow Stressor Egg incubatio nand emergenc e Goodwin Dam to Orange Blossom Bridge Life Stage (Locatio n) Dec-June Life Stage (Timing) Egg mortality from lack of interstitial flow; egg mortality from smothering by nest-building activities of other CCV steelhead or fallrun; suppressed growth rates Egg mortality, Embryonic deformities Individual Response and Ra tionale of Effect Jan. Jun. Dec-June Water temperatures warmer than life history stage requirements Bridge Egg incubatio nand emergenc e Goodwin Dam to Orange Blossom Suboptimal flow (March -June) Smolt emigratio n Stanislau s River High Frequenc y of Exposure High High Magnitud e of Effect Medium Medium Medium Weight of Evidence Reduced survival Severity of Stressor/Lev el of Benefit Medium Medium to High P robabl e C ha nge in Fitness Reduced sun•ival Medium (between 2%and 70%of eggs) High Lethal Sublethal and Lethal Medium Reduced sun•ival; Reduced diversity P roportio n of Populatio n Exposed Medium (between 2%and 70%of eggs) Sublethal and indirectly lethal via predation Biological Opinion for the Long-Term Operation of the CVP and SWP Division East Side Division East Side Division East Side Division Seasonal operations and Stepped Release Plan Fish do not leave reach of river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of predation 853 Seasonal operations and Stepped Release Plan Lack of overbank flow to inundate rearing habitat Stressor Juvenile rearing Goodwin Dam to Orange Blossom Bridge Juvenile rearing Goodwin Dam to Orange Blossom Bridge Life Stage (Locatio n) Year round Life Stage (Timing) Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Individual Response and Rationale of Effect Action Component Seasonal operations and Stepped Release Plan Reduction in rearing habitat complexity due to reduction in channel forming flows Juvenile rearing Goodwin Dam to Orange Blossom Bridge Year round, with temperat ure stress likely most acute JulySeptemb er Dec-Feb Year round Seasonal operations and Stepped Release Plan End of summer water temperatures warmer than life history stage requirements Sublethal Sublethal and indirectly lethal via predation Sublethal and indirectly lethal via predation Sublethal and indirectly lethal via predation Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Division East Side Division East Side Division East Side Division East Side Division Seasonal operations and Stepped Release Plan Spawnin g Goodwin Dam to Orange Reduced sui table spawning habitat; For individual: increased energy Excessive fmes in spawning gravel resulting from lack of 854 Proportio n of Populatio n Exposed Medium Medium Medium Medium Frequenc y of Exposure Magnitud e of Effect Medium Weight of Evidence Medium Reduced growth rates; Reduced survival Probabl e C hange in Fitness Reduced growth rates; Reduced survival Medium to High Reduced growth rates; Reduced survival Medium to High Medium to High Medium to High Medium Medium High High Medium High Reduced reproduc tive success Stressor Blossom Bridge Life Stage (Locatio n) Individual Response and Rationale of Effect Life Stage (Timing) overbank flow Severity of Stressor/Lev el of Benefit Medium Proportio n of Populatio n Exposed Sublethal Small Medium Jan.Jun. Missing triggers to elect anadromous life history; failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; Minor Beneficial: medium Juvenile steel head present upstream of action area Juvenile steelhead are primarily present upstream of OBB, however, few may be migrating through duri.ng summer months, and may be exposed to Dec-Feb Adult spawning Juvenile steelhead upstream ofOBB in summer Smoltific arion and ernigratio n Stanislau s River at mouth Spawning Habitat Temporary Low DO Barrier Water temperatures warmer than life history stage requirements (Mar- June) cost to attempt to "clean" excess fine material from spawning site Increased suitable spawning habitat; Biological Opinion for the Long-Term Operation of the CVP and SWP Division East Side Division Conservation Measure Spawning and Habitat Restoration Action Component East Side Division Seasonal operations and Stepped Re lease Plan East Side Division 2.5.7.1.3 Alteration of Stanisla1Us River Dissolved Oxygen Requirement (7.0 mg!L) 31 miles upstream to Orange 855 Frequenc y of Exposure High (Once completed , habitat will be available each year) Low (while June temps are unsuitable for smoltificat ion in 70%of years, very few steelhead likely smolt at that time) Low Medium High Weight of Evidence Low Reduced diversity. Increase d reproduc tive success Probabl e C hange in Fitness Magnitud e of Effect Low Medium Medium Low Action Component Blossom Bridge (OBB) Temporary Low DO Barrier Stressor Adult steelbead upstream ofOBB in summer Life Stage (Locatio n) Life Stage (Timing) Adult steelbead present upstream of action area Individual Response a nd Rationa le of Effect Minor Severity of Stressor/Lev el of Benefit Small Proportio n of Popula tio n Exoosed Biological Opinion for the Long-Term Operation of the CVP and SWP Division East Side Division 2.5.7.1.3 Alteration of Stanislaus River Dissolved Oxygen Requirement(7.0 mgfL) 31 miles upstream to Orange Blossom Bridge (OBB) reduced DO. This would be for a short period of time, and a difference of approximately 1-2 mg!L, which is not expected to have a significant effect. Adult steelhead are primarily present upstream of OBB, however, few maybe migrating through during summer months, and maybe exposed to reduced DO. This would be for a short period oftime, and a difference of approximately 1-2 mg!L, which is not expected to have a significant effect. 856 Frequenc y of Exposure Low Magnitud e of Effect Low Medium Weight of Evidence Low Probabl e C hange in Fitness Stressor Juvenile rearing Life Stage (Locatio n) Year round Year round Life Stage (Timing) Individual Response and Ra tionale of Effect Beneficial: low Minor Severity of Stressor/Lev el of Benefit Biological Opinion for the Long-Term Operation of the CVP and SWP Construction of Spawning and Rearing Habitat Juvenile rearing Division East Side Division Conservation Measure Spawning and Habitat Restorat1on Rearing Habitat Action Component East Side Division Conservation Measure Spawning and Habitat Restoration Short term behavioral disruption and displacement to alternate rearing habitat. Increased food supply; increased growth rates; refuge from predation; larger size at time of emigration 857 P roportio n of Populatio n Exposed Small Medium Frequenc y of Exposure High (goal is to place gravel every year) Medium (Once completed , habitat will be available each year, but extent likely to vary with flow, depending on design criteria) Low(due to extent of restoration compared to length of river) Low Magnitud e of Effect High High Weight of Evidence P robabl e C ha nge in Fitness Reduced growth Increase d survival, increased growth Biological Opinion for the Long-Term Operation of the CVP and SWP 2.8.5.2 Assess Risk to CCV Steelhead by Division and Associated Diversity Group Population viability is determined by four parameters: abundance, productivity, spatial structure, and diversity. Both population spatial structure and diversity (behavioral and genetic) provide the foundation for populations to achieve abundance levels at or near potential carrying capacity and to achieve stable or increasing growth rates. Spatial structure on a watershed scale is determined by the availability, diversity, and utilization of properly functioning conditions (habitats), as defined in McElhany et al. (2000), and the connections between such habitats. Thus, reductions in the quantity or quality of available habitat are assumed to reduce a population's spatial structure. 2.8.5.2.1 Northwestern California Diversity Group 2.8.5.2.1.1 Assess Risk to Clear Creek CCV Steelhead As described in section 2.5, habitat conditions in Clear Creek, the Sacramento River, and the Delta are negatively affected by the PAin a number of ways. CCV steelhead originating from the Clear Creek watershed are exposed to altered river flows that diminish the long-term sustainability of the population. Releases of water to the Clear Creek stream channel below Whiskeytown Dam are generally insufficient to sustain natural riverine processes and functions. In addition, dam releases are often insufficient to maintain adequate water temperature and flows below the dam for the entire year. These stressors, coupled with the additional stressors identified for the main stem Sacramento River and Delta, reduces the population's current spatial structure (by reducing habitat quantity and quality), which, in turn, reduces the likelihood of recovery for the Clear Creek CCV steelhead population. Adult CCV steelhead typically migrate into Clear Creek from late August through April. Spawning occurs from mid-December through April, with over 90 percent occurring by midFebruary (Schraml et al. 2018). Redds are located from Whiskeytown to the confluence, with the highest proportion located downstream of river mile 6 (Schaefer et al. 20 19). Early migrating adults and rearing juveniles located downstream of the compliance point at IGO may be exposed to unsuitable water temperature in the summer months. Exposure to stressful water temperatures during juvenile rearing is likely to reduce the spatial structure and factors that influence productivity (e.g., growth rate). The diversity of Clear Creek steelhead also may be affected by the PA. Water releases from Whiskeytown Dam has changed the thermal regime and likely the food web structure of Clear Creek. While further research is still needed on the mechanisms driving residency and anadromy in 0. mykiss, environmental conditions experienced in the early fresh water life stages (e.g., water temperature, fllow) may influence frequency of anadromy (Kendall et al. 2014). Without knowing the role that resident 0. mykiss play in population maintenance and persistence of anadromous 0. mykiss, it is difficult to assess whether the current conditions on Clear Creek, which may favor residency, are detrimental to the anadromous population in Clear Creek or not (Lindley et al. 2007). All of the above factors, which reduce the spatial structure, productivity and abundance of Clear Creek CCV steelhead, compromise the capacity for this population to respond and adapt to environmental changes. In addition to impacts to the spatial structure and productivity, the PA is 858 Biological Opinion for the Long-Term Operation of the CVP and SWP expected to result in direct mortality to CCV steelhead. PA-related sources of CCV steelhead mortality include: (1) entraining juveniles into the Central and South Delta (as described in detail in the supplemental Delta analysis in Section 2.5.5.11, revisions to DCC operations in the final PA somewhat reduce this effect relative to the original PA); (2) entraining and impinging juveniles at the pumps (both direct and indirect loss; as described in detail in the supplemental Delta analysis in Section 2.5.5.11, revisions to loss thresholds and commitments to review and technical assistance in the final PA provide some assurance that species risks will be conservatively managed and reduce this effect relative to the original PA); and (3) loss associated with the CHTR program. Future projections over the duration of the PA (i.e., through 2030), considering both increasing water demands and climate change, exacerbate risks associated with continuation of the PA, further increasing the risk of the population. 2.8.5.2.2 Basalt and Porous Lava Diversity Group 2.8.5.2.2.1 Assess Risk to Mainstem Sacramento River CCV Steelhead As described in Section 2.5 and summarized in Table 2.8.5-2, habitat conditions in the mainstem Sacramento River are negatively affected by the PA in a number of ways, including, but not limited to: (1) regulating flows in a way that impairs natural river processes; and (2) providing flows and water temperatures in the lower reaches Sacramento River spawning habitat that are stressful to CCV steelhead. These stressors, coupled with the additional stressors identified for the Delta, reduces the Sacramento River CCV steelhead! population's current spatial structure by reducing habitat quantity and quality. The diversity of mainstem Sacramento River CCV steelhead also may be affected by the PA. Water releases from Shasta Dam has changed the thermal regime and the food web structure of the Sacramento River (Lieberman et al. 2001) such that a resident life history strategy may have fitness advantages over anadromous forms (McEwan 2001, Lindley et al. 2006). Little is known about the relationship of resident and anadromous forms of 0. mykiss. Without knowing the role that resident 0. mykiss play in population maintenance and persistence of anadromous 0. mykiss, it is difficult to assess whether the current conditions on the Sacramento River, which may favor residency, are detrimental to the anadromous population in the Sacramento River or not (Lindley et al. 2007). Zimmerman et al. (2008) did demonstrate that resident rainbow trout can produce anadromous smolts and anadromous steelhead can produce resident rainbow trout in the Central Valley. However, the study indicated that the proportion of resident rainbow trout to anadromous steelhead in the Central Valley is largely in favor of the resident form, and is even more prominent in the Sacramento River where about 92 percent (142 out of 154) of 0. mykiss sampled were offspring of resident adults (Zimmerman et al. 2008). Only 1 out of the 154 0. mykiss sampled showed an anadromous migratory history, although the sampling was not intended to be selective for adults, so some fish sampled may not yet have made their downstream migration to the ocean. Revisions to the Cold Water Pool Management section of the final PA include the addition of Section 4.10.1.3.3 Upper Sacramento Performance Metrics. The objective of these performance metrics is to ensure that the performance of the PA operations for temperature management falls within the modeled range, and shows a tendency towards performing at least as well as the distribution produced by the simulation modeling of winter-run Chinook salmon temperature dependent mortality. This revision affects the steelhead analysis by increasing the certainty that 859 Biological Opinion for the Long-Term Operation of the CVP and SWP the analysis more accurately characterizes exposure and! risk to steelhead due to the PA operations. With this change, we consider our previous analysis of the modeled outcomes of temperature management - which is based on the central tendency to capture the most likely conditions - to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management do not change quantitatively due to the revisions included in the final PA, as this commitment to assess cold water management does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected longterm proportion of years in each Tier type. We do consider the PA components that are intended to offer as much protection as practicable in drought or extreme conditions, imcluding the process for development of an annual temperature management plan, the use of conservative forecasts, protection of the third cohort of winter-run Chinook salmon after two consecutive years of poor survival, and specific "at the ready" actions for drought and dry years. The temperature management plan may reduce the likelihood of exceeding the temperature target, which is used in the characterization of exposure to increased temperatures in the analysis. The conservation measures intended to protect the third cohort of winter-run Chinook salmon after two consecutive years of poor survival may allow opportunities for ac6ons to be implemented to reduce temperature-related effects on CCV steelhead despite the probability of year types that may occur. Finally, NMFS expects a reduction in extreme effects on the species throughout extended drought due to the Drought and Dry Year Actions. We note that potential benefit of a toolkit of actions to be taken in drought conditions, and the process by which early warnings of drought conditions may allow for clear and swift development of a drought contingency plan, but we also consider that managing a listed species in a crisis-management scenario is not a long-term strategy to avoiding extirpation. All of the above factors, which reduce the spatial structure, diversity, and abundance of mainstem Sacramento River CCV steelhead, compromise the capacity for this population to respond and adapt to environmental changes. In addition to impacts to the spatial structure and possibly life history diversity, the PA is expected to result in direct mortality to CCV steelhead. PA-reRated sources ofCCV steelhead mortality include: (1) redd dewatering in the upper Sacramento River; (2) entraining juveniles into the Central and South Delta (as described in detail in the supplemental Delta analysis in Section 2.5.5.11, revisions to DCC operations in the final PA somewhat reduce this effect relative to the original PA); (3) entraining and impinging juveniles at the pumps (both direct and indirect loss; as described in detail in the supplemental Delta analysis in Section 2. 5.5 .11, revisions to loss thresholds and commitments to review and technical assistance in the final PA provide some assurance that species risks will be conservatively managed and reduce this effect relative to the original PA); and (4) loss associated with the CHTR program. Future projections over the duration of the PA (i. e., through 2030), considering both increasing water demands and climate change, exacerbate risks associated with continuation of the PA, further increasing the risk of the population. 2.8.5.2.3 Northern Sierra Nevada Diversity Group 2.8.5.2.3.1 Assess Risk to American River CCV Steelhead As described above, habitat conditions in the lower American River are negatively affected by the PA to such a degree that the survival, growth, and reproductive success of multiple steelhead 860 Biological Opinion for the Long-Term Operation of the CVP and SWP life stages is reduced. For example, American River steelhead are exposed to stressful water temperatures during spawning, embryo incubation, juvenile rearing, and smolt emigration. Based on the entire effects analysis, it is apparent that the water temperatures and flows expected with implementation of the PA will continue to substantially limit the quantity and quality of habitat, thereby limiting the spatial structure of American River steelhead. These limitations to the spatial structure of a population which have already been blocked off from all of its historic spawning habitat certainly reduces the viability of American River steelhead. The behavioral and genetic diversity of American River steelhead also is expected to be negatively affected by the P A. Warm water temperatures in the American River under the proposed PA are expected to result in higher fitness for steelhead spawned early (e.g., January) in the spawning season, as eggs spawned later (e.g., March) would be exposed to water temperatures above their thermal r,equirements (see Assess Species Response, Section 2.5, above). This selective pressure towards earlier spawning and incubation would truncate the temporal distribution of spawning, resulting in a decrease in population diversity. The genetics of American River steelhead have been completely altered by Nimbus Fish Hatchery operations and the historical use of out of basin hatchery stocks. Nimbus Fish Hatchery Steelhead Program has been working to address these issues by examining the potential to replace the Nimbus Fish Hatchery steelhead broodstock with genetically appropriate sources, although a change in hatchery practices is uncertain. Release of juvenile hatchery steelhead inriver (Sunrise location) was also done experimentally in March 2019, and is expected to minimize straying of returning adults relative to Sacramento River release sites (Discovery Park location). In addition to the negative effects on the spatial structure and diversity, the PAis expected to reduce the abundance of American River steelhead. Direct mortality (e.g., redd dewatering, water temperature-related egg mortality) associated with proposed operations has been documented at both the egg and juvenile life stages. The fitness consequences from water temperature-related effects on juveniles (e.g., compromised immune system, increased predation, reduced energy for growth) also would be expected to negatively affect the population growth rate. The combined effects of the PA on the spawning, embryo incubation, juvenile rearing, and smolt emigration life stages of CCV steelhead in the American River, reduces the viability of the population and places the population, which was already at high risk of extinction (see Section 2.5 Status ofAmerican River Steelhead), at even greater risk. This notion is especially supported considering that Naiman and Turner (2000) demonstrated how even shght reductions in survival from one life stage to the next at each and every life stage can have serious consequences for the persistence of a population, and the P A reduces the survival of each CCV steelhead life stage, including the life stage transition from smolt to adult-sized fish in the ocean. Although the PA does not directly affect CCV steelhead in the ocean, it indirectly lowers their ocean survival because they are entering it in a weakened state. Increased water demand is expected to result in considerable challenges to flow and water temperature management for American River aquatic resources below Nimbus Dam, and will likely exacerbate the adverse habitat conditions already occurring in the river under present day water demands. In addition to increasing water demands, climate change is expected to further degrade the suitability of habitats in the Central Valley through increased temperatures, 861 Biological Opinion for the Long-Term Operation of the CVP and SWP increased frequency of drought, increased frequency of flood flows, and overall drier conditions (Lindley et al. 2007). All of the above factors, which reduce the spatial structure, diversity, and abundance of American River CCV steelhead, compromise the capacity for this population to respond and adapt to environmental changes. In addition to impacts to the spatial structure and life history diversity, the PA is expected to result in direct mortality to CCV steelhead. PA-related sources of CCV steelhead mortality include: (1) redd dewatering; (2) entraining juveniles into the Central and South Delta (as described in detail in the supplemental Delta analysis in Section 2.5.5.11, revisions to DCC operations in the final PA somewhat reduce this effect relative to the original PA); (3) entraining and impinging juveniles at the pumps (both direct and indirect loss; as described in detail in the supplemental Delta analysis in Section 2.5.5. 11, revisions to loss thresholds and commitments to review and technical assistance in the final PA provide some assurance that species risks will be conservatively managed and reduce this effect relative to the original PA); and (4) loss associated with the CHTR program. Future projections ov,e r the duration of the proposed PA (i.e., through 2030), considering both increasing water demands and climate change, exacerbate risks associated with continuation of the PA, further increasing the risk of the population. 2.8.5.2.4 Southern Sierra Nevada Diversity Group 2.8.5.2.4. 1 Assess Risk to Stanislaus River CCV Steelhead Habitat conditions in the Stanislaus River and Delta are negatively affected by the PA to such a degree that the survival, growth, and/or reproductive success of all inland life stages of CCV steelhead is reduced (see Table 2.8.5-2). For example, Stanislaus River steelhead are exposed to stressful water temperatures during adult immigration, embryo incubation, juvenile rearing, and smolt emigration. In addition, flow-dependent habitat availability is limited, particularly for the spawning, juvenile r,earing, and smolt emigration life stages. Based on the effects analysis throughout the CCV steelhead life cycle, it is apparent that the PA has substantial negative effects on the habitat, and therefore spatial structure, in the Stanislaus River and Delta. A further reduction to the spatial structure of a population which has already been blocked off from its historic spawning habitat certainly reduces the likelihood of recovery. Of equal importance to spatial structure in determining population viability is the presence of sufficient behavioral and genetic diversity within the population to allow it to be flexible and adapt to changing environmental conditions through utilization of a wide range of habitats. The combined effects of the P A on the adult immigration, spawning, embryo incubation, juvenile rearing, and smolt emigration life stages of CCV steelhead in the Stanislaus River, reduces the viability of the population and places the population, which was already at high risk of extinction due to extremely low abundance, at even greater risk. As previously described, Naiman and Turner (2000) demonstrated how even slight reductions in survival from one life stage to the next at each and every life stage can have serious consequences for the persistence of a populations. Considering that the P A reduces the survival of each CCV steelhead life stage, including the life stage transition from smolt to adult-sized fish in the ocean, Stanislaus River steelhead may not persist with implementation of the P A. 862 Biological Opinion for the Long-Term Operation of the CVP and SWP In addition to the negative effects on the spatial structure and life history diversity, the PAis expected to reduce the abundance of Stanislaus River steelhead. Mortality associated with the PA in the Stanislaus River is expected through such sources as potential water temperarure-related pre-spawn adult mortality, redd dewatering, and egg suffocation from deposition of fines. Once a juvenile CCV steelhead has survived moving downstream through the Stanislaus River tributary, it still must overcome the stressors located in the Delta, which include barriers constructed across waterways to preserve water elevations for irrigation, lack of a Head of Old River barrier (HORB) that helps keep water flow and CCV steelhead in the mainstem ofthe San Joaquin River, altered regional hydrodynamics resulting from the diversion of large volumes of water by the CVP and SWP, and direct entrainment and salvage within the export facilities related to those export actions. As described in detail in the supplemental Delta analysis in Section 2.5.5.11, revisions to loss thresholds and commitments to review and technical assistance in the fmal P A provide some assurance that species risks will be conservatively managed and reduce the effects of altered regional hydrodynamics and direct entrainment and salvage relative to the original P A. Results from Buchanan (2019) indicate overall mortality of juvenile CCV steelhead migrating from the San Joaquin River to Chipps Island range from 45 to 85 percent. Recent modelling (Buchanan 20 19) of the effects of the HORB presence on the estimated CCV steelhead survival from the HOR to Chipps Island indicates that survival is higher when the barrier is installed, compared to when it is not installed. The predicted difference in survival that was attributable to the presence of the barrier was estimated to range from 0. I 3 for a Vernalis flow of 3 I 9 cfs to 0.19 for a Vernalis flow of 3,889 cfs. Although there is high uncertainty in the predicted survival estimates for both conditions of the barrier's presence, and moderate uncertainty for the predicted effect ofthe barrier on survival, the predicted survival effect of the barrier was positive for all values of Delta inflows at Vernalis. Buchanan (20 19) cautions that this modelling is based on a limited data set (2011- 2016). Based on NMFS's current understanding of survival probabilities based on barrier condition at the Head of Old River, in years when flow conditions would have allowed HORB installation, the PA will lead to lower survival of steelhead juveniles emigrating from the San Joaquin River basin by 13-19 percent for flows of up to 5,000 cfs at Vernalis. Based on this information, Reclamation's PAis expected to create conditions that would reduce steelhead survival to Chipps Island for Stanislaus River steelhead and the entire Southern Sierra Nevada Diversity Group, further exacerbating the already diminished status of this diversity group. Future projections over the duration of the PA (i.e., through 2030), considering both increasing water demands and climate change, exacerbate risks to Stanislaus River steelhead. For example, climate change is expected to further degrade the suitability of habitats in the Central Valley through increased temperatures, increased frequency of drought, increased frequency of flood flows, and overall drier conditions (Lindley et al. 2007). 2.8.5.2.5 Population context It is possible that some of the loss modeled to occur at the export facilities under the PA flow conditions might have occurred due to far-field effects in the south Delta under COS conditions, but no modeling too[ is available that allows comparison of both direct loss and far-field effects under PA vs. COS conditions. 863 Biological Opinion for the Long-Term Operation of the CVP and SWP NMFS put the combined CCV steelhead loss in a population context (see full caveats in Section 2.5.5.8.3.1) by expressing the estimated annual combined loss as a percentage of the steelhead population in the Delta. These results should be considered a coarse screening level analysis due to limitations of the salvage-density method itself (limited historical time-frame of loss; relatively simple weighting of loss. by export changes and no other operational factors) and use of the average annual modeled loss rates (over the 15-year data period) scaled to both low and high population estimates. Since it is likely that annual observed loss in a particular year is correlated with population size, use of the average loss rate likely overestimates the population effect in a low-population year, and underestimates the population effect in a high-population year. Additionally, the revised loss thresholds related to OMR management in the final PA are expected to limit loss during April and May to levels less than estimated using the Salvage Density Model results, and to levels comparable to loss observed under the COS. Estimated annual combined loss from the COS is 6,560 juveniles, and estimated annual combined loss from the PA is 7 ,988. Good et al. (2005) estimated the CCV steelhead population at approximately 94,000-336,000 juveniles, and Nobriga and Cadrett (2001) estimated the CCV steelhead population at 413,069-658,453 juveniles. Applying the estimated annual combined loss to the lowest and highest juvenile population estimates provides ranges of 1 (6,560 -:- 658,453) to 7 (6,560 -:- 94,000) percent loss of the juvenile CCV steelhead population in the Delta for the COS, and 1 (7,988 + 658,453) to 8 (7,988 -:- 94,000) percent loss of the juvenile CCV steelhead population in the Delta for the PA. Because the revised loss thresholds in the original PA may limit loss to be more comparable with the COS scenario, the estimated screening-level population context under the final PAis likely less than the <1 to 8 percent estimated under the original PA. 2.8.5.3 Assess the Risk to the ESU/ DPS To assess the risk posed by the PA to the DPS of CCV steelhead, when combined with the status of the species, environmental baseline, and cumulative effects, NMFS determines if changes in population viability, based on changes in the VSP parameters of that population, are likely to be sufficient to reduce the viability of the species. In this assessment, we use the species' status, based on the current condition of the VSP parameters, (established in in Section 2.2 The Status of the Species of the Species and Critical Habitat) as our point of reference for the effects of the PA. Currently the CCV steelhead DPS is at moderate risk of extinction (National Marine Fisheries Service 20 16b). However, there is considerable uncertainty with regard to the magnitude of that risk, due in large part to the general lack of information and uncertainty regarding the status of many of its populations. Given this uncertain point of reference, but based on our knowledge of the population structure of the species, NMFS considers the consequences of a relative change in extinction risk to one or more of those populations and if that change would reduce appreciably the likelihood of both the survival and recovery of the species. Using the ESU/DPS-Level Recovery Criteria identified in the CCV steelhead 5-year status review (National Marine Fisheries Service 2016b), the combined risk to individual populations are evaluated to determine the risk to the DPS as a whole. As described in the Recovery Plan, watersheds in the four diversity groups were prioritized into three categories (Table 2.8.5-3). Core 1 watersheds possess the known ability or potential to support a viable population. For a population to be considered viable, it must meet the criteria for low extinction risk for Central Valley salmonids (Lindley et al. 2007). Core 2 populations meet, 864 Biological Opinion for the Long-Term Operation of the CVP and SWP or have the potential to meet, the biological recovery standard for moderate risk of extinction. Core 3 watersheds have populations that are present on an intermittent basis and require straying from other nearby populations for their existence. These populations likely do not have the potential to meet the abundance criteria for moderate risk of extinction. Although Core 3 watersheds are the lowest priority, they remain important because so many historic populations have already been extirpated, and, like Core 2 watersheds, they support populations that provide increased life history diversity to the ESU/DPS and are likely to buffer against local catastrophic occurrences that could affect other nearby populations. The diversity group .and population priority lens helps put the PA's potential impact on the CCV steelhead DPS into context in two key ways. First, the importance of the Clear Creek population to the CCV steelhead DPS is illuminated given that it is identified as a "Core 1" population and is likely the only population in the Northwestern California diversity group with the potential to meet the recovery criteria calling for one viable population in the diversity group. The combined effect of multiple stressors on Clear Creek steelhead with implementation of the PA is expected to reduce the population's viability. Relative to the Clear Creek population, the PA's potential impact on CCV steelhead occurring in the Sacramento, American, and Stanislaus rivers carry slightly less weight. However, given that most historic independent CCV steelhead populations have already been extirpated, NMFS considers that an expected appreciable reduction in any population's viability due to implementation of the PA would also appreciably reduce the viability ofthe population's diversity group and the DPS. The second way the diversity group/population priority lens provides context is that, while the Clear Creek population demonstrates the importance viable Core 1 populations for CCV steelhead, the DPS's survival and recovery is equally dependent on the occurrence of viable Core 2 populations in the San Joaquin River basin (i.e., southern Sierra Nevada diversity group). The expected impacts from the PA's increase in south Delta exports (albeit lessened by the revised loss thresholds in the OMR Management component of the final PA) and operation of south Delta agricultural barriers will likely inhibit populations in the southern Sierra Nevada diversity group. All of the juvenile CCV steelhead from the southern Sierra Nevada diversity group will be exposed to export-related impacts by either going by the "front door" of the export facilities via the Old River route since the PA has no HORB in place to block that route, or via the "backdoor" from the mainstem San Joaquin River if the fish stay in the SJR mainstem at the Head of Old River but then enter the interior channels of the south Delta at Turner Cut, Columbia Cut, or the mouths of Old River or Middle River. Any fish that goes the Old River route from the Head of Old River will more than likely be entrained into the TFCF or into CCF or predated upon trying to migrate north past the pumps. Fish in the mainstem San Joaquin River have a better chance to stay in the mainstem and survive to Chipps Island. The effects of the PA are expected to cause additional harm to the DPS, which is already at high extinction risk due to a harmful environmental baseline. While several factors contribute to that harmful environmental backdrop, the construction and operation of the CVP/SWP is prominent. The continued operation of the CVP/SWP as proposed in the ROC on LTO BA, based on the effects and VSP-based analyses, would likely decrease its likelihood of survival and recovery. 865 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.8.5-3. Central Valley Steelhead Diversity Groups and W atershed Prior itization. Divisions included in the PA are bold (modified from NMFS 2014). Diversity Group River or Creek Priority (number of viable populations needed to meet ESU level recovery criteria) Basalt and Porous Lava (2) Northwestern California (1) Northern Sierra Nevada (4) Southern Sierra Nevada (2) Battle Creek Core 1 Cow Creek Core 2 Sacramento River (downstream from Keswick) Core 2 Redding Area Tributaries Core 2 Putah Creek Core 2 Thomes Creek Core 2 Cottonwood/Beegum Creek Core 2 Clear Creek Core 1 Mokelumne River (downstream from Comanche) Core 2 American River (downstream from Nimbus) Core 2 Auburn Ravine Core 2 Feather River (downstream from Oroville) Core 2 Yuba River downstream from Englebright) Core 2 Butte Creek Core 2 Big Chico Core 2 Deer Creek Core 1 Mill Creek Core 1 Antelope Creek Core 1 Calaveras River (downstream from New Hogan) Core 1 Stanislaus River (downstream from Goodwin) Core 2 Tuolumne River (downstream from La Grange) Core 2 866 Biological Opinion for the Long-Term Operation of the CVP and SWP Diversity Group P riority River or Creek (number of viable populations needed to meet ESU level recovery criteria) Merced River (downstream from Crocker Huffman) Core 2 The VSP analysis shows that elements of the P A are expected to appreciably reduce the abundance VSP parameter for CCV steelhead populations of the Sacramento River and San Joaquin River basin, those of the Basalt and Porous Lava, Northwestern California, and Northern and Southern Sierra Nevada diversity groups. The VSP analysis shows that productivity, spatial structure, and diversity under the COS are currently degraded in the Sacramento River and San Joaquin River such that CCV steelhead remain at moderate risk of extinction (National Marine Fisheries Service 2016b). These VSP parameters are unlikely to improve under the PA and would likely deteriorate under increased water demands and climate change scenarios over the next decade. California's human population growth (see Section 2.7 Cumulative Effects) and the associated increase in water demand and climate change, will exacerbate risks associated with the PA, further increasing the risk to the population. In particular, the water temperature impacts expected with PA implementation are likely to be amplified by climate change. The PA is expected to expose individual CCV steelhead from Clear Creek, the main stem Sacramento River, the American River, and the Stanislaus River to stressors that have fitness consequences for each inland life stage. Cumulatively, these fitness reductions throughout the inland CCV steelhead life cycle, are expected to result in population level consequences for each of the four populations, reducing their viability. For Central Valley ESUs and DPSs, reductions in population viability are assumed to also reduce the viability ofthe diversity group the population belongs to as well as the species. Because the four diversity groups with extant CCV steelhead populations are represented by these four populations3 1, the viability of all four extant CCV steelhead diversity groups is expected to be decreased with impl ementation of the PA. In consideration of the status and baseline stress regime of the species, these diversity group- and population-level consequences identified above reduce the likelihood of survival and recovery of the species. Considering the effects of the PA, cumulative effects, and effects from interrelated and independent actions in the context of the status and environmental baseline of CCV steelhead, NMFS concludes that the PAis likely to appreciably reduce the likelihood ofboth the survival and recovery of the CCV steelhead DPS (Table 2.8.5-4). Table 2.8.5-4. Reasoning and decision-making steps for analyzing the effects of the proposed action on steel head. Dark shading identifies t he conclusion at each step of decision-making. Acronyms and abbreviations in the action column refer to not likely to adversely affect (NLAA) and not likely/likely to jeopardize (NLJ/LJ). A I the Available Evidence to Determine if... 31 True/False True Clear Creek belongs to the Northwestern California diversity group; the mainstem Sacramento River population belongs to the Basalt and Porous Lava diversity group; the American River belongs to the Northern Sierra Nevada diversity group; and the Stanislaus River belongs to the Southern Sierra Nevada diversity group. 867 Biological Opinion for the Long-Term Operation of the CVP and SWP Step Apply the Available Evidence to Determine if... The proposed action is not likely to produce stressors that have direct or indirect adverse consequences on the environment. Available Evidence: Proposed action-related stressors adversely affecting the environment include: (1) Sacramento River, Clear Creek, and Stanislaus River flow regulation disrupting natural river function and morphology; (2) warm water temperatures in the mainstem Sacramento River, Clear Creek, the American River, and the Stanislaus River; (3) low late-summer flows in Clear Creek and in the American and Stanislaus rivers; and (4) modified Delta hydrology associated with export operations (e.g., pulling water towards the Federal and State plants). CV steelhead individuals are not likely to be exposed to one or more of those stressors or one or more of the direct or indirect consequences of the proposed action. Available Evidence: (1) Allfreshwater life stages ofSacramento River, Clear Creek, and Stanislaus River steelhead will be exposed to regulated flows and their effects on river processes and morphology every year through 2030. {2) Each year through 2030, steelhead in Clear Creek, the mainstem Sacramento River, the American River, and the Stanislaus River are expected to be exposed to water temperatures warmer than life stage-specific requirements during multiple life stages, including egg incubation and juvenile rearing. (3) Steelhead rear in their natal stream year-round for I to 2 years, and thus are expected to be exposed to low late-summer flows in Clear Creek and in the American and Stanislaus rivers. (4) As water is movedfrom the north Delta and from the San Joaquin River to the Federal and State export facilities, each year through 2030,CCVsteelhead juveniles will have increased exposure to an abundant predator community, an aquatic environment degraded by pesticides and contaminants, and entrainment and loss at the{acilities. CV steelhead individuals are not likely to respond upon being exposed to one or more of the stressors produced by the proposed action. c Available Evidence: (1) Loss ofnatural river function resultingfromflow regulation in the Sacramento River, Clear Creek, and the Stanislaus River has reduced the quality and quantity ofrearing and migrat01y habitats, thereby reducing the growth and survival ofindividual steelheadjuveniles in those systems. (2) Exposure to warm water temperatures in Clear Creek, the mainstem Sacramento River, the American River, and the Stanislaus River is expected to cause eggs deposited later (i.e., March) in the spawning season to suffer increased mortality and structural deformities during incubation, particularly during critically dry years. Thermal stress responses (e.g. , reduced immune system function) are also expected to occur in individual juvenile CCV steelhead rearing over the summer in Clear Creek and the American River. (3) Low latesummer flows limit the availability ofquality rearing habitat, including predator refuge areas. Under these low flow conditions, juvenile steelhead have an increased susceptibility to predation and density dependent relatedfactors (e.g., disease and competition for prey and habitat). (4) Mortality ofjuvenile steelhead migrating from the San Joaquin River to Chipps Island is .expected to range from 45 to 85 percent based on results from acoustic tag studies. Mortality of salmonids mm LFR Chinook salmon study fish) that enter the Delta interior from the Sacramento River is expected to range from 66-96 percent, resulting in the loss ofapproximately I 3 -19 percent ofthe Sacramento River basin population ofthe California Central Valley DPS, assuming an average routing of 20 percent fish into the Delta interior. 868 True/False Action False Go to B True B False Go to c True NLAA False Go to D Biological Opinion for the Long-Term Operation of the CVP and SWP Step D E F 2.8.6 • Apply the Available Evidence to Determine if... Any responses are not likely to constitute "take" or reduce the fitness of the CCV steelhead individuals that have been exposed. Available Evidence: (1) "Take "ofsteelhead individuals in the form ofreduced growth and survival is expected due to the loss ofnatural river function associated with flow regulation in the Sacramento River, Clear Creek, and the Stanislaus river. (2) and (3) As described in step C, "take" ofsteelhead individuals, in the form ofmortality and sub-lethal effects, is expected with exposure to warm water temperatures particularly during the egg incubation and juvenile rearing life stages, and with exposure to low flows during juvenile rearing. (4) As described in step C, "take" ofsteelhead individuals, in the form of mortality, is expected in the Delta juvenile Any reductions in individual fitness are not likely to reduce the viability of the populations those individuals represent. True/False True False Action NLAA Go to E Available Evidence: The cumulative effects offlow regulation, warm water temperatures, low flows, project-related impacts in the Delta, and other projectrelated stressors (see Table 2.8.5-2) are expected to sufficiently reduce the survival, growth, and/or reproductive success ofsteelhead individuals at multiple life stages every year through 2030 such that key population parameters (i.e. spatial structure, diversity, and abundance) are appreciably reduced for steelhead populations in Clear Creek, the mains/em Sacramento River, the American River, and the Stanislaus River. Reductions in these parameters are ofsufficient magnitude for one to reasonably expect a reduction in the viability ofeach ofthe four populations. Any reductions in the viability of the exposed populations are not likely to reduce the viability of CCV steelhead the species. True NLJ False Go to F True NLJ Available Evidence: Considering the greatly diminished status ofthe CCV steelhead DPS, NMFS assumes that if a population-level effect on any ofthe populations within the DPS is expected from implementation ofthe proposed action, then a species-level effect will be expected as well. The proposed action is expected to reduce the viability ofat least four steelhead populations. Therefore, the viability ofthe DPS is expected to be significantly reduced with implementation ofthe proposed action. False LJ CCV Steelhead Critical Habitat Designated critical habitat (70 FR 52488 2005). 2.8.6.1 Status of Critical Habitat and Environmental Baseline As described in section 2.2 Rangewide Status of the Species and Critical Habitat, the geographical extent of designated critical habitat for CCV steelhead includes: the Sacramento, Feather, and Yuba rivers, and Deer, Mill, Battle, Clear, and Antelope creeks in the Sacramento River basin; the San Joaquin River, including its tributaries but excluding the mainstem San Joaquin River upstream of the Merced River confluence; and the waterways of the Delta. CCV steelhead critical habitat is composed of four physical or biological features that include freshwater spawning sites, freshwater rearing sites, freshwater migration corridors, and estuarine habitat. Stressors to CCV steelhead critical habitat PBFs include water diversions and water management, dams and other structures, loss offloodplain connectivity, loss of natural riverine 869 Biological Opinion for the Long-Term Operation of the CVP and SWP function, bank protection, dredging, sediment disposal, gravel mining, invasive aquatic organisms, and agricultural, urban, and industrial land use (McEwan 2001). The PBFs for the designated critical habitat were described for CCV steelhead in the following Federal Register notice: 70 FR 52488, September 2, 2005. CCV steelhead critical habitat includes the Delta - an ecosystem that has had dramatic habitat changes in recent years related to water quality, toxic algae blooms (e.g., M icrocystis), and invasive species (e.g., the aquatic macrophyte Egeria dens a). Based on the host of stressors to spawning, rearing, migratory, and estuarine habitats in the Central Valley, it is apparent that the current condition of CCV steelhead critical habitat is degraded, and does not provide the conservation value necessary for the survival and recovery of the species. 2.8.6.2 Summary of Proposed Action Effects on Critical Habitat Proposed action-related effects to CCV steelhead designated critical habitat are summarized in Table 2. 8.6-1 . Detailed descriptions regarding the effects of the PA on CCV steelhead designated critical habitat are presented in section 2.6. 870 Biological Opinion for the Long-Term Operation of the CVP and SWP PBFs Affected Clear Creek Response and Rationale of Effect Freshwater migration corridors Pulse flows increase turbidity, decrease barriers, and increase passage routes. Fresh water rearing sites Clear Creek Freshwater migration corridors Clear Creek Clear Creek Fresh water rearing sites Lack of flow variability leads to reduced habitat complexity. In Critical years, reduced base flows will reduce available rearing habitat. Flows may lack variability to create cues for juvenile emigration and adult migration, especially in Critical and Dry water year types. Pulse flows increase turbidity, decrease barriers, and increase passage routes. Clear Creek Freshwater migration corridors Location of Effect Table 2.8.6-1. Summary of proposed action-related effects on CCV steelhead critical habitat. Action Component Trinity (Clear Creek) Minimum instream base flows Division Trinity (Clear Creek) Channel maintenance pulse flows Spring attraction pulse flows Channel maintenance pulse flows Minimum instream base flows Trinity (Clear Creek) Trinity (Clear Creek) Trinity (Clear Creek) Pulse flows mobilize some gravel to form new habitat, and will temporarily increase rearing habitat availability. Magnitude, duration, and frequency is not likely to be great enough to shape the channel and inundate floodplains to improve or increase rearing habitat long-term. 871 Magnitude Weig ht of Evidence Low Reduced quality of migratory habitat for adults and juveniles. Medium. Medium Medium Medium Medium. Probable C ha nge in PBF Support in the Life History Needs of the Species Reduced quality of rearing habitat. Medium Medium Medium Medium Improved migratory corridor for juveniles and adults. Improved migratory corridor for juveniles and adults. Improved connectivity and increased available rearing habitat temporarily. Continued degradation of rearing halbitat if flows are not of magnitude to shape the channel. Clear Creek Clear Creek- Fresh water spawning sites Fresh water rearing sites PBFs Affected Clear Creek Response and Rationale of Effect Warm water temperatures downstream of compliance point degrade rearing habitat. Base flows provide suitable spawning habitat but lack variation that provides habitat complexity. In Critical water year types, reduced base flows will degrade spawning habitat. Warm water may block adult migration near mouth Fresh water rearing sites Ramp down following pulse flow create stranding habitat. Freshwater migration corridors Clear Creek Fresh water rearing sites Fresh water rearing sites Clear Creek Fresh water spawning sites Pulse flows mobilize some gravel to form new habitat, and will temporarily increase rearing habitat availability. Ramp down following pulse flow create stranding habitat.. Clear Creek Clear Creek Location of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Trinity (Clear Creek) Water temperature management: summer Action C omponent Trinity (Clear Creek) Minimum instream base flows Division Trinity (Clear Creek) Spring attraction pulse flows Water temperature management: summer Trinity (Clear Creek) Channel maintenance pulse flows Spring attraction pulse flows Trinity (Clear Creek) Spring attraction pulse flows Trinity (Clear Creek) Trinity (Clear Creek) Pulse flows mobilize and disperse some spawning gravel, and decrease fines, which improve spawning habitat. 872 Magnitude Weigbtof Evidence Low Low Improved connectivity to rearing halbi tat temporarily.. Degraded migratory corridor. Reduced quality of spawning habitat. Medium Low Degraded rearing halbi tat Low Low Degraded rearing halbi tat Probable Change in PBF Support in the Life His tory Needs of the Species Reduced quality of rearing habitat Low Low Low Low Medium Low Low Low Some increased quality and quantity of spawning habitat. Summer Cold Water Management (2.5.2.1.3) Channel maintenance pulse flows Action C omponent Upper Sacramento River Upper and middle Sacramento River Clear Creek Location of Effect Weigbtof Evidence Medium Magnitude Low Response and Rationale of Effect Fresh water spawning sites Pulse flows mobilize and disperse some spawning gravel, and decrease fines, which can improve spawning habitat. Magnitude and duration is not likely to be great enough to shape the channel and adequately route spawning gravel and improve spawning habitat. High Medium Temperatures in excess of 57.5°F can lead to sub-lethal affects to adult salrnonids as well as abnormal development or mortality of eggs and larvae. PBFs Affected Biological Opinion for the Long-Term Operation of the CVP and SWP Division Trinity (Clear Creek) Shasta Shasta Fall and Winter Refill and Redd Maintenance (2.5.2. 1.4.1) High: Supported by multiple scientific and technical publications that include quantitative models specific to the region and species. Medium: Supported by select technical publications specific to the region and species. Quantitative results include month to Decreased month to month flows resulting in stranding caused by a loss of floodplain inundation and sidechannel habitat. Water temperatures between 42.557.SOF (5.814.1 °C) for successful spawning, egg incubation, and fry development, Freshwater Spawning Sites Adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, Freshwater Spawning Sites 873 Probable Change in PBF Support in the Life His tory Needs of the Species Some increased quality and quantity of spawning habitat. Continued degradation of spawning habitat if flows are not of magnitude to shape the channel. Decreased access to suitable water temperatures Decreased flow limiting the downstream transport of juveniles Division Action C omponent Upper Middle Sacramento River Location of Effect PBFs Affected Decreased flows in September and November resulting in increased travel time and a decrease in survival because of increased predator interactions. Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Fall and Winter Refill and Redd Maintenance (2.5.2. 1.4.1) Adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, Access downstream so that juveniles can migrate from the spawning grounds to San Francisco Bay and the Pacific Ocean, Freshwater Migration Corridors 874 Magnitude Medium Weigbtof Evidence month change. Medium: Supported by select technical publications specific to the region and species. Quantitative results include month to month change. Probable Change in PBF Support in the Life His tory Needs of the Species Decreased flow limiting the downstream transport of juveniles Division Spring Pulse Flow (2.5.2. 1.2. 1) Action C omponent Upper Sacramento River Upper Sacramento River Location of Effect PBFs Affected Increased habitat carrying capacity (WUA) at lower flows providing increased feeding conditions, and decreased competition and predation. Spring pulse flows could provide flows high enough to flush fine sediments from spawning substrates. Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Shasta Fall and Winter Refill and Redd Maintenance (2.5.2.1.4.1) Availability of clean gravel for spawning substrate, Adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, Freshwater Spawning Sites Adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, Freshwater Spawning Sites 875 Weigbtof Evidence Medium Medium: Correlation of flow and migration supported by multiple scientific and technical publications but magnitude of benefit uncertain. Magnitude Low High: Supported by multiple scientific and technical publications specific to the region and species. Quantitative results include WUA analysis. Probable Change in PBF Support in the Life His tory Needs of the Species Increased or improved quantity/quality of spawning substrate Increased habitat carrying capacity necessary for successful spawning, incubation of eggs, fry development and emergence Division Fall and Winter Refill and Redd Maintenance (2.5.2. 1.4.1) Action C omponent Upper Middle Sacramento River Location of Effect Riparian habitat that provides for successful juvenile development and survival, Freshwater Rearing Sites PBFs Affected Increased habitat carrying capacity (WUA) at lower flows providing increased feeding conditions, and decreased competition and predation. Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Shasta Upper Sacramento River Spawning Gravel Injection (2.5.2.3.2.1) Availability of clean gravel for spawning substrate, Freshwater Spawning Sites As part of adaptive management reclamation would implement spawning gravel injection project(s) in the action area. This action component would directly affect the quantity and quality of available substrate suitable for spawning. 876 Magnitude Low Low (Uncertain) Weigbtof Evidence Medium: Supported by technical publications specific to the region and species. Quantitative results include WUA analysis and month to month floodplain inundation. Low: (Programma! ic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Probable Change in PBF Support in the Life His tory Needs of the Species Increased access to riparian habitat that provides for successful juvenile development and survival Increased or improved quantity/quality of spawning substrate Division Action C omponent Side-Channel habitat (2.5.2.3.2.2) Location of Effect PBFs Affected Middle Sacramento River Upper Middle Sacramento River Programmatic action component. Construction activities are not described but operation is assumed to comply witih NMFS and CDFW fish screening guidance. As part of adaptive management reclamation would implement sidechannel habitat restoration project(s) in the action area. This action component would directly affect access to areas suitable for spawning whlch includes increased flow to those areas as well as the quantity and quality spawning substrate. Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Shasta Small Screen Program (2.5.2.3.2.3) Availability of clean gravel for spawning substrate, Adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, Freshwater Spawning Sites Access downstream so that juveniles can migrate from the spawning grounds to San Francisco Bay and the Pacific Ocean, Freshwater Migration Corridors 877 Weigbtof Evidence Low (Uncertain) Low: (Programma! ic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Magnitude Low (Uncertain) Low: (Programma! ic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Probable Change in PBF Support in the Life His tory Needs of the Species Increased or improved quantity/quality of spawning substrate in freshwater spawning sites Increased access to and through Freshwater Migration Corridors Division Water temperature management Adult rescue (2.5.2.3.3.1.2) Lower Intakes near Wilkins Slough (2.5.2.3.1.2) Action C omponent Middle Sacramento River Access downstream so that juveniles can migrate from the spawning grounds to San Francisco Bay and the Pacific Ocean, Freshwater Migration Corridors Programmatic action component. Increased stress and mortality related to capture and handling. Minimization measure intended to increase relative survival of adult salmonids entrained in water diversions (e.g. Yolo and Sutter Bypasses). Programmatic action component. Construction activities are not described but operation is assumed to comply with NMFS and CDFW fislu screening guidance. Response and Rationale of Effect Middle Sacramento River Access from the Pacific Ocean to appropriate spawning areas in the upper Sacramento River, Freshwater Migration Corridors PBFs Affected Nimbus to confluence Location of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Shasta Shasta American River Spawning/incub ation and freshwater rearing and migratory habitat Incubation, rearing, and migration (smoltification) habitat may be degraded by temperatures especially in dry and critically dry years 878 Magnitude Low (Uncertain) Low (Uncertain) high Weigbtof Evidence Low: (Programma! ic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Low: (Programma! ic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. high- water temperature monitored/m odeled and in excess of suitable ranges of some life Probable Change in PBF Support in the Life His tory Needs of the Species Increased access to and through Freshwater Migration Corridors Increased access to and through Freshwater Migration Corridors Reduced quality of incubation and rearing/smoltific ation habitat Water Transfer Spawning and rearing habitat restoration Flow management and flood control Action C omponent Framework programmatic action component. Redd siltation or dewatering (lethal), fry and juvenile stranding Response and Rationale of Effect Spawning/incub ation and freshwater rearing habitat improved spawning substrate and floodplain access for rearing PBFs Affected specific named sites Spawning/incub ation and freshwater rearing habitat Nimbus to confluence Location of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division American River American River Delta Freshwater Rearing Habitat for Juveniles: Lower Sacramento River and Delta Adequate river flows for successful downstream transport of juveniles; water quality and forage supporting juvenile salmonid development; I) Improved flow conditions may improve water temperature conditions in the mainstem Sacramento River. 2) Improved flow conditions may improve dissolved oxygen conditions through improved mixing of water column and water surface- air interface. 3) Improved water quality in fall may improve primary and secondary productivity benefitting forage base. 879 Magnitude medium medium MediumImproved flows and water quality elements will affect a small proportion of the juvenile CCV steel head Sacramento River Basin population emigrating downstream in the fall during the transfer window due to timing of juvenile CCV steelhead migration behavior. Most of the adult CCV steel head population from Weigbtof Evidence stage in nearly all years high- flow fluctuations occur as routine operations mediumhabitat restoration is ongoing, benefits uncertain Mediummultiple peer reviewed papers confirm benefits to water quality with increased flows. Effects to primary and secondary productivity from increased flows in Sacramento River less certain. Probable Change in PBF Support in the Life His tory Needs of the Species reduced quality of spawning, incubation, and rearing halbi tat. Spawning gravels/redd scour improved incubation and rearing halbitat Increased flows due to water transfers from upstream reservoir releases will improve water temperatures and water quality conditions in the lower Sacramento River and upper Delta waterways. Effect will be temporary and related to the volume and frequency of transfers. Division Action C omponent Location of Effect PBFs Affected I) Access to the interior Delta through open DCC gates reduces the survival of migrating juveniles, reduces the value of the mainstem migratory corridor. 2) Operations of the DCC gates can alter the extent of tidal influence in the river reaches downstream of the DCC location, delaying migration or rerouting juveniles into alternate migratory routes with lower survival. 3) Operations of the DCC gates reduces the upstream migratory function of the mainstem Sacramento River to adults, enhances straying and migratory delays. 4) Enhanced flows from Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Delta I) DCC Gate operation, 2) Water transfer, 3) North Bay Aqueduct Operations, 4) CCWD Rock Slough Freshwater Migratory Corridors for Outmigrating Juveniles and Spawning Adults: Sacramento Rivermainstern, Delta, and SF BayFreshwater migratory corridor for adults and juveniles Freshwater migration corridors free of obstruction and excess predation with water quantity and quality conditions and natural cover such as submerged and overhanging large woody objects, aquatic vegetation, large rocks and boulders, side channels, and undercut banks supporting juvenile and adult mobility and survival. 880 Magnitude the Sacramento River Basin will be migrating upstream during the water transfer window and are expected to benefit from improved water quality and migratory cues inducing upstream movements Medium - Open DCC gates will redirect a portion of the Sacramento River flow into the Delta interior, negatively impacting downstream flow characteristics for juvenile migration. A proportion of downstream migrating juveniles will be routed into the Delta Interior, reducing survival of migrating fish in routes with more adverse habitat conditions (predation, longer Weigbtof Evide nce HighMultiple peer reviewed studies and reports, coupled with modelling support conclusions. Probable Change in PBF Support in the Life His tory Needs of the Species DCC gate operations may provide access to the Delta interior reducing survival of juveniles utilizing these inferior routes. Closing the gates will prevent rerouting into the Delta interior via the DCC gates and enhance downstream hydrodynamics and reduce tidal intrusion into riverine reaches of the Sacramento Division Action C omponent Freshwater Rearing Habitat for Juveniles: San Joaquin Delta Location of Effect PBFs Affected water transfers can benefit juvenile CCV steelhead migrating downstream in October and November, as well as adults migrating upstream due to stronger flow and olfactory cues. 5) Operations ofNBA/ Barker Slough Pumping Plar1t may delay migration of juveniles due to alterations to flow patterns created by the export of water Medium - Most oftheCCV steelhead population will remain in the north Delta and be minimally affected by operations in the South Delta. CCV steelhead from the San travel distances and travel time). Adults that stray into the Mokelumne River system due to open gates and then encountering subsequently closed gates will be delayed in their upstream migration. Magnitude I ) Increased exports during transfer wi ndow will increase the risk of entrainment of CCV steelhead juveniles; 2) exports in general over the calendar year will increase CCV steelhead entrainment into the CVP and SWP facilities; 3) Operations of the south Delta Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Delta Contra Costa Water District-Rock Slough, Water Transfer, CVP and SWP Export Facilities, South Delta Agricultural Barriers Adequate river flows for successful downstream transport of juveniles; water quality and forage supporting juvenile salmonid development; 881 Weigbtof Evide nce High numerous studies have examined the effects of theCVP and SWP export facilities, the south Delta agricultural ba.rriers, and the survival Probable Change in PBF Support in the Life His tory Needs of the Species River mainstem. Closed gates reduce the probability of adult straying and migration delay by c[osing offfalse attractant flows. Lesser effect in final PA due to revised DCC operations in DecemberJanuary. Water transfers may enhance ambient Sacramento River flows, providing better freshwater migratory conditions for juvenile and adult SH. Increased exports entrain more fish into theCVP and SWP facilities, where loss occurs; lesser effect in final PA due to revised loss thresholds. Constructi63.5°F), Medium(8% of days >71.5) Medium (45 - 68% of years) Medium, High Sublet hal, Lethal Medium (3 1% of days >63.5°F at Hamilton City) Low Low (5 7%of years) Sublet hal Large hal Large Medium (<75% of years) Sublet Benefi cia I: Mediu m Weight of Evidence Medium: Supported by multiple scientific and technical pub!ications, however not specific to the region and species. Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Low Medium: Correlation of flow and migration supported by multiple scientific and technical pub!ications. Probable Change in Fitness Reduced reproductive success, Reduced survival probability Reduced reproductive success Decreased reproductive success; decreased survival probability Improved reproductive success Action Compone nt SpringMgmt. of Spawning Locations Tier 2 (Shasta Cold Water Pool Mgmt.) Stressor Water Temperature Water Temperature Life Stage (location) Adults (Upper Sacramento River) Spawning Adults, EggsfLarval, (BSF gauge- Hamilton City) Individual Response and Ration.ale of Effect Benefi cial: Mediu m t Severi ty of Stress or/Lev el of Benefi March - July (April - May) Lower temperatures may benefit pre-spawn females by ensuring that eggs are not damaged and normal embryo development occurs after spawning Sublet hal benefit females migrating upriver by ensuring that eggs are not damaged before spawning. April - July (May 15- July), May- August (May 15August) Life Stage Timing (Work W indow Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento! Shasta Division Upper Sacramento{ Shasta Division PA temperature ranges from temps associated with abnormal development of eggs and larvae (Sublethal) to decrease in egg survival (Lethal) in lab studies. 905 Proportion of Population Exposed Frequenc y of Exp osure Medium Magnitu de of Effect Low Uncertain Low Medium (17- 35% of years) Large Medium (42%ofdays >63.5°F) Weight of Evidence Low: A number of scientific and technical pub!ications have suggested a relationship between temperature and salmonid spawning but a direct effect is sti II unknown. Effects to green sturgeon are more uncertain. Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Probable Change in Fitness Improved reproductive success Reduced reproductive success Action Compone nt Tier 3 (Shasta Cold Water Pool Mgmt.) Wi lkins Slough intakes (Cold water pool mgmt.) Juvenile Trap and Haul (tier 4 intervention) Stressor Water Temperature Passage lmped i ments!Barri ers, Flow Conditions, Loss of Riparian Habitat and Instream Cover Life Stage (location) Spawning Adults, Eggs/Larval, (BSF gauge- Hamilton City) Adults, Juveniles (Middle Sacramento River) Juveniles (Upper Sacramento River) Individual Response and Ration.ale of Effect April - July (May 15 - July), May- August (May 15 . August) PA temperature ranges from temps associated with abnormal development of eggs and larvae (Subletbal) to decrease in egg survival (Lethal) in lab studies. May- August (Uncertain) MarchSeptember (Construction: June September), May - October (Construction: June - October) Life Stage Timing (Work W indow Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Monitoring, Maintenance, Research Studies, etc. (minimization for Water Temperatures) Framework programmatic action component, construction activities are not described. NMFS assumes that construction would occur during an appropriate in· water work window and include BMPs and minimization measures to limit potential effects to species. Uncertain. Framework programmatic action component to be implemented in Tier 4 years when river conditions are unsuitable for juvenile winterrun Chinook salmon rearing. Depending on 906 Severi ty of Stress or/Lev el of Benefi t Sublet hal Sublet hal Sublet hal Frequenc y of Exp osure Magnitu de of Effect Weight of Evidence Probable Change in Fitness Reduced reproductive success Proportion of Population Exposed Medium: Supported by multiple scientific and technical pub!ications, however not specific to the region and species. Reduced survival probability Low Low Low: (uncertain) very little information available as to how this action component would be implemented (construction ). Low (7 15%of years) Uncertain Low Reduced survival probability Medium (67% of days >63.5°F) Small Uncertain Low (7% of years) Low: (Programma! ic action component) very little information available as to how this action component would be implemented Stressor Fall and Winter Refill and Redd Maintenance Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function Action Compone nt Small Screen Program (Spawninglreari ng habitat restoration) Construction or installation of fish screens on water diversions. Passage lmpediments/Barri ers, Flow Conditions, Loss of Riparian Habitat and lnstream Cover Winter Minimum flows Juveniles (Upper Sacramento River) May - August (little overlap with October/Novem ber operations) Life Stage (location) Adults, Juveniles (Middle Sacramento River) Juveniles (Upper Sacramento River) May -August (little overlap with December Februa.ry operations) MarchSeptember (Uncertain), May - October (Uncertain) Life Stage Timing (Work W indow Intersection) Framework programmatic action component. Construction activities are not described but assumed construction effects related to installation of fish screens include: changes in flow, stranding (installation of coffer dams), and handling. Decreased flows may reduce access to channel margin and side channel rearing habitats timing and location of trap and haul operations, juvenile green sturgeon could also be collected and returned to the river or relocated. Decreased flows may reduce access to channel margin and side channel rearing habitats Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss ofNatural River Morphology and Function 907 Severi ty of Stress or/Lev el of Benefi t Minor Sublet hal Minor Proportion of Population Exposed Uncertain Low Uncertain Frequenc y of Exp osure Uncertain Low (Uncertai n) Uncertain Magnitu de of Effect Low Low Low Weight of Evidence or as to its effects. Low: minimal information on flow and habitat requirements for juvenile green sturgeon Low: (Programmat ic action component) very little information available as to how this action component would be implemented (construction ). Low: minimal information on flow and habitat requirements for juvenile Probable Change in Fitness Reduced growth rate and survival probability Reduced reproductive success, Reduced survival probability Reduced growth rate and survival probability Action Compone nt Wilkins Slough intakes (Cold water pool mgmt.) Spawning Gravel Injection (Spawninglreari ng habitat restoration) Stressor Entrainment/lmpin gement at water diversions Spawning Habitat Availability, Loss of Riparian Habitat and Instream Cover, Physical Habitat Alteration Riparian vegetation, Loss of Riparian Habitat and Instream Cover, Physical Habitat Alteration Life Stage (location) Juveniles (Middle Sacramento River) Adults, Juveniles (Upper Sacramento River) Adults, Juveniles (Middle Sacramento River) May - October Framework programmatic action component, operation is assumed to comply with NMFSand CDFWfish screening guidance. Benefi cia!: Low (Uncer tain) Low (Benef icial) t Severi ty of Stress or/Lev el of Benefi MarchSeptember (Uncertain), May- August (Uncertain) Increased habitat quality and quantity. Framework programmatic action component. Programmatic action component, no description of timing, location or extent of effects. Benefi cia!: Low Individual Response and Ration.ale of Effect MarchSeptember (Uncertain), May - October (Uncertain) Life Stage Timing (Work W indow Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Division Side-Channel habitat (Spawninglrcari ng habitat restoration) Increased habitat quality and quantity. Framework programmatic action component. no description of timing, location or extent of effects. 908 Proportion of Population Exposed Small Low Uncertain Frequenc y of Exp osure Low High (Permane nt) High (Permanc nt) Magnitu de of Effect Low Low Low Weight of Evidence green sturgeon Low: (uncertain) very little information available as to how this action component would be implemented or its effects when operated. Low: (Programmat ic action component) very little information available as to how this action component would be implemented or the extent of its effects. Low: (Programma! ic action component) very little information available as to how or where this action component would be Probable Change in Fitness Increased survival probability Increased reproductive success and survival probability Increased growth rate Action Compone nt Small Screen Program (Spawninglreari ng habitat restoration) Adult rescue (tier 4 intervention) Operation of a Shasta Dam Raise Stressor Operation of new or repaired fish screens on water diversions. Entrainment!Impin gement at water d.iversions Passage Impediments/Barri ers, Entrainmentllmpin gement at water diversions NA Life Stage (location) Adults, Juveniles (Middle Sacramento River) Adults (Middle Sacramento River) NA March September (Uncertain), May - October (Uncertain) Life Stage Timing (Work W indow Intersection) Framework programmatic action component. Construction activities are not described but operation is assumed to comply with NM FSand CDFW fish screening guidance. Individual Response and Ration.ale of Effect NA MarchSeptember (Uncertain) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Upper Sacramento/ Shasta Division Upper Sacramento/ Shasta Divis ion Upper Sacramento/ Shasta Division Uncertain. Framework programmatic action component. Increased stress and mortality related to capture and handling. Minimization measure intended to increase relative survival of adult salmonids entrained in water diversions (e.g., Yolo and Sutter Bypasses). None. Reclamation has committed to no change in operations with the inclusion of a 909 t Severi ty of Stress or/Lev el of Benefi Benefi cia!: Low Benefi cia!: Low NA Proportion of Population Exposed Uncertain Uncertain (Intervention measure may not apply to green sturgeon?) NA Frequenc y of Exp osure Low Magnitu de of Effect NA Low High (Permane nt) Uncertain (Low: tier 4 years= 7%ofall years) NA Weight of Evidence implemented or the extent of its effects. Low: (Programma! ic action component) very little information available as to how this action component would be implemented (construction ) or its effects when operated. Low: (Programma! ic action component) very little information available as to how this action component would be implemented or as to its effects. NA Probable Change in Fitness Increased survival probability (NMFS/CDF W fish screening criteria 5% loss) Increased reproductive success, Increased survival probability NA Life Stage (location) None (Species not present in Battle Creek) Stressor NA Juveniles - Sacramento River -Delta Juveniles - Sacramento River -Delta Altered hydrodynamics in South Delta/ routing Entrainment and loss at the South Delta export facilities Year round presence Year round presence NA Life Stage Timing (Work W indow Intersection) Individual Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Battle Creek Restoration (Cold water pool mgmt.) Division Upper Sacramento/ Shasta Division Action Compone nt Delta CVP/SWP South Delta Exports Delta CVP/SWP South Delta Exports Shasta Dam raise such that there will be no change in the frequency of meeting manage ment criteria nor will there be any change in the timing and volume of releases. Covered under 2005 NMFSIUSFWS Biological Opinions Mortality or decreases in condition due to migratory delays in response to altered hydrodynamics in channels of the South Delta. Loss of appropriate migratory cues. Delays increase transit time and exposure to predators, poor water quality, and contaminants. Entrainment of juvenile green sturgeon into the fish salvage facilities, un.k nown vulnerability to 910 t Severi ty of Stress or/Lev el of Benefi NA Sublet hal to Lethal Sublet hal to Lethal Proportion of Population Exposed Frequenc y of Exp osure Magnitu de of Effect Weight of Evidence Probable Change in Fitness None (included in the baseline) NA Reduced survival, reduced growth; likely lesser effect in final PA due to revised Ioss thresholds associated withOMR management. NA Medium Medium to Higheffects of hydrodynami cswell studied and modelled. Effects of hydrodynami cs on green sturgeon migrations in South Delta less certain. Reduced survival; lesser effect in final PA due to revised Ioss thresholds associated NA Highyearround exports High Mediumstudies have evaluated the effect of screening facilities, and NA Medium- small highyear round exports Mediumsustained high frequency exposure on small proportio n of Action Compone nt DCC Gate operations - DCC Gate operations · Stressor Routing Routing Life Stage (location) Adults · Sacramento River · Delta Juveniles • Sacramento River- Delta Year round presence Year round presence Life Stage Timing (Work W indow Intersection) Movement into and through the Mokelumne River system, increased transit distance to/from western Delta predation or loss through louvers. Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Movement into the Mokelumne River system from the Sacramento River increased routing distance to the western Delta 911 t Severi ty of Stress or/Lev el of Benefi Minor Minor Proportion of Population Exposed High · Sacramento River basin is only known spawning area, DCC adjacent to main migratory route for adults High-all juvenile green sturgeon emigrate downstream in the Sacramento River. DCC gates are open from mid-June through the end of October. Closed Febmid-May Frequenc y of Exp osure highgates open every year during the summer, closed during winter highgates are open every year during the summer allowing re-routing into Delta interior. Magnitu de of Effect populatio n Medium Medium Weight of Evidence predation on green sturgeon, but not specifically related to loss as well as survival through at the facilities Low · There is little information regarding green sturgeon migratory movements through the DCC- Low- There is little information regarding green sturgeon migratory movements through the DCC - Probable Change in Fitness withOMR management. Delayed migration, possible reduction of spawning success Minimal negative change in fitness, potential exposure to lower quality rearing habitat; lesser effect in final PA due to revised DCC operations in DecemberJanuary. Action Compone nt DCC Gate operations - DCC Gate operations - Stressor Transit times Life Stage (location) Juveniles - Sacramento River -Delta Juveniles - Sacramento River -Delta Year round presence Year round presence Life Stage Timing (Work W indow Intersection) Increased migration times to western Delta Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Altered Hydrodynamics downstream of DCC location When gates are closed, riverine reach of Sacramento extends farther downstream, less tidal infliuence, faster transit times. When gates are opened, more routing into Delta interior 912 Severi ty of Stress or/Lev el of Benefi t Minor Minor Proportion of Population Exposed High - all juvenile green sturgeon emigrate downstream in the Sacramento River. DCC gates are open from mid-June through the end of October. Closed Febmid-May Highopening of gates reduces the proportion of riverine reaches adjacent to the DCC location; closing of gates extends the riverine reaches farther downstream. Entire summer and fall season of emigration occurs with gates in open position. Frequenc y of Exp osure Medium Magnitu de of Effect Medium Highgates are operated every year open during the summer, closed during the Febmid-May period. highgates are operated every year open during the summer, closed during the Feb mid-May period. Weight of Evidence Low - There is little information regarding green sturgeon migratory movements through the DCC- Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Low- There is little information regarding green sturgeon migratory movements through the DCC - Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Probable Change in Fitness Minimal negative change in fitness, potential exposure to lower quality rearing habitat; lesser effect in final PAdue to revised DCC operations in DecemberJanuary. Minjmal negative change in fitness, potential exposure to lower quality rearing habitat; lesser effect in final PA due to revised DCC operations in DecemberJanuary. Action Compone nt South Delta Agricultural Barriers Stressor transit times transit times Life Stage (location) Juveniles - South Delta Adults - South Delta Year round presence Life Stage Timing (Work W indow Intersection) Individual Response and Ration.ale of Effect Year round presence Delayed migration and increased transit times with potential for i.ncreased mortality due to increased exposure to poor water quality and high water temperatures Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta South Delta Agricultural Barriers Delayed migration and increased transit times with potential for increased mortality due to increased exposure to poor water quality and high water temperatures 913 t Severi ty of Stress or/Lev el of Benefi Sublet hal to Lethal Sublet hal to Lethal Proportion of Population Exposed High Frequenc y of Exp osure Magnitu de of Effect High Small Small Medium installatio n of barriers occurs every year from April/Ma y through the end of Novernbe rand blocks off free passage through the three main channels of the South Delta Mediuminstallatio n of barriers occurs every year from Aprii!Ma y through the end of Novernbe rand blocks off free passage through the three main channels of the Reduced survival Probable Change in Fitness Medium several studies have indicated that the barriers increase transit time through the South Delta and increase exposure to ambient water quality conditions Reduced survival Weight of Evidence Mediumseveral studies have indicated that the barriers increase transit time through the South Delta and increase exposure to ambient water quality conditions Action Compone nt CCF aquatic weed control Stressor exposure to herbicides exposure to herbicides Life Stage (location) Adults - Sacramento River - Delta Juveniles - Sacramento River - Delta Year round presence Year round presence Life Stage Timing (Work W indow Intersection) adverse physiological effects (i.e., reduced growth and survival), due to exposure to hannful compounds in the water Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division De lta Delta CCF aquatic weed control Adverse physiological effects (i.e., reduced growth and survival), and increased vulnerability to predation due to exposure to hannful compounds in the water 914 t Severi ty of Stress or/Lev el of Benefi Sublet hal to Lethal Sublet hal to Lethal Proportion of Population Exposed Small Small Frequenc y of Exp osure High High Magnitu de of Effect Probable Change in Fitness Reduced survival Weight of Evidence Medium Medium several ecotoxicolog ical studies on the herbicides to be used. The majority of the studies are on surrogate fish species. Reduced survival South Delta Medium Mediumseveral ecotoxicolog ical studies on the herbicides to be used. The majority of the studies are on surrogate fish species. Action Compone nt DCC Gate operations - North Bay Aqueduct Stressor Increased entrainment and loss at the South Delta Exports facilities Life Stage (location) Juveniles - Sacramento River -Delta Juveniles - Sacramento River -Delta Year round presence Year round presence Life Stage Timing (Work W indow Intersection) Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Entrainment and impingement onto fish screens Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. 915 Severi ty of Stress or/Lev el of Benefi t Sublet hal to Lethal Minor Proportion of Population Exposed Small to Medium Small Magnitu de of Effect Reduced survival; lesser effect in final PA due to revised DCC operations in DecemberJanuary and revised loss thresholds. Probable Change in Fitness Frequenc y of Exp osure Medium numerous studies have evaluated the potential risk to salmonids entering the Delta interior and becoming vulnerable to entrainment at the fish salvage facilities. Unknown applicability to green sturgeon Minimal negative change in fitness Weight of Evidence High Low sustained populatio n effects on a small to medium proportio n of the populatio n present in the Delta Highmonitoring has few observations of green sturgeon at this location, multiple studies regarding efficiency of positive barrier fish screens high Lowscreens are designed for delta smelt criteria, few green sturgeon expected to be present at screen location Action Compone nt North Bay Aqueduct North Bay Aqueduct Stressor Routing Entrainment during sedime nt cleaning Life Stage (location) Juveniles - Sacramento River -Delta Juveniles - Sacramento River -Delta Juveniles - Sacramento River -Delta Year round presence Year round presence Injury or death due to entrainment into dredge or impingement onto fish screens Increased migration times to western Delta Individual Response and Ration.ale of Effe ct Year round presence Life Stage Timing (Work W indow Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division De lta De lta De lta North Bay Aqueduct Impingement/ capture during aquatic weed cleaning Injury or death due to impingement, capture by grappling hooks during weed removal 916 Severi ty of Stress or/Lev el of Benefi t Minor Sublet hal to Lethal Sublet hal to Lethal Proportion of Population Exposed high Frequenc y of Exp osure Magnitu de of Effect Small Low . Sediment removed infrequent ly Small Small Low. Aquatic weeds removed infrequent ly Lowvery small proportio n of populatio nwill be present in Barker Slough, low impacts of diversion volumes on hydrodyn amics Low fish unlike ly to be in area of screens dur ing cleaning Lowfish unlikely to be in area of screens during cleaning Weight of Evidence Low - There is little information regarding green sturgeon migratory movements through the Delta Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Low. No reports or studies available Low. No reports or studies available Probable Change in Fitness Minimal negative change in fitness Mini mal change in fitness Minimal change in fitness Action Compone nt CCWD Rock Slough water diversions Predator removal studies Stressor routing capture in sampling gear Temporary change in water flow/water quality (20 days Oct-May, 60 days June-Sept) Life Stage (location) Juveniles - Sacramento River -Delta Juveniles • Sacramento River -Delta Adults and juveniles may migrate through the area on their way to spawning grounds or as outrnigrating juveniles. Year round presence Year round presence Life Stage Timing (Work W indow Intersection) Increased vulnerability to injury and predation due to entanglement/entr apment in sampling gear Delayed migration and increased transit times Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division De lta De lta Delta 2.5.6.8.1.1.4 Suisun Marsh Roaring River Distribution System Food Subsidy Studies SMSCGops from October through May coincides with the upstream migration of green sturgeon and late winter and spring downstream juvenile migration. During summer ops, juvenile and adult green sturgeon may be present. During the annual 70 to 80 days of periodic operation, individual adult green sturgeon may be delayed in their spawning migration from a few hours to several days. Green sturgeon are less affected since they spawn in deep turbulent sections of the upper reaches of the Sacramento River. 917 Severi ty of Stress or/Lev el of Benefi t Minor Sublet hal to Lethal Minor Frequenc y of Exp osure Magnitu de of Effect Low. No reports or studies available regarding green sturgeon presence in front of the fish screens Weight of Evidence Proportion of Population Exposed Small Low small numbers offish are likely to be i.n the vicinity of the fish screens and intake Probable Change in Fitness Minimal change in fitness high pumping through the Rock Slough diversion occurs every year Reduced survival, potential injury from gear or handling Low Medium · Several reports from previous predator removal studies, literature on sampling methods. Minimal SmaU Low Low- data on green sturgeon migration and rearing in Suisun Marsh is low Low infrequent sampling over two to three years of study Low Low frequency for adult migration period (<10% of days) Action Compone nt 2.5.6.8. I. I .4 North Delta Food Subsidies/ Colusa Basin Drain Stressor Temporary water quality (July/Sept) Altered hydrodynamics and migration routing in the Ship Channel Adult green sturgeon migrate through the area on their way to spawning grounds or as outrnigrating juveniles Du.ring agricultural drainage into the N Delta, juvenile and adult green sturgeon are likely to be exposed to potential increase in contaminants. Potential increase in water temp from ag ditch water (not described in ROConLTO BA). Life Stage (location) Adults and Juveniles Year-round presence in Delta Life Stage Timing (Work W indow Intersection) Individual Response and Rationale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division De lta Delta Sacramento Deep Water Ship Channel Food Study May be temporarily exposed to increased contamjnants from agricultural drainage from Colusa Basin Drain to Cache Slough during July and September. Exposure would likely be limited and short-term. Given the short time period, significant effects are not expected. Potential delays and false attraction to the opening and closing of the boat locks, potential diversion from Sacramento River into Deepwater ship channel when boat locks are open, exposure to reduced water quality in Port of Sacramento and Deepwater ship channel, increased exposure to angling and poaching, increased exposure to 918 Severi ty of Stress or/Lev el of Benefi t Minor Sublet hal to Lethal Frequenc y of Exp osure Magnitu de of Effect Proportion of Population Exposed Weight of Evidence Probable Change in Fitness Minimal Low Low nutrient suppleme ntation in area of Cache Slough Low - little information available regarding the effects of proposed nutrient supplemental ion on green sturgeon Low initially study will last a few years, conducted during the July through Septembe r period Reduced fitness Low Low Low Low - little information on sturgeon migration behavior and use within the Sacramento Deepwater ship channel, and Port of Sacramento Action Compone nt Water Transfer Window Extension Stressor Low fall flows Temporary change in water flow/water quality Life Stage (location) Adults and Juveniles Sacramento River Delta Adults and Juveniles Individual Response and Ration.ale of Effect Year-round presence Elevated flows in October or November due to additional water being transferred may decrease transit times to the Delta in riverine reaches shipping traffic and ship strikes Year-round presence in Delta Life Stage Timing (Work W indow Intersection) Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta De lta Fall Delta Smelt Habitat Operations Potential changes in Delta hydrodynamics due to export reductions and increased Delta inflow from upstream may reduce entrainment at the export facilities and create better foraging opportun ities, induce downstream migrat ions 919 Severi ty of Stress or/Lev el of Benefi t Benefi cia!: Low Benefi cia!: Low Proportion of Population Exposed Frequenc y of Exp osure Magnitu de of Effect Weight of Evidence Probable Change in Fitness Minimal benefit Low Low, very little information available on green sturgeon migratory behavior in relation to flow levels. Minimal benefit Medium Low - little information available on green sturgeon regional movements in the Delta and their foraging behavior. Medium Medium Medium (Septemb erand October of above normal and wet water year types) Low adult and juvenile green sturgeon already can move to find suitable foraging areas in the Delta Action Compone nt PA Conditions Stressor Life Stage (location) Adults and juveniles -San Joaquin River between the confluence with the Stanislaus River and Mossdale Life Stage Timing (Work W indow Intersection) Potential for decreased survival or growth due to increased exposure to poor water quality and high water temperatures Individual Response and Ration.ale of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Eastside/San Joaquin Reductions in spring flows and associated temperatures, water quality, water depth, contaminant concentrations, wetland function. Adults and juveniles present year round, but responses to flow and temperaturerelated stressors most likely during winter and spring, when the PA has the most limiting effect on flows. 920 Severi ty of Stress or/Lev el of Benefi t Sublet hal Small Proportion of Population Exposed Low Frequenc y of Exp osure Low Magnitu de of Effect Weight of Evidence Low information available on groon sturgeon use of the lower San Joaquin River between Mossdale and the confluence of the Stanislaus River Probable Change in Fitness Reduced survival or reduced growth Biological Opinion for the Long-Term Operation of the CVP and SWP sDPS Green Sturgeon Abundance As it is for salmonids, the three key attributes of the abundance VSP parameter require that the relative size of a spawning population be large enough to: (1) have a high probability of surviving environmental variability, (2) allow compensatory process to provide resilience from environmental and anthropogenic disturbance, and (3) maintain its genetic diversity (McElhany et al. 2000). Although, the ability to derive a reliable estimate of sDPS green sturgeon population abundance is challenging, the current, best estimate of annual abundance of sDPS green sturgeon adults is 2,1 06 [95 percent CI = 1,246-2,966 (Mora 201 6a)]. To evaluate the effects of the PA on the abundance VSP parameter of sDPS green sturgeon, NMFS assesses if the probable change in fitness attributed to the effects of a stressor would result in "reduced survival" or "reduced reproductive success" (identified in Table 2.8.7-1) for a significant proportion of adults. Changes to the juvenile and sub-adult populations are also considered; however, those affects are reflected in the assessment of the productivity VSP parameter, because juveniles and sub-adults are not part of the effective population and changes to the fitness of these life stages are not considered in the assessment of the abundance VSP parameter. NMFS expects primarily low and medium magnitude impacts to sDPS green sturgeon from the P A such that only a small portion of the population are likely to experience mortality or substantial injury, and elements ofthe PA that affect medium to large portion of the population will be of lower severity (i.e., behavioral). Examples of these impacts include reduced reproductive success for individuals spawning in lower reaches of the Sacramento River due to elevated water temperatures and migration delays due to the DCC and South Delta agricultural barriers. Presumably, adult sDPS green sturgeon exposed to elevated water temperatures would adjust spawning to somewhere in the nearly 100-mile stretch of progressively cooler spawning habitat upstream of Hamilton City. Thus, temperature effects are only expected to temporarily impact a small number of individuals and are unlikely to constitute a reduction in the effective population size ofthe sDPS. Migration delays are likely to reduce the fitness and eventual spawning success of exposed adults, which, would constitute a reduction in the effective population size of the sDPS. In rare instances, some adults could be permanently re-routed into the South Delta and experience reduced survival. However, migration delays in the Delta are only expected to affect a small portion of the adult population for a relatively short duration (i.e., temporary reduction in reproductive success). Thus, effects of the P A are unlikely to significantly reduce the abundance VSP parameter of sDPS green sturgeon. Southern DPS Green Sturgeon Productivity The productivity VSP parameter for sDPS green sturgeon, is described by the key attributes of a population' s ability to reproduce itself, and the survival of early life stages. For salmonids, the productivity VSP parameter is also described by a popu1ation's resilience to the infllllence of hatchery-produced spawners, but since sDPS green sturgeon is not supplemented by a hatchery, this attribute does not factor into the consideration of productivity VSP parameter. Based on the attributes remaining for sDPS green sturgeon, the common metric used to assess the productivity VSP parameter is the population growth rate (or decline). Lindley et al. (2007) further identified that the population growth rate (10-year trend estimated from the slope of log-transformed estimated run size), must not show a decline in order for a salmonid population to be considered at a low risk of extinction. If the population is experiencing a decline within last two generations to annual run size 500 spawners, or run size > 500 but declining 10 percent per year, that 921 Biological Opinion for the Long-Term Operation of the CVP and SWP population would be considered at high risk of extinction. Direct measurements of productivity, such as larval count data at the RBDD rotary screw traps is highly variable and because of potential high mortality of the larval life stage and slow maturation of the species, trend detection dependent upon these types of data sets is extremely difficult. Given the limitations of using the metric of population growth rate (based on trend estimates) to assess changes in the sDPS green sturgeon population•s productivity VSP parameter, we examine the relative effect of actions that would impact the juvenile population. Specifically, if the probable change in fitness attributed to the effects of a stressor would result in "reduced survival" or "reduced growth" (identified in Tables 2-259 and 2-260) for a significant proportion of the juvenile population (2:: 10 percent) in a given year, that would be considered a reduction of the productivity VSP parameter of the population. NMFS expects that the PA will have multiple impacts that will affect the abundance and fitness ofjuvenile sDPS green sturgeon, but these impacts are unlikely to affect the productivity VSP parameter of sDPS. Most of the effects are expected to have a low to medium magnitude of impact to exposed sDPS green sturgeon individuals such that they are unlikely to result in mortality or substantial injury. As described in Section 2.5.1.2 Operation Effects, under the PA, Delta operations and agricultural barriers continue to alter the natural hydrograph of the Delta and its waterways. This impacts the productivity VSP parameter of sDPS green sturgeon (i.e., growth and recruitment) because of potentially increased travel times of juveniles and exposure to degraded habitats. The PA also includes operations ofthe existing South Delta fish salvage facilities and increased reverse flows in the South Delta compared to current conditions, which will result in additional negative effects such as direct mortality of early life stages at and around the South Delta fish salvage facilities (e.g., entrainment, impingement:). Based on extremely low sampling numbers and reports, only a small proportion of the juvenile population is believed to experience significant migration delays or entrainment into the South Delta. This suggests proposed Delta operations and barriers will only have a small effect on sDPS green sturgeon recruitment and production, which may be further reduced by the revisions to the loss thresholds associated with OMR management in the fmal PA The PA also includes restoration of Delta habitat, which has the potential to benefit the productivity VSP parameter of sDPS green sturgeon and offset impacts associated with South Delta operations and agricultural barriers. Other actions associated with the PA that are considered to have impacts on the productivity of sDPS green sturgeon include water temperature and flow management in the upper Sacramento River. These actions are expected to affect sDPS green sturgeon productivity by reducing fitness of a small to medium proportion of larvae and juveniles that rear near the downstream extent of the spawning reach. As described above, it is presumed that during low flow conditions, spawning and rearing of the majority of the sDPS green sturgeon population would occur in more suitable habitats upriver and offset potential poor spawning production of downriver reaches. Revisions to the Cold Water Pool Management section of the final PA include the addition of Section 4.10.1.3.3 Upper Sacramento Performance Metrics. The objective ofthese performance metrics is to ensure that the performance of the PA operations for temperature management falls within the modeled range, and shows a tendency towards performing at least as well as the distribution produced by the simulation modeling of winter-run Chinook salmon temperature dependent mortality. This revision affects the green sturgeon analysis by increasing the certainty that the analysis more accurately characterizes exposure and risk to green sturgeon due to the PA 922 Biological Opinion for the Long-Term Operation of the CVP and SWP operations. With this change, we consider our previous analysis of the modeled outcomes of temperature management - which is based on the central tendency to capture the most likely conditions- to be a more accurate characterization of projected and expected operations. The results described in Section 2.5.2.3.3.1 Summer Cold Water Pool Management do not change quantitatively due to the revisions included in the final P A, as this commitment to assess cold water management does not affect the modeling results used to characterize the exposure of the species to the stressor of increased water temperature, or the risk based on the expected longterm proportion of years in each Tier type. We do consider the project components that are intended to offer as much protection as practicable in drought or extreme conditions, including the process for development of an annual temperature management plan, the use of conservative forecasts, protection of the third cohort of winter-run Chinook salmon after two consecutive years of poor survival, and specific "at the ready" actions for drought and dry years. The temperature management plan may reduce the likelihood of exceeding the temperature target, which is used in the characterization of exposure to increased temperatures in the analysis. The conservation measures intended to protect the third cohort of winter-run Chinook salmon after two consecutive years of poor survival may allow opportunities for ac6ons to be implemented to reduce temperature-related effects on green sturgeon despite the probability of year types that may occur. Finally, NMFS expects a reduction in extreme effects on the species throughout extended drought due to the Drought and Dry Year Actions. We note that potential benefit of a toolkit of actions to be taken in drought conditions, and the process by which early warnings of drought conditions may allow for clear and swift development of a drought contingency plan, but we also consider that managing a listed species in a crisis-management scenario is not a long-term strategy to achieving viability. Based on the available information, NMFS assumes the effect of water temperature and flow management in the upper Sacramento River, Delta operations, agricultural barriers, and restoration will not significantly reduce sDPS green sturgeon production. However, annual recruitment monitoring does not exist (and is not included in the PA) and our understanding of the effect of the PA on sDPS green sturgeon production may change with improved measures of production. Southern DPS Green Sturgeon Spatial Structure The spatial structure parameter of a VSP is determined by the availability, diversity, and utilization of properly functioning habitats and the connections between such habitats. Southern DPS green sturgeon are primarily limited in spatial structure as they comprise only one population that spawns in the Sacramento River but also spawns opportunistically in the Feather and Yuba rivers. The listing highlighted this as a major threat to the species, and to reduce this risk, consistent spawning is needed in at least one additional location outside the mainstem Sacramento River. Given the relative lack of habitat available to sDPS green sturgeon in the baseline, there could be considerable impact to the spatial structure VSP parameter if it is further reduced. Stressors, attributed to the PA, that would increase or further limit access to available habitats would be expected to affect the spatial structure VSP parameter. As described in Section 2.5, and given the level of exposure to sDPS green sturgeon to the agricultural barriers and South Delta exports, the PA could result in further limiting the species ability to move between habitats. However, these elements of the PA are not anticipated to impact a large proportion of the juvenile or adult population with our current understanding of 923 Biological Opinion for the Long-Term Operation of the CVP and SWP sDPS green sturgeon habitat usage and migration. In Section 2.5.1.2.1 Increased Upstream Temperature, temperatures under the PA were above the suitable threshold for sDPS green sturgeon spawning and incubation during certain months of a percentage of years. These temperature-related effects are not expected to significantly impact sDPS green sturgeon spatial structure, however, because under normal conditions suitable temperatures for spawning and incubation are available in a relatively large reach of spawning habitat on the Sacramento River. Therefore, the PA would not result in Delta or upstream conditions in the Sacramento River that would diminish the spatial structure VSP parameter in a way that is expected to limit the appropriate exchange of spawners or the expansion of a population into underutilized habitat. Southern DPS Green Sturgeon Diversity The diversity VSP parameter comprises the three key attributes of ( 1) variation in traits such as run timing, age structure, size, fecundity, morphology, behavior and genetic characteristics; (2) resilient gene flow among populations that is limited; and (3) maintenance of ecological variation (McElhany et al. 2000). Diversity is related to population viability because it allows a species to exploit a wider array of environments, protects against short-term spatial and temporal changes in the environment, and provides the raw material for surviving long-term environmental changes. At this time, we do not have methods to directly measure diversity or compare or assess changes to the present and historical levels of diversity. However, stressors, attributed to the PA that would limit the variation in sDPS green sturgeon traits, or that would select for a particular behavior or life history, would be expected to in·fluence the diversity VSP parameter of the sDPS green sturgeon population. Overall, the PA is not expected to exert any additional selective pressures on sDPS green sturgeon and the div·ersity VSP parameter of the population is expected to remain unchanged. Given the higher temperature tolerances of the early life stage of sDPS green sturgeon compared to salmonids (and the recent decommissioning ofRBDD in 2012), appropriate conditions for spawning and incubation are present year-round in accessible reaches of the Sacramento River. This allows for the potential for multiple spawning runs of sDPS green sturgeon in the Sacramento River in most years. Therefore, the PA is not expected to alter the diversity VSP parameter of the sDPS green sturgeon population. 2.8.7.3 Assess the Risk to DPS Given that the entire sDPS green sturgeon is represented by a single population, the discussion points above apply equally to both the population level analysis and that of the DPS as a whole. As described in the VSP analysis above, effects of the P A are unlikely to significantly reduce the abundance and productivity, diminish the spatial structure, or alter the diversity of sDPS green sturgeon. Thus, as summarized above and described in Section 2.5 Effects ofthe Action on Species, the PA is expected to have a negative effect on the population, but it will not appreciably reduce the survival or viability of sDPS green sturgeon. The sDPS green sturgeon recovery plan (National Marine Fisheries Service 2018g) describes criteria for determining sOPS green sturgeon population recovery and alleviation of threats. Demographic recovery criteria are population metrics that if achieved demonstrate population recovery and alleviation of threats. Threat-based recovery criteria involve actions that would result in population recovery and are as follows: 924 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • • • • Access to spawning habitat is improved through barrier removal or modification in the Sacramento, Feather, and/or Yuba rivers such that successful spawning occurs annually in at least two rivers. Volitional passage is provided for adult green sturgeon througlh the Yolo and Sutter bypasses. Water temperature and flows are provided in spawning habitat such that juvenile recruitment is documented annually. Adult contaminant levels are below levels that are identified as limiting population maintenance and growth. Operation guidelines and/or fish screens are applied to water diversions in mainstem Sacramento, Feather, and Yuba rivers and San Francisco Bay Delta Estuary such that early life stage entrainment is below a level that limits juvenile recruitment. Take of adults and subadults through poaching and state, federal and tribal fisheries is minimal and does not limit population persistence and growth. The PA does not include actions on the Feather or Yuba rivers that would support an alternate sDPS green sturgeon spawning river (criteria number 1 above). Passage through the Yolo and Sutter bypasses are also not included in the P A (criteria number 2). Factors directly affecting adult contaminant levels and take are not included in the PA (criteria numbers 4 and 6). For criteria that are associated with the PA, the influence on recovery is uncertain. Water temperatures and flows necessary for sDPS green sturgeon recruitment are poorly understood. Southern DPS green sturgeon larval abundance and juvenile recruitment both appear to be related to elevated fl.ows in the Sacramento River, although specific operational targets to support spawning and recruitment (e.g., Sacramento River temperature compliance point) have not been developed (criteria number 3). Conversely, recruitment ofsDPS green sturgeon in critically dry years is likely poor, but without knowledge of the specific mechanism for recruitment failure (e.g., decline of riverine or estuarine habitat) the effect of the PA on recruitment is unclear. The proposed small screen program may reduce early life stage entrainment of sDPS green sturgeon and increase juvenile recruitment if implemented strategically or on a large scale (criteria number 5). With our current understanding of sDPS green sturgeon, the PA does not include actions that specifically preclude recovery. After reviewing and analyzing the current status of the listed species, the environmental baseline, the effects of the proposed action, any effects of interrelated and interdependent activities, and cumulative effects, it is NMFS' biological opinion that the proposed action is not likely to reduce appreciably the likelihood of both survival and recovery of the Southern DPS of North American green sturgeon (Table 2.8.7-2). 925 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.8.7-2. Reasoning and decision-making steps for analyzing the effects of the proposed action on green sturgeon. Darker shade identifies the conclusion at each step of decision-making. Acronyms a nd abbreviations in the action column refer to not likely to adversely affect (NLAA) and not likely/likely to jeopardize (NLJ/LJ). Step True/False Action True End False Go to B True NLAA False c True NLAA c Listed individuals are not likely to respond upon being exposed to one or more of the stressors produced by the proposed action. Available Evidence: Multiple stressors, including but not limited to passage barriers and operations will rise to a level ofeffect that will engender a response from exposed individuals. False Go to D True NLAA D Any responses are not likely to constitute " t ake" or reduce the fitness of the individuals that have been exposed. Available Evidence: Multiple stressors, including but not limited to those associated with agricultural barriers and operations are expected to result in a reduction ofoverall fitness ofindividuals which could rise to the level of "take. " False Go to E NLJ E Any reductions in individual fitness are not likely to True reduce the viability of the populations those individuals represent. Available Evidence: The overall reduction in fitness of individuals caused by the PA is expected to reduce some of the False parameters describing a viable population; however, those reductions would not constitute a reduction in viability ofthe population or an increase in extinction risk for the species. F True NLJ A B Apply the Available Evidence to Deter mine if.. . The proposed action is not likely to produce stressors that have direct or indirect a dverse consequences on the environment. Available Evidence: The PA will produce multiple stressors that will adversely affect green sturgeon including, but not limited to: impingement and entrainment, and effects related to reduced Delta flows. Listed individuals are not likely to be exposed to one or more ofthose stressors or one or more of the direct or indirect consequences of the proposed action. Available Evidence: A medium proportion of individuals from the sDPS population are expected to be exposed to impacts from operations in the P A throughout the year over multiple years. 926 Go to Go to F Biological Opinion for the Long-Term Operation of the CVP and SWP Step Apply the Available Evidence to Determine if•.. Any reductions in the viability of the exposed populations are not likely to reduce the viability of the species. Available Evidence: Not Applicable 2.8.8 • True/False Action False LJ Green Sturgeon Critical Habitat Critical habitat designated October 9, 2009 (74 FR 52300) 2.8.8.1 Status As described in Section 2.6, critical habitat for sDPS green sturgeon consists of several physical and biological features occurring in freshwater, riverine, estuarine, and marine habitats that are essential for the conservation of the species. Designated! critical habitat for sDPS green sturgeon is composed of seven PBFs that are shared among different life stages across the different habitat types. All ofthose PBFs are considered necessary habitat features that facilitate successful spawning, rearing, and migration. Therefore, we have evaluated the effect of the P A in terms of its effect on the PBFs present in the freshwater and estuarine habitats for rearing juveniles and migrating juveniles, adults, and sub-adults. As described in Section 2.2 Rangewide Status of the Species and Critical Habitat, many of the PBFs of sDPS green sturgeon designated critical habitat are currently degraded or impaired and provide limited high quality habitat. Features that lessen the quality of migratory corridors and rearing habitat for juveniles include unscreened or inadequately screened diversions, altered flows in the Delta, and the presence of contaminants in sediment. Although the current conditions of sDPS green sturgeon critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain in both the Sacramento/San Joaquin River watersheds and the Delta are considered to have high intrinsic value for the conservation of the species. Summary of Proposed Action Effects on Designated Critical Habitat Detailed descriptions regarding the impacts to designated critical habitat caused by stressors associated with the P A are presented in Section 2.6, Effects of the Action to Critical Habitat. The PA-related effects to sDPS green sturgeon designated critical habitat have been further separated by life-stage specific habitat type and assessed by the effects on the PBFs found therein. Much like the effects to the species, the effects to sDPS green sturgeon designated critical habitat are summarized in Table 2.8.8-1. Habitat for Spawning Adults, Incubation of Eggs, and Rearing Larvae and Juveniles With the P A, NMFS does not expect an appreciable reduction in the PBFs of sDPS green sturgeon critical habitat used for spawning of adults and rearing for larvae and juveniles. Specifically, the PAis not expected to adversely impact the PBFs of these habitats, including: substrate type or size, water flow, and water quality. The PA will have periods of higher temperature in lower reaches of spawning habitat, but suitable spawning and incubation temperature is available in accessible upstream areas. The PA also does not describe any specific 927 Biological Opinion for the Long-Term Operation of the CVP and SWP in-water activity that would appreciably disturb, contaminate, remove, or otherwise degrade the substrate type or size within the known spawning and freshwater rearing range for sDPS green sturgeon in the Sacramento River. Based on related entries in Table 2. 8.8-1, the combined effects of the PA, environmental baseline, and cumulative effects are not expected to negatively affect these PBFs. Freshwater and Estuarine Rearing and Migratory Corridors for Juveniles and Adults The PA is expected to result in some degradation to the migratory PBFs for juvenile and adult life stages in the lower Sacramento River and Delta. The effects of combined exports present an entrainment issue that could delay migration, expose individuals to poor rearing habitat, or decrease survival through entrainment into the fish salvage facilities themselves. Southern DPS green sturgeon may be exposed to these effects year-round and for the duration of the PA with effects increasing in magnitude the closer to the export faci lities the fish are located. Export effects may be reduced, compared to the original PA, by the revisions to loss thresholds associated with OMR management in the final PA Likewise, DCC gate operations and the operation of the South Delta agricultural barriers enhance the potential to delay movement and migratory behavior in the channels of the South Delta. Juvenile and adult sDPS green sturgeon may be trapped behind the barriers after construction/operation for varying periods of time. Revisions to the DCC operations in the final PA may lead to more closures, which may enhance the potential for migratory delays for sDPS green sturgeon but may reduce the routing of juveniles into the interior Delta. While the PBFs in the designated freshwater riverine and estuarine habitat are degraded by the PA, they still function in providing access from the upper river habitat to the marine environment. 928 Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component Summer Cold Water Management (2.5.2. 1.3) Upper Middle Sacramento River (Cottonwood Creek to Hamilton City) Middle Sacramento River Middle Sacramento River Spawning Gravel Injection (2.5.2.3 .2. 1) Seasonal Operations (2.5.2.1) Summer Cold Water Management (2.5.2. 1.3) Location of Effect Response and Rationale of Effect Water Quality PA temperatures in excess of 63.5°F (39% of days) can lead to Sublethal abnormal development of eggs and larvae. Temperatures higher than 71. 5°F (<1% of days) would cause a decrease in egg survival. Water Flow, Food Resources, Sediment Quality, Depth Water Flow PBF can determine access to the quantity and quality of the other PBFs (Food Resources, Sediment Quality, and Depth) in the freshwater rearing habitat. Small increases in flow onto the bypasses (Yolo and Sutter) would provide a small increase to freshwater rearing habitat for juvenile green sturgeon. Water Quality Substrate Type or Size PA temperatures in excess of66.2°F (7% of days) are sub optimal for green sturgeon reariog, leading to reduced growth. PBFs Affected Table 2.8.8-1. Summary of PA related effects on sDPS green sturgeon critical habitat. Division Shasta Shasta Shasta Shasta Upper Middle Sacramento River (Cottonwood Creek to Hamilton City) Framework programmatic action component. As part of adaptive management Reclamation would implement spawning gravel, injection projcct(s) in the action area. This action component could increase the quantity and quality of available substrate suitable for spawning. 929 Medium Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Decreased Water QualityPBF Decreased Water QualityPBF W eight of Evidence Low High: Supported by multiple scientific and technical publications that include lab studies to verifY temperature thresholds for optimal Increased Water Flow PBF, increased access to Food Resources, Sediment Quality, and Depth PBFs Probable C hange in PBF Supportin g the Life History Needs of the Species Low Medium: Supported by scientific and technical publications that include modeled flow conditions specific to the action area. Increased qu antity/quality of spawning Substrate Type or Size PBF Magnitude of E ffect Low (Uncertain) Low: (Programmatic action component) very little information available as to how or where th is action component would be implemented or the extent of its effects. Action Comp()nent Side-Channel habitat (2.5.2.3.2.2) Small Screen Program (2.5.2.3.2.3) Lower Intakes near Wilkins Slough (2.5.2.3.1.2) SWP and CVP South Delta Operations Middle Sacramento Ri vcr Middle Sacramento River Upper Middle Sacramento River (Cottonwood Creek to Hamilton City) Location of Effect Migratory Corridors Migratory Corridors Water Flow, Substrate Type or Size Framework programmatic action component. Construction activities (?) are not described but design and diversion operation is assumed to comply with NMFS and CDFW fish screening guidance. Framework programmatic action component. Construction activities (?) arc not described but design and diversion operation is assumed to comply with NMFS and CDFW fish screening guidance. Framework programmatic action component. As part of adaptive management Reclamation would implement sidechannel habitat :restoration project(s) in the action area. This action component could increase access to areas suitable for spawning which includes increased flow to those areas as well as the quantity and quality spawning substrate. Response and Rationale of E ffect water flow, migratory corridors Operations of the CVP and SWP exports alter the flows in the channels of the South Delta, degrading the functioning of the channels as a migratory corridor to reach the western Delta a.nd SF Bay. Effects of the altered flow conditions increases the exposure to entrainment into the export facilities. PBFs Affected Biological Opinion for the Long-Term Operation of the CVP and SWP Division Shasta Shasta Shasta Delta Freshwater Riverine Habitat for Juveniles and Sub-adults: Lower Sacramento, San Joaquin, and American Rivers and Delta [Freeport to Golden Gate (GG) Bridge) 930 Weight of Evidence Low (Uncertain) Low: (Programmatic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Magnit ude of E ffect Low (Uncertain) Low (Uncertain) Low: (Programmatic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Low: (Programmatic action component) very little information available as to how or where this action component would be implemented or the extent of its effects. Medium - Numerous peer reviewed studies on salmonids have shown how altered hydrodynamics in the channels surrounding the exports arc impacting migratory behavior. However, there are no studies directed at green sturgeon; thus uncertainty as to the magnitude of impacts. MediumExtended duration of residency in the Delta increases the frequency of exposure to altered migratory corridors for green sturgeon, and increases the vulnerability to entrainment into the export facilities. Probable Change in PBF Supporting the Life H istory Needs ()f the Species Increased Water Flow PBF (spatial), increased quantity/quality of spawning Substrate Type or Size PBF Increased access to Migratory Corridors PBF Increased access to Migratory Corridors PBF OMR Reduction in the quality of the migratory corridor; lesser effect in final P A due to revised loss thresholds associated with managem ent. Action Comp()nent Water transfers Freshwater Riverine Habitat for Juveniles and Sub-adults: Lower Sacramento, San Joaquin, and American Rivers and Delta (Freeport to GG Bridge) Location of Effect water flow, migratory corridors Water flow, water quality, migratory corridor, food resources PBFs Affected Increased flow may aid downstream migration ofjuveniles and adults during the extended water transfer window (July I to November 30) and improve water quality parameters (dissolved oxygen, temperature). Improved flows and water quality may improve primary and secondary productivity, which enhances the forage base for green sturgeon. Low - volumes of transfers may not be enough to sustain changes in flow or water quality for very long. Dependent on frequency and volumes of released transfer water from upstream reservoirs. Magnitude of E ffect Operations of the DCC gate and exports at the NBA and CCWD may alter the migratory corridors used by green sturgeon. Alternative routes may have better, less, or equal quality habitat for green sturgeon. Extended residence time of green sturgeon within the Delta indicates that multiple waterways and habitats will be utilized during their time in the Delta. Response and Rationale of E ffect Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta DCC Gate operations, NBA Operations, CCWD Rock Slough Operations Freshwater Riverine Habitat for Juveniles and Sub-adults: Lower Sacramento, San Joaquin, and American Rivers and Delta (Freeport to GG Bridge) Low -export volumes at the NBAandCCWD are relatively small and any migratory delays are small compared to the time green sturgeon spend in the Delta; rerouting of green sturgeon through the DCC into the Delta interior may not impact survival of green sturgeon over the duration of their residency in the Delta. 931 Weight of Evidence Medium - numerous studies and reports regarding water quality requirements for green sturgeon, less so for flows. Modeling is generally too coarse to get fine scale resolution of hydrodynamic changes based on the size of releases. Temporary improvement in flows and water quality as a result of the releases of transfer water during the extended transfer window. Better water quality and higher flows may improve food resources for green sturgeon. Probable Change in PBF Supporting the Life H istory Needs ()f the Species Low- few studies exist that track the migratory behavior through the Delta for juvenile or adult lifestages, and those studies do not examine fine scale movements or use of Delta habitats. Unknown which Delta habitats are preferred by each life stage category and how they are utilized. Impacts of migratory delays or re-routing are unknown with certainty, but will be increased due to operations. Revisions to the DCC operations in the final PA may lead to more closures, which may enhance the potential for migratory delays for sOPS green sturgeon but may reduce the routing ofjuveniles into the interior Delta. Action Comp()nent South Delta Agricultural Barriers 2.5.6.8.1.1.1 Fall Delta Smelt Habitat (X2) Location of Effect Freshwater Riverine Habitat for Juveniles and Sub-adults: Lower Sacramento, San Joaquin, and American Rivers and Delta (Freeport to GG Bridge) Suisun Marsh and vicinity SDWSC downstream to Sacramento River confluence water flow, water quality, migratory corridor water flow, water quality, migratory corridors The action may result in changes to low salinity location, flow volume, and water temperatures. A small change in low salinity zone (X2) location would likely result in minimal effects to salmonid and green sturgeon critical habitats. Water temperatures may be altered have an effect on prey abundance, water quality, and migration corridor. Short-term changes to tidal flow patterns in Montezuma Slo·ugh due to operation of the SMSCG are not expected to significantly change habitat availability or suitability for· rearing green sturgeon. Operations of the barriers will create physical barriers, which will impede the free movement of both adult and juvenile green sturgeon within the waterways of the affected South Delta waterways. It is unlikely that fish will pass over the barrier crests, and passage through the tidally operated culverts will be restricted to entry from the downstream side of the barrier during flood tides for almost all of the irrigation season when the barriers are operated. Fish trapped by the barriers will be exposed to reduced water quality, and potentially a diminishment of food resources above the barriers. Response and Rationale of E ffect Low Low Low- The frequency of use of the South Delta channels by adult and juvenile green sturgeon is unknown, thus the impacts of the severely reduced quality of the migratory corridors may not affect a substantial proportion of the population. Magnit ude of E ffect Low Low Low- few reports exist that track the migratory behavior through the South Delta for juvenile or adult green sturgeon lifestage, and those reports do not examine fine scale movements or use of South Delta habitats. Weight of Evidence Low Low Reduction in the function of the Freshwater Riverine Habitat for water quality, migratory corridors, adequate water flows, and potentially food resources Probable Change in PBF Supporting the Life H istory Needs ()f the Species PBFs Affected flow, water quality, and migration corridors free of passage impediments Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Delta 2.5.6.8. 1.1.3 Sacramento Deep Water Ship Channel Food Srudy Reconnecting the SDWSC to the Sacramento River will allow flow through the sh.ip channel which will improve conditions (water temp, flow), but will impact habitat downstream by mobilizing contaminants and other water quality parameters. 932 Action Comp()nent 2.5.6.8.1 .1.4 North Delta Food Subsidies I Colusa Basin Drain and Suisun Marsh Roaring River Distribution System Food Subsidy Studies 2.5.6.8. 1.1.4 Suisun Marsh Roaring River Distribution System Food Subsidy Studies PA conditions Location of Effect North Delta Suisun Marsh Water quality would be temporarily affected by the Colusa Basin drainage into the N Delta, which would temporarily expose fish to agricultural drainage water potentially containing contaminants (pesticides, nutrients) during two months of the year. Exposure would be limited and temporary and would not likely affect survival. Low Low Low Low Low Low Weight of Evidence Low Low Probable Change in PBF Supporting the Life H istory Needs ()f the Species Response and Rationale of E ffect food resources, water quality. Fish passage will be affected by the operation of the SMSCG. The tidallyoperated gates are also expected to influence water currents and tidal circulation periodically during the 70-80 days of annual operation. However, these changes in water flow will be limited to the flcod portion of the tidal cycle and will generally be limited to a few days during each periodic operational episode. Short-term changes in tidal flow are not expected to significantly change habitat avai lability or suitability PBFs Affected Green sturgeon PBFs in estuarine areas: food resources, water flow, water quality, migratory corridor, water depth, and sediment quality. Channelized river limits availability of varied rearing and migratory habitat. Magnit ude of E ffect Food resources, water flow and water quality, and migratory corridor. Reduced quality necessary for normal behavior, growth, and survival. Biological Opinion for the Long-Term Operation of the CVP and SWP Division Delta Delta Eastside/San Joaquin River San Joaquin River between the confluence with the Stanislaus River and Mossdale 933 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.8.8.2 Impact to the Critical Habitat of the Species at the Designation Level Individual PBFs are diminished to varying degrees as a result of the PA. However, the magnitude of these impacts is generally low within the context of the broader designated critical habitat as a whole. Further, conservation measures (e.g., habitat restoration, small screen program) may partially restore PBFs in some areas. Therefore, considering the relative size and scale of the exposed areas, the context of these areas within the broader designated critical habitat as a whole, and conservation measures proposed! in the PA, critical habitat and associated PBFs are still expected to function at a level necessary to support conservation of the species. After reviewing and analyzing the current status of the critical habitat, the environmental baseline, the effects of the proposed action, any effects of interrelated and interdependent activities, and cumulative effects, it is NMFS' biological opinion that the proposed action is not likely to appreciably diminish the value of the critical habitat for the conservation of the Southern DPS ofNorth American green sturgeon. Table 2.8.8-2. Reasoning and decision-making steps for analyzing the effects of the proposed action on designated critical habitat for sDPS green sturgeon. Darker shade identifies the conclusion at each step of decision-making. Acronyms and abbreviations in the action column refer to not likely to adversely affect (NLAA) and destruction or adverse modification of critical habitat (DIAD MOD). Step Apply the Available Evidence to Determine if... The proposed action is not likely to produce stressors that have direct or indirect adverse consequences on the environment. A Available Evidence: The PA will produce multiple stressors that will adversely affect the Migratory Corridors and Habitat for Rearing including, but not limited to: impingement and entrainment, and effects related to altered flows and temperatures. Areas of designated critical habitat are not likely to be exposed to one or more of those stressors or one or more of the direct or indirect consequences of the proposed action. B Available Evidence: Areas ofdesignated critical habitat for sDPS green sturgeon will be exposed to multiple stressors produced by the PA, including to habitats such as: Freshwater Rearing Habitat for Juveniles; Freshwater Migratory Corridors for Outmigrating Juveniles and Spawning Adults; and Estuarine Habitat for Rearing and Migration. c 934 True/False Action True End False GotoB True NLAA False GotoC True NLAA Biological Opinion for the Long-Term Operation of the CVP and SWP Step Apply the Available Evidence to Determine if•. . The quantity or quality of any physical or biological features or primary constituent elements of critical habitat or capacity of that habitat to develop those features over time are not likely to be reduced upon being exposed to one or more of the stressors produced by the prO[POSed action. False GotoD Any reductions in the quantity or quality of one or more physical or biological features or primary constituent elements of critical habitat or capacity of that habitat to develop those features over time are not likely to reduce the value of critical habitat for the conservation of the species in the exposedl area. True NLAA Available Evidence: The reductions in quantity and quality of PBFs, as well as the reductions in the capacity of the critical habitat to develop these features over time is expected to reduce the value of the habitat; particularly with regard to juvenile and adult migratory corridors in the Delta. False Go to E True DIAD Available Evidence: In multiple instances the quantity and quality ofthe P BFs ofgreen sturgeon designated critical habitat, will be reduced by the PA. For example, suitability of water temperature and flow in lower reaches ofspawning habitat are expected to be reduced by operation ofthe PA. D Any reductions in the value of critical habitat for the conservation of the species in the exposed area of critical habitat are not likely to appreciably diminish the overall value of critical habitat for the conservation of the species. Available Evidence: Although individual PBFs in several exposed areas will be diminished, the exposed areas represent a small portion ofhabitat within the broader context of the available designated critical habitat with intact PBFs. Therefore, considering the relative size and scale ofthe exposed areas within the context ofthe broader designated critical habitat as a whole, the overall value ofthe critical habitat for the conservation of the species is not expected to be appreciably diminished. E 2.8.9 • True/False Action Southern Resident Killer Whale Listed as endangered (70 FR 69903; November 18, 2005) 935 No MOD False DIAD MOD Biological Opinion for the Long-Term Operation of the CVP and SWP Detailed information regarding the life history and status of federally listed SRKW distinct population segment (DPS) of killer whales can be found in Section 2.2.5 Rangewide Status of the Species and Critical Habitat. 2.8.9.1 Status oftllte Species and Environmental Baseline In summary, the SRKW DPS is at a high risk of extinction primarily from low abundance and impaired survival and fecundity, especially in recent years. Major threats to this species include limitations in available preferred prey (Chinook salmon), vessel and sound impacts, contaminants, and climate change. SRKWs would benefit from the recovery of Chinook salmon populations and increased access to prey, as well as protections to reduce the impacts of vessels and sound, as well as reduced exposure to contaminants in prey items and in the marine environment. At present, the SRKW population has declined to the lowest levels seen in over thirty years. Recent updates to population viability analyses suggest a continued downward trend in population growth projected over the next 50 years (National Marine Fisheries Service 2016e). This downward trend is in part due to the changing age and sex structure of the population, but also related to the relatively low fecundity rate observed over the period from 2011 to 2016 (National Marine Fisheries Service 2016e). Recent analyses have concluded the effects of prey abundance on fecundity and survival have a large impact on the potential population growth rate (Lacy et al. 2017). When prey is scarce, SRK.Ws likely spend more time foraging than when prey is plentiful. Increased energy expenditure and prey limitation can cause poor body condition and nutritional stress. Nutritional stress is the condition of being unable to acquire adequate energy and nutrients from prey resources and as a chronic condition, can lead to reduced body size of individuals and to lower reproductive and survival rates of a population (Trites and Donnelly 2003). Recent aerial surveys of the SRKW population have detected declines in the body condition before the death of seven individuals and provided evidence of a general decline in SRKWs body condition in recent years (Trites and Rosen 2018). The diet data indicate that Chinook salmon is the primary prey for SRKWs year round, presumably because of Chinook salmon's large size, high fat and energy content, and year-round occurrence in the whales' geographic range. Sighting reports, satellite-linked tag deployments, and other data indicate that K and L pods use the coastal waters along Washington, Oregon, and California during the winter and spring; occasionally as far south as Monterey Bay. Preliminary analysis of prey remains and fecal samples sampled during the winter and spring in coastal waters indicate that Chinook salmon from the Columbia River, Central Valley, Puget Sound, and Fraser River Chinook salmon comprise over 90 percent of the whales' coastal Chinook salmon diet during that time period (NWFSC unpublished data). In general, over the past decade, some Chinook salmon stocks within the range ofSRKWs have had relatively high abundance (e.g. Washington and Oregon coastal stocks, some Columbia River stocks) compared to the previous decade, whereas other stocks originating in the more northern and southern ends of the whales' range (e.g. most Fraser stocks, Northern and Central British Columbia stocks, Georgia Strait, Puget Sound, and Central Valley) have declined. Changing ocean conditions driven by climate change may influence ocean survival of Chinook and other Pacific salmon, further affecting the prey available to SRKWs. On average since the early 1980s, it appears that CV Chinook salmon (as represented by the SI) constitutes about 20 percent of the total catch and escapement of all Chinook salmon populations 936 Biological Opinion for the Long-Term Operation of the CVP and SWP that are likely encountered by SRKWs from British Columbia to California, although this proportion varies from about 10-30 percent each year depending on varying strengths in run size (Kope and Parken 2011 ). As a result, we conclude that CV Chinook salmon make up a sizeable and significant portion of the total abundance of Chinook salmon available to SRKWs throughout their range in most if not all years; likely at least several hundred thousand individual fish other than during years of exceptionally low abundance for CV Chinook salmon. In addition, the known distributions of Chinook salmon along the coast suggest that CV Chinook salmon are an increasingly significant prey source (as SRKWs move south along the U.S. West Coast) during any southerly movements ofSRKWs along the coast of Oregon and California that may occur during the winter and spring, constituting the majority offish along some areas of the U.S. West Coast at times (Weitkamp 2010, Bellinger et al. 2015, Shelton et al. 2019). In addition, DDT fingerprints suggest fish from California form a significant component of their diets (Krahn et al. 2007, Krahn et al. 2009, O'Neill et al. 2012). In total, the available data suggest that CV Chinook salmon constitute a sizeable percentage of Chinook salmon that would be expected to be encountered by SRKWs in coastal waters off California and Oregon, and at least a small portion of Chinook salmon in the ocean as far north as British Columbia. As a result, we conclude that CV Chinook salmon are an important part of the diet for most SRKWs during portions ofthe year when SRKWs occur in coastal waters off the North American coast, especially south of the Columbia River, which includes the times of potential reduced body condition and increased diet diversity that received additional weight during the recent prey prioritization process. There are numerous additional factors that are affecting Chinook salmon and the availability of prey in the action area. Chasco et al. (20 17) concluded that these increases in marine mammal predation of Chinook salmon could be masking recovery efforts for salmon stocks, and that competition with other marine mammals may also be limiting the growth of the SRKW population. The harvest of Chinook salmon that may overlap with SRKWs occurs at a large international scale; generally, on the order of approximately 20 percent of Chinook salmon that may be available as prey for SRKWs. As part of the recent the Pacific Salmon Treaty negotiation, the U.S. agreed to develop a targeted funding initiative to mitigate the effects of harvest and other limiting factors by investing in habitat and hatchery actions to increase prey available for SRK.Ws (National Marine Fisheries Service 2019b). However, Chinook salmon from these hatcheries may only overlap with the small proportion of Chinook salmon from the Central Valley that range up to the Columbia River area and northward. Recently, NMFS completed consultation on the operation of the Klamath River water project from 2019-2024, which included measures to address disease concerns for juvenile Chinook salmon and coho salmon in the Klamath Basin (National Marine Fisheries Service 2019a). The analysis concluded that hundreds or thousands of more adult Chinook salmon from the Klamath River will be available for SRKWs off the coast of California and Oregon during some years over the next decade, especially for brood years that may have been exposed to more stressful conditions. 2.8.9.2 Summary of Proposed Action Effects Overall, the productivity of CV Chinook salmon, especially the dominant fall-run population, appears to be decreasing over time. This is likely a result of many important factors, including the ongoing effects of water operations on the survival of productivity of all CV Chinook salmon populations. Individual stressors resulting from the PA such as increased water temperatures, 937 Biological Opinion for the Long-Term Operation of the CVP and SWP reduced survival from routing through the Delta, redd dewatering, and entrainment/salvage in water operations negatively affect the fitness and survival of individuals from all CV Chinook salmon populations runs. In particular, these factors may be especially significant for non-ESA listed Chinook salmon populations such as fall-run Chinook salmon, because there are fewer measll!res under the PA to minimize the impacts of operations on the non-ESA listed populations. In the past, there has been some analysis (National Marine Fisheries Service 2009b) showing decreased productivity for natural populations of fall- and late fall-run Chinook salmon as a result of water operations on the order of 10 percent. While it is uncertain how that compares to operations under the PA, it seems likely that the PA continues to reduce productivity of the CV Chinook salmon at least at similar levels as before. For ESA-listed Chinook salmon ESUs in the Central Valley, we conclude that population level effects for ESA-listed species and critical habitats overall under the PA are significant across multiple VSP parameters, including abundance. Generally, we expect that non-ESA-listed populations are similarly impacted by the same stressors across the spectrum ofVSP parameters. With respect to the PA compared to COS, a relatively small decrease in overall productivity for Chinook salmon in total under PA was estimated (<1 percent), largely as a result of the decrease in productivity expected for the dominant fall-run Chinook salmon populations. However, we recognize that these estimates could not account for all stressors on all Chinook salmon populations affected by the PA. We expect a reduction in productivity under the PA to lead to an additional reduction in the number of adults in ocean (on average) compared to COS, on top of the ongoing perpetual reduction and limitation of productivity that is expected to occur under cos. The June 14, 2019 final PA included a number of additional elements and conservation measures that may help to minimize impacts to CV Chinook salmon populations. As described 2.5.8.2 Supplemental Analysis ofJune 14, 2019, none ofthese measures are quantitatively assessed within any framework similar to the results presented in Section 2.5.8.1.4 Changes in Chinook Salmon Productivity under the PA compared to COS at this time. Some of the revised PA elements, such as Revisions to the Cold Water Pool Management and development ofUpper Sacramento Performance Metrics (Section 4.10.1.3.3), or Revisions to the Governance Sections ofthe PA to include additional Drought and Dry Year Actions (Section 4.12.5) and Chartering of Independent Panels (Section 4.12.6) and Four-Year Reviews (Section 4.12.8) ultimately do not affect the modeling results used to characterize the exposure of the species to stressors such as increased water temperature, or the risk based on the exjpected long-term proportion of years in each Tier type. There are expectations for revised PA elements such as OMR management and performance objectives intend to limit impacts (i.e., salvage loss) under the PA to levels comparable to what would occur under the COS. However, as described in 2.5.8.2 Supplemental Analysis ofJune 14, 2019 there are some uncertainties in how new approaches will be implemented and uncertainties associated with effects. For other elements, such as the SRSC Partnership establishment and implementation of the Mainstem Sacramento River Integrated Water and Fish Science and Monitoring Partnership, studies into alternate release strategies for hatchery fall-run Chinooks salmon from CNFH, and construction of a fish trapping and sorting facility at CNFH, it is not possible to describe their benefits more specifically at this time based due to limited information on their effectiveness and/or uncertainty on how these actions will ultimately be incorporated into future project operations. 938 Biological Opinion for the Long-Term Operation of the CVP and SWP Finally, Reclamation identified a number of these restoration actions or programs that have been occurring, and which are expected to continue into future, in addition to proposing restoration actions linked to the P A. These ongoing and new restoration actions are expected to improve Chinook salmon habitat. Based on the analysis, it is likely that conditions under the PA where SRKWs are exposed to and affected by reductions and limitations in the abundance of Chinook available as prey as a result of the PA will continue and increase over time. The analysis determined that this exposure would lead to changes in the foraging behavior of SRKW in the action area and increased risks of nutritional stress for individual SRKWs, and that all members ofK and L pod are expected to be harmed through the increased risk of impaired foraging due to decreased Chinook salmon abundance in the ocean resulting from these effects. While revised P A measures and proposed restoration actions offer some benefit for Chinook salmon productivity compared to the original P A, there is not enough information to clearly indicate that Chinook salmon productivity in the Central Valley will not continue to diminish over time under the P A. The effect of perpetual and/or additional nutritional stress over time for individual SRKWs that are already experiencing and showing signs of nutritional stress is an additional reduction in fitness that increases the risk of reduced survival and/or reproductive success for at least some members ofthe SRKW population that are already compromised, or potentially contributing to diminishing the fitness of individuals to a compromised state over time where reduced survival and/or reproductive effects become increasingly likely to occur. 2.8.9.3 Assess Risk to the Population!DPS The available information presented in Section 2.2.5 Rangewide Status of the Species indicates that a number of SRKW individuals have been showing signs of nutritional stress, poor health; and some of these individuals have subsequently died. In addition, and at least partly as a result of these recent developments, the most recent assessments of the SRKW population indicate that fecundity of the population has been low and that the population is expected to continue to decline in the future if the population dynamics of the population (survival and fecundity) do not Improve. The available information indicates that CV Chinook salmon (especially the fall-run populations) is a significant source (10-30 percent) of Chinook salmon abundance during the winter and spring time in coastal waters where SRKWs occur during the time period when we believe prey resources are most limiting for SRKWs. The available information also indicates that CV Chinook salmon are increasingly prominent and dominant components of available Chinook salmon prey resources as SRKWs head south along their range. Given the significance of CV Chinook salmon to the abundance of Chinook, we conclude that reductions and limitations in the productivity of CV Chinook salmon would affect the foraging behavior of SRKWs. Under the PA, our analysis concludes that SRKWs will continue to be exposed to decreased abundances of CV Chinook salmon as a result of reduced productivity as a result of the PA and limited by the overall low rates of juvenile Chinook salmon survival in the Central Valley. As proposed, the P A does not improve prospects for available Chinook salmon prey resources for SRKWs; but instead the PA would further contribute to additional nutritional stress of at least some SRKW individuals. Over the long term, the reduction in Chinook salmon productivity in the Central Valley will likely not rdent under the P A, but instead will likely continue to escalate if the productive capacity of the Central Valley system, especially for fall-run Chinook salmon, 939 Biological Opinion for the Long-Term Operation of the CVP and SWP continues to diminish and as some ESA-listed Chinook salmon populations are increasingly unlikely to recover and head closer to extinction. We conclude that the P A is expect·ed to diminish VSP parameters and increase extinction risk of ESA-listed units of salmon. In the NMFS 2009 Opinion, we concluded the continued decline and potential extinction of winter-run and CV spring-run populations, and consequent interruption in the geographic continuity of salmon-bearing watersheds in the SRKWs' coastal range, was likely to alter the distribution of migrating salmon and increase the likelihood of localized depletions in prey, with adverse effects on the SRKWs' ability to meet their energy needs. The PA removes some of the RPA measures that were required in 2009; and does not contain many protective measures designed to address significant stressors for the non-listed populations that are responsible for a large portion of Chinook salmon production in the Central Valley. The trend in Chinook salmon productivity in the Centra1 Valley is of concern to the long-term outlook for available prey resources for SRKWs. Currently, overall productivity of this system depends heavily on modified hatchery release practices to minimize impacts from the PA and other factors in the Central Valley. As a result, the P A w ill continue to exacerbate the proportional larger impact of water operations on the natural production of Chinook salmon from the system, which illustrates the fundamental limitations on productivity that exist in this system, in part as a result of the PA. The increased risks of reduced survival and/or reproductive success for at least some members of the SRKW population, the diminished productivity of all Chinook salmon populations including fall-run Chinook, and the increased risks of extinction for ESA-listed Chinook salmon, that are expected to occur as a result of the P A have significant implication for the viability ofthe SRKW population. Given the current forecast of population declines for this small population, risks of additional mortality and/or reduced fecundity would likely expedite population declines and present significant obstacles to the recovery and ultimate survival of this population. The available information suggests that large changes in individual survival and reproduction rates are necessary in order for SRKW to recover (and even survive). The prospect for persistent and escalating risks of reduced survival and reproductive success associated with reduced prey resources and diminishing Chinook productivity from the Central Valley heading into the future increasingly limit the possibility that SRKWs can recover given the compromised status of the population and signals of poor health for numerous individuals that are already being observed. Considering the effects of the P A, cumulative effects, and effects from interrelated and independent actions in the context ofthe status and environmental baseline ofSRKWs, NMFS concludes that the PA is likely to appreciably reduce the likelihood of both the survival and recovery of SRKWs. Conclusion 2.9 After reviewing and analyzing the current status of the listed species and critical habitat, the environmental baseline within the action area, the effects ofthe ROC on LTO, any effects of interrelated and interdependent activities, and cumulative effects, it is NMFS' biological opinion that the ROC on LTO is: • likely to jeopardize the continued existence of Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and likely to destroy or adversely modify any of their designated critical habitats; 940 Biological Opinion for the Long-Term Operation of the CVP and SWP • • likely to jeopardize the continued existence of Southern Resident killer whales; and not likely to jeopardize the continued existence of the southern DPS ofNorth American green sturgeon, and not likely to destroy or adversely modify its designated critical habitat. 2.10 Reasonable and Prudent Alternatives "Reasonable and prudent alternatives" (RPA) refer to alternative actions identified during formal consultation that can be implemented in a manner consistent with the intended purpose of the action, that can be implemented consistent with the scope of the Federal agency's legal authority and jurisdiction, that are economically and technologically feasible, and that would avoid the likelihood of jeopardizing the continued existence of listed species or resulting in the destruction or adverse modification of critical habitat (50 CFR 402.02). Regulations also require that NMFS review all relevant information provided by the Federal agency or otherwise available, evaluate the current status of the listed species or critical habitat, evaluate the effects of the action and cumulative effects on the listed species or critical habitat, and discuss the basis for any findings and any RPAs with the action agency and utilize the action agency's expertise in formulating the RPA (50 CFR 402.14(g)(5)). This RPA was developed through a thoughtful and reasoned analysis of the key causes of the jeopardy and adverse modification findings, and a consideration of alternative actions within the legal authority of Reclamation and DWR to alleviate those stressors. The actions in this RPA have been discussed in the context ofNMFS recommendations to Reclamation over the course of multiple Tiger Team meetings in November through December, during the development of the draft biological assessment; and during meetings that were held throughout the consultation period, between February 5 and June 14, during which NMFS provided verbal and written recommendations to Reclamation to address significant adverse effects of the PA. These recommendations were not included by Reclamation in changes to the February 5, April 30 or June 14 revisions to the proposed action. NMFS concentrated on actions that have the highest likelihood of alleviating the stressors with the most significant ,effects on the species, rather than attempting to address every project stressor for each species or every PBF for critical habitat. For example, water temperatures lethal to incubating eggs often occur downstream of Shasta and Keswick reservoirs when the air is warm and flows are low. Fish cannot reach spawning habitat with colder water at higher elevations if it is above currently impassable dams. Accordingly, NMFS' near-term measures provide suitable water temperatures below dams in a higher percentage of years, and long-term measures provide passage to cooler habitat above dams as soon as practicable. Reducing egg mortality from high water temperatures is a critical step in slowing or halting the decline of Central Valley salmonids. There are several ways in which water operations adversely affect listed species that are addressed in this RPA. We summarize the most significant here: 1) Water operations result in elevated water temperatures that have lethal and sub-lethal effects on egg incubation and juvenile rearing in the upper Sacramento River. The immediate operational cause is lack of sufficient cold water in Shasta Reservoir to reduce 941 Biological Opinion for the Long-Term Operation of the CVP and SWP 2) 3) 4) 5) 6) downstream temperatures at critical times and meet other project demands. This elevated temperature effect is particularly pronounced in the Upper Sacramento River for winterrun Chinook salmon. The RPA includes a new year-round storage and temperature management program for Shasta Reservoir and the Upper Sacramento River, as well as long-term passage prescriptions at Shasta Dam and re-introduction of winter-run Chinook salmon into its native habitat in the McCloud and/or Upper Sacramento rivers to minimize these effects to ecologically acceptable levels for winter-run Chinook salmon. PA operations in Clear Creek are expected to result in suboptimal flows and water temperatures for portions of the CV spring-run Chinook salmon holding, spawning, egg incubation periods in some years. The RPA calls for improved approaches to achieve essential flows and water temperatures during these life stages. Both Reclamation and DWR's winter and spring operations associated with retention of natural flows result in adverse effects through reduced frequency and magnitude of rearing habitat inundation. To minimize these effects, the PA includes "scheduling" action components (spring pulse flows) and "collaborative planning" action components (habitat restoration). The 2016 FERC opinion includes related actions in the Feather River. This RPA contains additional both short-term and long-term actions necessary to minimize effects to juvenile rearing habitat in the Lower Sacramento River and northern Delta. The effects analysis shows that juvenile CCV steelhead migrating out from the San Joaquin River Basin are exposed to significant high magnitude stressors and have low survival rates due to the proposed action. The RPA mandates additional measures to improve survival of San Joaquin CCV steelhead smelts, including both increased San Joaquin River flows and export curtailments. Given the uncertainty of the relationship between flow and exports, the RP A also prescribes a significant new study of acoustic tagged fish in the San Joaquin Basin to evaluate the effectiveness of the RPA and refme it over the lifetime of the project. The Nimbus Fish Hatchery steelhead program contributes to both loss of genetic diversity and mixing of natural and hatchery stocks of steelhead, which reduces the viability of natural stocks. The Nimbus Fish Hatchery program for non-listed fall-run Chinook salmon also contributes to a loss of genetic diversity, and therefore, viability, for fall-run Chinook salmon. To minimize these effects, the PA includes development of Hatchery and Genetic Management Plans (HGMP) to improve genetic diversity of both steelhead and fall-run Chinook salmon, the latter ofwhich is an essential prey base ofSRKW. The RPA sets some specific requirements for HGMP development and requires additional development and implementation of plans for alternative hatchery release strategies/increased hatchery production with the goal of increasing survival of all fallrun Chinook salmon as part of the HGMP for fall-run Chinook salmon at Nimbus Fish Hatchery. The effects analysis shows that Chinook salmon productivity in the Central Valley, including especially non-listed fall-run Chinook salmon populations, is increasingly diminished by the PA, which increases the risks associated with reduced Chinook prey availability for SRKW. The RP A requires measures designed to minimize significant stressors for Chinook salmon in both upstream areas and through the Delta, actions to improve Chinook salmon productivity in the Central Valley to reduce these risks for 942 Biological Opinion for the Long-Term Operation of the CVP and SWP SRKW, along with initiatives to support development of information and tools that can be used to inform and improve these measures over time. An RPA must avoid jeopardy to listed species in the short term, as well as the long term. Essential short-term actions are presented for each division and are summarized for each species to ensure that the likelihood of survival and recovery is not appreciably reduced in the short term (i.e., one to five years). In addition, because the proposed action is operation of the CVP/SWP until 2030, this consultation also includes long-term actions that are necessary to address projectrelated adverse effects on the likelihood of survival and recovery of the species over the next decade. NMFS considered the consistency with the scope of the intended purpose of the proposed action, Reclamation and DWR's legal authority and jurisdiction, and made considerations regarding the economic and technological feasibility in several ways when developing actions in this RPA. The RPA also allows for tailored implementation of many actions in consideration of economic and technological feasibility without compromising the RPA's effectiveness in avoiding jeopardy and adverse modification of critical habitat. The RPA includes opportunities for independent scientific review of all actions to further the scientific understanding of the stressors and actions and to create a process for adaptively managing actions based on the findings and recommendations of these review. 2.10.1 Organization of the RPA The specific actions in the RPA are detailed below. That section begins with overarching actions that apply to operations in all geographic divisions of the project, including procedures for orderly functioning of the many technical teams that assist with decision making, research and adaptive management, and monitoring. These are followed by suites of actions specific to most geographic divisions of the propos.e d action: Shasta, American River, East Side (Stanislaus River), and the Delta. Notwithstanding specific attribution to Reclamation below, RPA actions are to be implemented jointly by Reclamation and DWR. The RPA also includes a species-by-species explanation ofhow each action contributes to avoiding jeopardy or adverse modification for that species, and the basis for NMFS' conclusion that the RP A actions are likely to avoid jeopardizing the species or adversely modifying or destroying its critical habitat. 2.10.1.1 RPA Actions By Division Trinity River Division (Clear Creek) Action CC.1: Improvements to Flow and Water Temperature Management in Clear Creek Objective: Decrease risk to Clear Creek CV spring-run Chinook salmon and CCV,steelhead populations through improved flow and water temperature management. Action CC.l.a: Reservoir Water Temperature Model Reclamation shall develop a water temperature model for Whiskeytown Reservoir, expanding the Watercourse Engineering model for Keswick and Shasta Reservoirs, to capture the inter943 Biological Opinion for the Long-Term Operation of the CVP and SWP connections of the Trinity-Sacramento River systems for efficient use of cold-water resources. A model would enable better forecasting and planning for Clear Creek to provide protective water temperatures for CV spring-run Chinook salmon during holding, spawning, and egg incubation. Water temperature impacts from hydropower peaking shall be considered during model development. Final model, including recommendation for implementation, due August 1, 2022, toNMFS. Action CC.l.b: Whiskeytown Dam Structural Improvement Evaluation Reclamation shall evaluate feasibility and fish benefits of structural improvements to Whiskeytown Dam to improve cold-water pool availability. Improvements to be evaluated include, but are not limited to: the locations of outlets and options for configurations; siphon; and temperature control device that allows for selective withdrawal. Draft report due August 1, 2023, to NMFS. Final report, including recommendation for implementation, due August I, 2024, to NMFS. Action CC.l.c: Long-term Flow and Water Temperature Prescription Reclamation shall develop a long-term flow and water temperature prescription (plan) to achieve various ecological functions in Clear Creek. The plan shall include incorporation of the reservoir water temperature model, and consideration of monitoring data on CV spring-run Chinook salmon and CCV steelhead and best available scientific publications on ecological channel function, fluvial processes, sediment transport, flow regimes, and fish habitat needs. Reclamation shall develop a plan that to the extent possible shall include the following prescriptions: 1. ii. 111. tv. encourage upstream movement of CV spring-run Chinook salmon to preferred habitat in July and August, including water temperature or flow adjustments operate between 53°F and 56°F at JGO, September I 5 through October 31 shift the water temperature compliance point from IGO at river mile 11.0 downstream to Clear Creek Road Bridge at river mile 8.59 protect earlier egg incubation if present (prior to September 15), and any redds downstream of!GO, by implementing a gradual flow increase and water temperature cooling Reclamation shall operate flow releases and water temperatures as described in the proposed action until the long-term flow and water temperature plan is developed. Alternative operations developed in the plan are subject to NMFS review and concurrence. Rationale: Operations in Clear Cr,e ek are expected to result in suboptimal flows and water temperatures for listed salmonids in Clear Creek. These measures would support optimization of flows and water temperatures on Clear Creek. Shasta Division Action SD.l: Shasta Cold Water Pool Management- Develop Temperature Dependent Egg Mortality and Egg to Fry Survival Objectives The P A, as updated on June 14, 2019, contains new performance measures that NMFS fully supports. These will be helpful in tracking whether the PA performs as modeled. However, due to the ongoing effects of temperature related mortality and its contribution to NMFS' finding of jeopardy and adverse modification of critical habitat for winter-run Chinook salmon, NMFS 944 Biological Opinion for the Long-Term Operation of the CVP and SWP concludes the following supplemental tier frequency and associated temperature dependent egg mortality and total survival objectives are necessary to maintain population viability. Objective: Reduce temperature dependent egg mortality and egg to fry mortality by creating management objectives that support population-scale viability for winter-run Chinook salmon below Shasta and Keswick dams. SD.l.a - Tier Frequency Objectives a. Reclamation shall operate to Tier 1 conditions in at least 2 out of 3 years, and shall operate to Tier 2 or Tier 3 conditions in no more than 1 out of 4 years. Reclamation shall operate to Tier 4 conditions in no more than 1 out of 10 years. b. Reclamation shall make operational adjustments as necessary to meet these objectives, including, but not limited to: retaining storage in April, May, June and July, if effective in meeting objectives, by limiting Keswick Dam releases and resulting downstream deliveries; re-operating to meet downstream needs through releases at Folsom and Oroville reservoirs, provided operational minimum requirements are met and notwithstanding incurring COA debt; foregoing hydropower; and further limiting fall releases. c. If Reclamation operates to a Tier 2 or 3 year with greater frequency than what is expected (described above) for more than two consecutive years, or a Tier 4 year for more than 1 out of 10 years, an independent review panel shall be established by the end of the calendar year to determine the degree to which operational decisions affected the frequency. The panel shall review whether the above water operation in subsection "b" actions were taken to maintain a Tier, and if so, analyze whether Reclamation made all possible operational adjustments to attempt to meet the objectives in subsection "a"; or conversely, whether hydrology/meteorology provided conditions that under which meeting the objectives was beyond Reclamation's control . The panel will make recommendations on actions that may be taken to reduce the likelihood for tier frequency exceedance. Reclamation shall submit a report to NMFS within two months of the panel report on what changes, if any, Reclamation plans to make as a result ofthe review. SD.l.b - Survival Objectives in Tier 1 Years a. Reclamation shall not exceed an annual temperature dependent mortality (TDM) of2 percent (based on the Martinet al. 2017, model ofTDM) OR b. Reclamation shall operate such that total egg-to-fry survival (ETF) is at least 32 percent (as calculated by CDFW winter-run Chinook salmon escapement estimates and USFWS' estimated juvenile winter-run Chinook salmon passage counts at RBDD). c. If neither of these metrics are met, this year may be considered a Tier 2 or Tier 3 year for the purposes of accounting for the probability of operating in a Tier as long as the survival objectives in Tier 2/3 are met. If the survival objectives of a Tier 2/3 year are not met, then this shall be considered a Tier 4 year for purposes of accounting for expected frequency. However, if considering the current year as a higher tier year would exceed the expected frequency of operating in that tier, reinitiation of consultation would be required. 945 Biological Opinion for the Long-Term Operation of the CVP and SWP SD.l.c - Survival Objectives in Tier 2 and Tier 3 Years a. Reclamation shall not exceed an annual TDM of 12 percent TDM (based on the Martinet al. 2017 model ofTDM) OR b. Reclamation shall operate such that total ETF survival is at least 27 percent (as calculated by CDFW winter-run Chinook salmon escapement estimates and USFWS' juvenile winter-run Chinook salmon passage counts at RBDD). c. The first 5 years of implementing the opinion will be operated such that there are no more than three consecutive years of Tiers 2, 3, or 4 in any combination. d. If neither of these metrics in subsections "a" and "b" are met, this year may be considered a Tier 4 year for the purposes of accounting for the probability of operating in a Tier. However if considering the current year as a Tier 4 year would exceed the expected frequency of operating in that tier, reinitiation of consultation would be required. SD.l.d - Survival Objectives in Tier 4 Years a. Reclamation shall target ETF survival of 15 percent or greater; AND b. Reclamation shall target end-of-September carry-over storage of at least 1.9 MAF; AND c. Reclamation shall implement intervention measures in consultation with NMFS. SD.l.e - Collaborative Strategy Provisions a. Reclamation may, at any time during the implementation of the Opinion, convene, with NMFS, an independent panel to review the Tier Frequency, temperature dependent egg mortality and total survival objectives described in SD.l.a- SD.l.d to review and develop alternative objectives that they shall operate to, subject to NMFS review and concurrence. b. If Reclamation decides to initiate such a review, Reclamation shall charter an independent panel consistent with "Chartering oflndependent Panels" under the "Governance" section of the June 14, 2019, fmal PA. c. Reclamation may at any time request that NMFS provide relief from meeting these objectives, and/or reassess the biological necessity of meeting these objectives below Shasta Dam, due to successful acceleration of reintroduction efforts in Battle Creek and McCloud rivers, per actions below. Rationale: Winter-run Chinook salmon require conditions that prevent frequent high mortality events and support viability of the species despite demands of operations. The species is likely to absorb the stress associated with an infrequent (i.e., 1 in 10 year) high-mortality year. However, to support viability, survival rates should not be low for several consecutive years, and should be at levels similar to or improved upon recent rates. NMFS considers the multiple mortality sources and potential opportunities to increase survival through non-flow actions by identifying temperature-dependent mortality metrics and overall egg-to-fry survival metrics. Note that exceedance of an objective is not equivalent to exceeding take or being considered out of compliance. See the ITS for more details on the amount or extent of take exempted. Action SD.2 - Shasta Fish Passage Pilot Program 946 Biological Opinion for the Long-Term Operation of the CVP and SWP Beginning in January 2020, Reclamation shall undertake a 10-year phased winter-run Chinook salmon pilot passage program to evaluate the long-term feasibility of reintroducing winter-run Chinook salmon into their historical holding, spawning, and rearing habitats above Shasta Dam. Objective: Reduce extinction risk of Sacramento River winter-run Chinook salmon and mitigate for CVP water project operation effects. SD.2.a - Interagency Fish Passage Steering Committee Reclamation shall re-convene the Interagency Fish Passage Steering Committee (Committee) by January 2020. The Committee shall be re-established in consultation with and the approval of NMFS. The Committee shall include experienced biologist and engineers with expertise in fish passage design and operation, reintroduction techniques, permitting, and salmonid biology. All membership to the committee must be approved by Reclamation and NMFS. Committee membership shall include one lead member and one alternate. If a formal charter for the Committee, pursuant to F ACA, is delayed for more than three months following the re-start of the Committee, Reclamation shall provide updates to all interested members of the public on Committee decisions a minimum of three times a year. SD.2.b- Adult Winter-run Chinook Salmon Release Site(s) Above Shasta Dam and Winter-run Chinook Salmon Juvenile Release Site(s) Below Keswick Dam Reclamation shall transport adults to habitats above Shasta Dam and juveniles (from spawning above Shasta Dam) to habitats below Keswick Dam using safe, timely and effective release methods and protocols. Transport and release locations and methods shall follow existing State and Federal protocols. With assistance from the Committee, and in coordination with applicable landowners and stakeholders, Reclamation shall complete construction of all selected adult and juvenile release sites by October 3 1, 2021. SD.2.c- Juvenile Fish Collection Prototypes Since 2010, Reclamation has made considerable progress on concepts for juvenile fish collection facilities above Shasta Dam. Reclamation shall continue the development ofjuvenile fish collection facilities above Shasta Dam. Pilot efforts already explored include installation of two prototype juvenile salmonid collection facilities in the lower riverine portion of the McCloud River and the upper McCloud arm of Shasta Reservoir. By September 1, 2020, Reclamation shall fund, design, construct, install, and operate both collection systems. SD.2.d- Broodstock SR Winter-run Chinook Salmon from the Livingston Stone National Fish Hatchery From January 1, 2020 through December 31, 2023, Reclamation shall use juvenile and adult winter-run Chinook salmon broodstock from the Livingston Stone NFH during the initial stages of the reintroduction program. Reclamation shall provide funding for broodstock production and, if necessary, expansion of the Livingston Stone NFH broodstock program within one year of a determination by the Committee. Expansion may be required if adequate numbers of fish are not available to assess the effectiveness of the reintroduction program or adequately seed upstream habitat during years of low natural adult returns. SD.2.e - Transition to Natural Winter-run Chinook Salmon 947 Biological Opinion for the Long-Term Operation of the CVP and SWP By December 31,2023, ifthe Committee determines the preliminary stages ofthe pilot project are successful (e.g., adult holding, spawning, and juvenile survival and collection), Reclamation shall transition to using natural winter-run Chinook salmon obtained from the Keswick Dam fish collection faci lity. The Steering Committee, in collaboration with the NMFS SWFSC, shall develop strategies that minimize risk to the existing natural population below Keswick Dam. Numbers of natural adult SR winter-run Chinook salmon to be used for reintroduction shall be set by the Steering Committee in consultation with the NMFS Southwest Fisheries Science Center. SD.2.f- Project Effectiveness, Monitoring and Evaluation for Winter-run Chinook Salmon From January 1, 2020, through December 31, 2030, Reclamation shall fund and implement all phases of the pilot program for winter-run Chinook salmon. The objective is to gather sufficient biological and technical information to assess the relative effectiveness of the program, including the foUowing; (a) the biological response ofwinter-run Chinook salmon to historical habitats above Shasta Dam, (b) juvenile collection efficiency, and (c) preliminary estimates of cohort replacement rates. A report shall be provided to the Committee for review and comment by March 31 of year 5 and a final report of the pilot effort shall be completed by year 10. Prior to issuing the final report, Reclamation submit the draft final report for independent scientific peer review. All of the reports shall summarize the findings from SD.2a through SD.2.c, above. The final report shall include recommendations regarding long-term fish passage actions. SD.2.g- Dynamic Distribution Model and Plan By year 4, Reclamation, in cooperation with NMFS, shall draft a Dynamic Distribution Model and Plan detailing how LSNFH practices (including annual supplementation, captive broodstock and drought year production supplementation), and fish reintroduction actions (Battle Creek and McCloud River) can be used, in synchrony with Reclamation's Tier 3 and Tier 4 water temperature management plans and the intervention measures proposed for Tier 4, to reduce the exposure and risk of winter-run Chinook salmon downstream from Shasta and Keswick dams, and allow for long-term recovery. The model and plan shall be submitted for independent review, and shall inform related annual actions in the PA and this RPA following peer review. Reclamation shall complete a finaE model and plan by year 8. Rationale: The analysis in the opinion finds that even after all discretionary actions are taken to implement the 4-tiered approach to Shasta Cold Water Pool Management Program the risk of temperature-dependent egg mortality persists, especially in critically dry years. This mortality can be significant at the population level. The analysis also leads us to conclude that due to climate change, the frequency of critically dry years will increase. Additionally, the longer an action impedes recovery of an ESU with a single spawning population, the more it increases the risk of extinction due to continued exposure to stochastic events and a declining background environmental conditions. Existing habitat that was historically occupied by winter-run Chinook salmon in the McCloud River remains in excellent condition for holding, spawning, egg incubation and rearing. The concept for reintroduction above Shasta is not new and was first proposed in the NMFS 2009 opinion and identified in the NMFS 2014 recovery plan as a high priority recovery action. Additionally, from 2010 through Ju ly, 2018, Reclamation has led, and provided necessary funding for, the Shasta Dam Fish Passage Evaluation project. This RPA action will continue that effort to and will improve the scientific and management understanding of how reintroducing 948 Biological Opinion for the Long-Term Operation of the CVP and SWP winter-run Chinook salmon to historic habitat in the McCloud River can be used to reduce risk to winter-run Chinook salmon, particularly during Tier 3 and 4 years when temperature-dependent egg mortality below Keswick Dam can be very high. Specifically, Reclamation accomplished the following steps: • • • • • • • • • Formation of an Interagency Fish Passage Steering Committee along with various subcommittees; Completion of an evaluation of habitat in the upper Sacramento and McCloud rivers; Completion of a pilot implementation plan; Funded DWR for critical engineering work which resulted in a contract being awarded for construction, installation and preliminary testing of juvenile collection facilities; Requested NMFS designate winter-run and CV spring-run Chinook salmon as nonessential experimental populations when above Shasta Dam; Funded an expansion of the Livingston Stone NFH to provide winter-run Chinook salmon broodstock for the initial reintroduction efforts; Conducted extensive public outreach and workshops; Funded U.S. Geological Survey to assess juvenile reservoir transit and other critical future aspects of the pilot program; and Completed a draft National Environmental Policy Act document ready for public comment. Action SD.3 - Battle Creek Restoration and Winter-·run Reintroduction Acceleration Program Objective: Implement key actions necessary to accelerate the Battle Creek Restoration Program and implement the Battle Creek winter-run Chinook salmon Reintroduction Plan. SD.3.a- Reclamation Shall Complete a Battle Creek Acceleration Plan by December 31, 2020 and Provide all Necessary Funding to Ensure Timely Implementation. a. The purpose of the plan is to ensure continued funding additional actions that are necessary to assist with the completion of the Battle Creek Salmon and Steelhead Restoration Program and to support the certainty of establishing an additional population of winter-run Chinook salmon. b. The plan shall be developed with technical assistance from the NMFS, USFWS and CDFW and shall: 1. Identify and implement, to the maximum extent practicable, a suite of no-regrets actions that can be planned and carried out while the disposition of the PG&E hydroelectric project is in process. For the purpose of this RPA, "no regrets" actions are defined as those actions that can move forward on Battle Creek that are not directly tied to future decisions related to the disposition PG&E's hydroelectric license on Battle Creek; n. Describe a strategy for integrating the Battle Creek winter-run Chinook salmon jump-start project with the long-term Battle Creek Winter-nm Chinook Salmon Reintroduction Plan; 949 Biological Opinion for the Long-Term Operation of the CVP and SWP m. tv. v. Develop the infrastructure necessary to complete the Battle Creek Reintroduction Plan for Winter-run Chinook Salmon (as described in Table 15 ofthe 2016 Battle Creek Winter-run Chinook Salmon Reintroduction Plan); Fund the ongoing operational costs of the Battle Creek Reintroduction Plan for Winter-run Chinook Salmon (as described in Table 15 of the 2016 Battle Creek Winter-run Chinook Salmon Reintroduction Plan); and Identify and support science actions such as marking and tagging/survival studies for Battle Creek Reintroduction. For the purpose of this RPA, technical assistance is not meant to infer NMFS concurrence with an action, but rather that NMFS is afforded the opportunity to provide scientific or technical recommendations for Reclamation's consideration. SD.3.b - Reclamation Shall Provide the Unmet Funding Needs to Complete the Battle Creek Winter-run Chinook Salmon Reintroduction Plan a. The unmet funding needs are described in Item #2 in the attachment to the June 19, 2019, letter from FWS to NMFS (Appendix C), and also in Table 15 of the 2016 Battle Creek Winter-run Chinook Salmon Reintroduction Plan, and include: • Construction of a fish culture facility on the North Fork of Battle Creek. • Additional supporting facilities and capital equipment at the Coleman Weir, such as holding tanks, water chillers, fry capture equipment and fish transport trucks. • Annual operations costs for fish culture, power and water and monitoring activities, including, but not limited to data collection and processing, tagging, genetic evaluations. SD.3.c- Reclamation Shall Construct a Fish Sorting Facility at the Coleman National Fish Hatchery a. Design and construct a fish sorting facility at Coleman National Fish Hatchery (CNFH) to support the Battle Creek monitoring program and restoration and facilitate hatchery operations and evaluation. b. Design and implement a strategy to document the benefits of fish sorting on the survival and productivity of all Chinook salmon populations that are impacted by the sorting. Rationale: In the PA, Reclamation proposed to accelerate the Battle Creek Restoration Program but did not provide any details about how this would be accomplished. The USFWS provided additional detail in a letter dated June 19, 2019, on the status, including funding certainty, of hatchery-related actions, including those necessary for Battle Creek reintroduction. Beginning in 2017, early implementation of the winter-run Chinook salmon reintroduction was initiated through the Winter-run Chinook Salmon Reintroduction Jump-start Project. In 2019, CDFW and USFWS executed a funding agreement to fund initial stages of the Battle Creek Winter-run Chinook Salmon Reintroduction Plan. Accelerating the Battle Creek Restoration Program will increase habitat availability for winter- and spring-run Chinook salmon and CCV steelhead that will contribute to improvements in their spatial, genetic and life-history diversity, abundance and growth rates. SD.4 - Middle and Lower Sacramento River Habitat Restoration Objective: To restore and enhance floodplain, side-channel and in-channel habitat for salmon and steelhead in order to improve the growth and survival of emigrating juveniles 950 Biological Opinion for the Long-Term Operation of the CVP and SWP SD.4.a- Reclamation shall develop and implement a middle and lower Sacramento River Habitat Restoration Plan. a. The goal of the Habitat Restoration Plan shall be to restore at least 2,000 acres of mainstem Sacramento floodplain and side-channel habitat. b. The draft plan shall be developed and submitted to NMFS for Jreview by December 31, 2021. The plan shall include proposed actions and locations and a funding and implementation strategy. c. A final plan shall be completed by June 1, 2022. d. Actions may be taken as soon as possible but shall begin no later than July 2020, prior to completion of the final plan. e. NMFS understands and expects that these projects will be partially or wholly funded by public funding sources such as the CVPIA program, the PCSRF/FRGP NOAA funds for salmon recovery and or State bond funds (e.g. Prop 1) in addition to PWA funds and other non-state and federal sources. NMFS further understands that each of these funding programs have their own processes, and expects Reclamation, DWR and local sponsors to compete for these funds. Furthermore, NMFS understands that PWAs will apply for funds, and if funded, implement several projects on this list. SD.4.b- Reclamation Shall Consult with NMFS and CDFW to Study, Develop and Implement an Eight Year Science-based Predator Hotspot Management Experiment a. The draft experimental design shall be developed and submitted to NMFS for review by December 31, 2021. The plan shall include proposed actions and locations and a funding and implementation strategy. b. NMFS WCR and NMFS SWFSC shall be consulted on the experimental design, including the objectives, scope, locations, timing, questions/hypotheses, and methods. c. A final plan shall be completed by June 1, 2022. d. Actions may be taken as soon as possible but shall begin no later than July 2022. e. Reports summarizing the effectiveness of the experiment are due by July 2025, and July 2030. SD.S- Reclamation Shall Provide the Unmet Funding Needs to Improve Livingstone Stone National Fish Hatchery Objective: Ensure that funding applied to hatchery improvements that are necessary to support the winter-run Chinook salmon population Supplementation Program and also actions that may be necessary during Tier 3 and Tier 4 years. a. The unrnet funding needs are described in Item # 1 in the attachment to the June 19, 2019, letter from FWS to NMFS (Appendix C). Reclamation shall: • either secure an emergency/alternate water supply when Shasta and Keswick reservoirs reach elevations below the current penstocks, or acquire (either purchase or rent) water chillers to ensure that adequate water temperatures are provided during critical winter-run Chinook salmon life stages (e.g., adult holding, egg incubation, and juvenile rearing). • coordinate with NMFS and the USFWS to evaluate the need for modjfications or improvements to Keswick Dam Fish Trap and Elevator, or operational 951 Biological Opinion for the Long-Term Operation of the CVP and SWP • • adjustments to reduce the likelihood of injury or death to adult fish entering or attempting to enter the trap. coordinate with NMFS and USFWS to investigate the feasibility of installing an alternative winter-run Chinook salmon collection facility on the south side of the Sacramento River at the ACID fish ladder. The study shall begin in January 2020. If the results of the investigation determine that a collection facility would be technically and economically feasible, Reclamation shall install such a facility within 2 years of the recommendation. coordinate with the USFWS on the need to install a drum screen to remove solids from the hatchery's. effluent. The purpose of the drum screen would be to provide more flexibility to use medicated feed to prevent disease. If, at any time, the USFWS determines that such infrastructure is necessary to prevent disease, particularly during Tier 3 and 4 years, Reclamation shall install this infrastructure. Rationale: Due to the variability in the abundance of the naturally-produced winter-run Chinook salmon population in the Sacramento River, the Livingston Stone National Fish Hatchery is used to supplement the abundance of the population. Also, during droughts and as proposed in Tier 4 years, demands on the hatchery are likely to increase. It is necessary to ensure that all of the infrastructure needs are in place to ensure this demand can be met. SD.6- Use of Power Bypasses for Temperature Control Objective: The objective is to ensure that all actions necessary to control water temperatures in the Sacramento River are consider·ed. a. Reclamation shall implement power bypasses when needed for additional cold water resources. Rationale: During certain condition, it may be necessary to use the power bypasses at Shasta and Keswick dams to meet water t·emperature objectives. American River Division Action AR.l - Preparation of Hatchery Genetic Management Plan (HGMP) for steelhead and fall-run Chinook salmon at the Nimbus Fish Hatchery Objective: Improve genetic and life history diversity of American River steelhead by ensuring the timely completion of the Nimbus HGMP and to reduce the operational hatchery management effects on fall-run Chinook salmon in order to improve prey availability of SRKWs. AR.l.a - Reclamation Shall Fund Genetic Screening at the Nimbus Fish Hatchery for Steelhead to Determine the Most Ecologically Appropriate Broodstock Source a. This action shall be completed by March 31, 2021. AR.l.b- Reclamation Shall Fund a Study Examining the Potential to Replace the Nimbus Fish Hatchery Steelhead Broodstock, with Genetically More Appropriate Sources. a. This action sihall be completed by March 31, 2022. 952 Biological Opinion for the Long-Term Operation of the CVP and SWP AR.l.c - Reclamation Shall Fund Development and I mplementation of Plans for Alternative Hatchery Release Strategies and/or Increased Hatchery Production with the Goal of Increasing Survival and Ocean Abundance of Fall-run Chinook Salmon as Part of the Nimbus HGMP for Fall-run Chinook Salmon. a. The HGMP should establish a plan for implementing alternative release strategies, as determined appropriate through studies and consultation with NMFS. The HGMP should include plans for documenting the ongoing effectiveness of alternative hatchery release strategies and their impact on Chinook salmon abundance and diversity. b. The HGMP should establish a plan for evaluating and implementing increased hatchery production goals in concert with alternative hatchery release strategies. c. This action slhall be completed by March 31, 2022. Rationale: Hatcheries have been established on CVP and SWP rivers to offset effects of dams and project operations. Since these hatcheries were initially put into operation, additional knowledge has been developed that has advanced NMFS understanding of how hatchery operations can affect listed and non-listed salmonids. Nimbus Fish Hatchery steelhead broodstock is predominantly Eel River stock. Maintaining this genetic broodstock has adverse effects on listed steelhead in the CCV steelhead DPS (Garza and Pearse 2008). An HGMP is necessary to minimize effects ofthe ongoing steel head hatchery program on steelhead contained within the DPS. Additionally, SRKWs depend on Chinook salmon as prey. Preparation of a hatchery management plan for fall-run Chinook salmon at Nimbus Fish Hatchery is necessary to reduce operational effects on SRKW prey. Improving the genetic diversity and diversity of run timing of Central Valley fall-run Chinook salmon will decrease the potential for localized prey depletions and, thereby, provide a more consistent food source even in years with overall poor productivity. AR.2- Use of Power Bypasses for Temperature Control Objective: The objective is to ensure that all actions necessary to control water temperatures in the American River are considered. a. Reclamation shall implement power bypasses when needed for additional cold water resources, not just during the limited circumstances (i.e., "Reclamation proposes to limit power bypass operations solely to respond to emergency or unexpected events or during extreme drought years when a drought emergency has been declared by the Governor of California") identified in the PA (Appendix A3) Rationale: During certain conditions, it may be necessary to use the power bypasses at Folsom Dam to meet water temperature objectives. Delta Division Action DD.l- San Joaquin Basin Steelhead Protections Objective: To reduce the vulnerability of emigrating CCV steelhead within the lower San Joaquin River to entrainment into the channels ofthe South Delta and at the export facilities due 953 Biological Opinion for the Long-Term Operation of the CVP and SWP to the diversion of water by the export facilities in the South Delta by undertaking a suite of flow and non-flow actions. DD.l.a - Reclamation Shall Initiate an Interim Action 2:1 Inflow to Export Ratio for April and May for the 2021 Water Year Only While the Study Plan Described in DD.l.b, below, is Developed. If an Alternative Study is not Agreed to, then Reclamation Shall Operate to the Following Inflow to OMR Relationship Starting in 2022. Allowable OMR flows depend on gaged flow measured at Vernalis32, and will be determined by a linear relationship. IfVernalis flow is below 5,000 cfs, OMR flows will not be more negative than -2000 cfs. If Vernalis is 6,000 cfs, OMR flows will not be less than + 1000 cfs. If Vernalis is 10,000 cfs, OMR flows will not be less than +2,000 cfs. IfVernalis is 15,000 cfs, OMR flows will not be less than +3,000 cfs. If Vernalis is at or exceeds 30,000 cfs, OMR flows will not be less than+ 6,000 cfs. DD.l.b- Multi-species March-May Q-west or Vernalis Adaptive Management Program (VAMP)-Iike Action a. Reclamation shall create an interagency workgroup to develop a science-based experimental alternative that provides similar protection to the San Joaquin Inflow-toExport (I:E) ratio, protects multiple species in Delta during this period, and submit to NMFS for review at a project specific level. b. The alternative shall be an adaptive management action that is based on an experimental design with a suite of different action considerations based on variable flow and fishery conditions. c. Reclamation shall charter an independent panel consistent with "Chartering of Independent Panels" under the "Governance" section of the final P A (Appendix A3) to review the design and impl ementation concepts, and adaptive management provisions of the action and shall seek NMFS technical assistance on all recommendations that result from the panel review for consideration. d. Reclamation shall seek NMFS technical assistance on workgroup membership, experimental design, and selection of contractor. NMFS shall be invited to co-author annual and final reports. e. Reclamation shall make a long-term investment in tagged fish studies as part ofthis effort. f. Reclamation shall seek NMFS concurrence on the action under this section prior to implementation. DD.l.c- Reclamation Shall Install the Head of Old River Barrier so that it is Operational by April 1st, and During the April and May Period, Whenever Feasible, and Shall Consult with NMFS for Concurrence on Feasible Conditions. Rationale: Existing protections for San Joaquin Basin CCV steelhead are not sufficient and will reduce the spatial diversity, abundance and productivity of the DPS. The modeling conducted for the original PA depicts that OMR flows will become substantially more negative in April and May without the I:E ratio which restricted export rates to a ratio of the inflow of the San Joaquin River as measured at Vernalis during April and May. NMFS expects that, even under the fmal 32 When OMR target is based on Vernalis flow, will be a function of 5-day average measured flow. 954 Biological Opinion for the Long-Term Operation of the CVP and SWP PA, OMR flows during April and May will likely be more negative in April and May than under current operations, just less so than under the original P A. Recent modeling (Buchanan 2019) of the effects of the HORB presence on the estimated CCV steelhead survival from the HOR to Chipps Island indicates that survival is higher when the barrier is installed, compared to when it is not installed. Based on NMFS' current understanding of survival probabilities based on barrier condition at the Head of Old River, the PA will lead to lower survival of steelhead juveniles emigrating from the San Joaquin River basin by up to 20 percent for flows between 3,800 cfs and 5,000 cfs at Vernalis. Action DD.2 - SRKW Protections Objective: To ensure the effects of Delta Operations on all Central Valley salmon populations and overall Chinook salmon productivity are minimized by developing operational loss thresholds for all Chinook salmon populations. DD.2.a- Reclamation, in Coordination with NMFS, Shall Develop and Implement Loss Thresholds for Operations at TFCF and SDFPF for all Chinook Salmon Populations in the Central Valley. The final PA does not include loss thresholds that are specifically protective of all Chinook salmon in the Central Valley, fall-run Chinook salmon in particular. In order to ensure that the effects of Delta operations on the prey availability of Chinook salmon are minimized, Reclamation shall work with NMFS to develop and implement loss thresholds for all Chinook salmon populations, including fall-run, late fall-run, and CV spring-run Chinook salmon, that are at least consistent with the intent of the performance measures designed specifically for winterrun Chinook salmon and CCV steelhead. As part of this process, Reclamation and NMFS may consider a "combined" approach where performance measures for all Chinook salmon in total may achieve the objective of this measure. Loss thresholds for all Chinook salmon populations shall be developed by, and implemented beginning in, Water Year 2020, and may be revised with the review and concurrence ofNMFS. East-side Division Action ED.l: San Joaquin Basin Steelhead Protections Objective: To reduce the vulnerability of emigrating CCV steelhead within the lower San Joaquin River to entrainment into the channels of the South Delta and at the pumps due to the diversjon of water by the export facilities in the South Delta by undertaking a suite of flow and non-flow actions. ED.l.a - Reclamation Shall Implement Floodplain Restoration at the San Luis National Wildlife Refuge and Shall Support the Following Lower San Joaquin River Habitat Projects Consistent with the Collaborative Planning Action described in the PA. a. Franks tract or other San Joaquin corridor specific restoration actions in the southern Delta. b. Sturgeon Bend Floodplain Restoration c. Durham Ferry State Recreation Area floodplain restoration 955 Biological Opinion for the Long-Term Operation of the CVP and SWP Rationale: Existing protections for San Joaquin Basin CCV steelhead are not sufficient and will reduce the spatial diversity, abundance and productivity of the DPS. The RPA actions will increase the growth San Joaquin origin CCV steelhead to improve the likelihood of their survival as they migrate downstream through the lower San Joaquin River and Delta. Juvenile listed salmonids emigrate downstream in the main channel of the San Joaquin River during the winter and spring period. Juvenile CCV steelhead from the San Joaquin River basin, the Calaveras River basin, and the Mokelumne River basin also utilize the lower reaches of the San Joaquin River as a migration corridor to the ocean. G.l.- Upon expiration of contracts, Reclamation shall renew contracts to provide linkage to this consultation. Similar to language that has recently been negotiated on American River contracts, Reclamation shall include the following language in contract renewals: "This contract is subject to the requirements of the Endangered Species Act (ESA) and all other applicable laws. The Contractor shall operate in accordance with all requirements of any applicable biological opinion(s) in effect during the term of this Contract, including but not limited to all biological opinions for the joint operations of the Central Valley Project and the State Water Project. The Contracting Officer and the Contractor acknowledge and agree that Reclamation also must act in accordance with the requirements of the ESA, including any shortages or operational restrictions necessary to comply with applicable biological opinions." Rationale: Past practices have occasionally created confusion over the linkage between the biological opinion and individual contracts. This provision will clarify the legal mechanism by which contracts receive coverage under this biological opinion or its successor. 2.10.2 RPA Consistency with the Proposed Action The purpose and need for modifications to the long-term operation of the CVP and SWP (Projects) is to operate the Projects in a manner than enables Reclamation and DWR to maximize water deliveries and optimize marketable power generation consistent with applicable laws, contractual obligation, and agreements; and to augment operational flexibility by addressing the status of listed species (82 FR 61790, Dec. 29. 20 17). The RPA is consistent with the intended purpose of the action because it builds on concepts and policies already proposed in the action. According to the BA, "[t]he proposed action is the continued operation of the CVP and SWP." Specifically, Reclamation and DWR propose to operate the CVP and SWP to divert, store, and convey CVP and SWP water consistent with applicable law and contractual obligations. Changes in operation of the Projects to avoid jeopardizing listed species or adversely modifying their critical habitats require that additional sources of water for the Projects be obtained, or that water delivery be made in a different way than in the past or that amounts of water that are withdrawn and exported from the Delta during some periods in some years be reduced. These operational changes do not, however, preclude operation ofthe Projects. NMFS developed focused actions ,c onsidering the full range of authorities that Reclamation and DWR may use to implement these actions. These authorities are substantial. The CVPIA, in particular, makes "mitigation, protection, and restoration of fish and wildlife" authorized purposes of the Central Valley Project and provides Reclamation with ample authority to provide benefits for fish and wildlife through measures such as purchasing water to augment in-stream flow, implementing habitat restoration projects, and taking other beneficial actions. 956 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.10.3 Consistency with the Scope of the Federal Agency's Legal Authority and Jurisdiction, that is Economically and Technologically Feasible The RPA can be implemented consistent with the scope of the federal agency's legal authority and jurisdiction. The Rivers and Harbors Act of 193 7, which established the purposes of the CVP, provided that the dams and reservoirs of the CVP "shall be used, first, for river regulation, improvement of navigation and flood control; second, for irrigation and domestic uses; and, third, for power." (ROC on LTO BA, p. 1-2). The CVP was reauthorized in 1992 through the CVPIA, which modified the 1937 Act and added mitigation, protection, and restoration offish and wildlife as project purposes. The CVPIA provided that the dams and reservoirs of the CVP should be used "first, for river regulation, improvement of navigation, and flood control; second, for irrigation and domestic uses and fish and wildlife mitigation, protection and restoration purposes; and, third, for power and fish and wildlife enhancement." (ROC on LTO BA p. 1-3) One of the stated purposes of the CVPIA is to address impacts of the CVP on fish and wildlife. CVPIA, Sec. 3406(a). The CVPIA gives Reclamation broad authority to mitigate for the adverse effects of the projects on fish and wildlife, and nothing in the Rivers and Harbors Act of 1937 requires any set amount of water delivery. In addition to adding protection offish and wildlife as second tier purposes of the CVP, the CVPIA set a goal of doubling the natural production of anadromous fish in Central Valley rivers and streams on a long-term sustainable basis, by 2002. Sec. 3406(b)(1 ). This goal has not been met. Instead, as detailed in this opimion, natural production of anadromous fish has declined precipitously. A 2008 report on the CVPIA anadromous fish program by independent reviewers (Cummins et al. 2008), recommended by the Office of Management and Budget and requested by Reclamation and the USFWS, stated that: [The agencies} "should develop a more expansive view of the authorities at their disposal to address the problems, especially with regard to water management and project operations. The agencies have followed a more restrictive view of their authorities than appears legally necessary or appropriate to the seriousness ofthe mission. Most relevant to this consultation, the review panel observed that: "[i]t would seem that CVPIA activities and personnel should be central to the OCAP plan, the Section 7 consultation, and the agencies' efforts to satisfY the requirements of the ESA (that is, after all, one ofthe directives ofthe CVPJA). The panel received no information or presentations on the involvement of the CVPIA program or personnel in the ESA consultation effort ... and in the determination ofwhat actions the agencies should be taking to meet the ESA. " Reclamation and DWR operate their respective projects in close coordination, under a Coordinated Operations Agreement (COA). The COA was authorized by Congress in Public Law 99-546. Consequently, the COA " is the federal nexus for ESA section 7 consultation on operation of the SWP. Because of commitments expressed in the COA and the Congressional mandate to Reclamation to operate the CVP in conjunction with the SWP, the operations of the two projects are linked ... " 957 Biological Opinion for the Long-Term Operation of the CVP and SWP DWR, like Reclamation, has broad authority to preserve and enhance fish and wildlife. State law gives DWR authority to provide for needs of fish and wildlife independent of the connection of the two water projects. [DWR] "is required to plan for recreational and fish and wildlife uses ofwater in connection with State-constructed water projects and can acquire landfor such uses (Wat. Code Sec. 233, 345,346, 12582). The Davis-Do/wig Act (Wat. Code Sec. 1190011925) establishes the policy that preservation offish and wildlife is part ofState costs to be paid by water supply contractors, and recreation and enhancement offish and wildlife are to be provided by appropriations from the General Fund. " The Preamble to the ESA consultation regulations states that "a Federal agency's responsibility under section 7(a)(2) permeates the full range of discretionary authority held by that agency," and that the Services can prescribe a RPA "that involves the maximum exercise ofFederal agency authority when to do so is necessary, in the opinion of the Service, to avoid jeopardy." 51 Fed. Reg. 19925, 19937 (June 3, 1986). The independent review panel concluded that despite Congressional authorization and direction more than 16 years ago to restore anadromous fish populations in Central Valley rivers and streams, Reclamation continues to take an unduly narrow view of its authorities in carrying out Congress' mandate. The legal foundation of this RPA is a broader view of Reclamation's authorities, one that is consistent with the CVPIA, the ESA, and the independent review panel's recommendations. Project Costs In addition to water costs, Reclamation and DWR will incur project costs associated with certain RPA actions (e.g., the fish passage program). The State of California has authorized over 20 billion in water-related general obligation bonds since 2000, and these bonds often contain provisions for environmental conservation related purposes (LAO, 2008). Similarly, the CVPIA AFRP funds eligible restoration projects, using federal authorities. Some of the projects in the RPA may qualify for those sources of funds. Additionally, Reclamation and DWR signed an MOU in December 2018 providing for funding to implement the NMFS 2009 opinion, including the RPA actions, which shows they have the resources, capacity and authority to implement a complex RPA, including the ability to recover costs from water contractors, if necessary. Although NMFS has not had time to complete a thorough economic analysis, given the scope of the NMFS 2009 opinion RPA (72 RP A actions), as compared to the scope of this RP A, the actions contained in this RP A are not more costly than those actions, and are likely less costly both in terms of water and dollars. 2.10.4 Avoids the Likelihood of Jeopardizing the Continued Existence of Listed Species or Resulting in the Destruction or Adverse Modification of Critical Habitat This section presents NMFS' rationale for concluding that with adoption of this RPA, Reclamation would avoid jeopardizing the listed species and adversely modifying their designated critical habitats. This rationale is presented for the following species and critical habitats that NMFS concluded would be jeopardized or adversely modified by the proposed action: • Sacramento River winter-run Chinook salmon and its designated critical habitat, 958 Biological Opinion for the Long-Term Operation of the CVP and SWP • • • CV spring-run Chinook salmon and its designated critical habitat, CCV steelhead and its designated critical habitat, and Southern Resident killer whales Each section summarizes the main stressors and the actions within the RPA that alleviate those stressors. The supporting biological information for each action is contained in the "objective" and "rationale" sections for each RPA action. Each action of the RPA is linked to at least one main stressor for at least one speci,es, identified in the effects analysis and the integration and synthesis sections of this opinion. Sacramento River Winter-Run Chinook Salmon and its Designated Critical Habitat Throughout this opinion, NMFS has explained that a species' viability (and conversely extinction risk) is determined by the VSP parameters of spatial structure, diversity, abundance, and productivity. In addition, NMFS has explained the need for the proper functioning of the PBFs that comprise the critical habitat designation. Currently, only the one small population of winter-run Chinook salmon spawning downstream of Keswick Dam exists, making this species particularly vulnerable to environmental pressures such as the 2012-2015 drought. This vulnerability manifested with the drought as three consecutive year classes suffered heavy losses due to an inability to release cold water from Shasta Reservoir throughout the egg and fry life stages. Warm water releases from Shasta Reservoir contributed to egg-to-fry mortality rates of85 percent in 2013,94 percent in 2014, and 96 percent in 2015, the highest levels since estimates of that statistic began in 1996. Mortality decreased after the drought ended with 76 percent mortality in 2016 and 56 percent mortality in 2017. The Sacramento River winter-run Chinook salmon ESU is at high extinction risk because there is only one naturally-spawning population, and it is not within its historical range (Lindley et al. 2007, National Marine Fisheries Service 2016c). Of over 165 species that NMFS protects under the Endangered Species Act, the winter-run Chinook salmon ESU is considered one of just nine33 species that are most at risk of extinction in the near future, per the Species in the Spotlight initiative (National Marine Fisheries Service 2015e). As described in the Status of the Species section of this Opinion, weaknesses in all four VSP parameters -- spatial structure, population size, population growth rate, and diversity -contribute to this risk. In particular: (1) multiple populations of this ESU have been extirpated; the ESU now is composed of only one population, and this population has been blocked from all of its historical spawning habitat; (2) habitat destruction and modification throughout the mainstem Sacramento River have dramatically altered the ESU's spatial structure and diversity; (3) the ESU is at risk from catastrophic events including drought; (4) the population has a "high" hatchery infll!lence (Lindley et al. 2007); and (5) the population experienced an almost seven fold decrease in 2007. In addition, many of the physical and biological features of critical habitat that are essential for the conservation of winter-run are currently impaired and provide limited habitat value. The extinction risk ofthe winter-run Chinook salmon population has increased since the 2007 assessment. Based on the Lindley et al. (2007) criteria, the population is at high extinction risk in 2019. High extinction risk for the population was triggered by the hatche1y influence criterion, 33 The NMFS Species in the Spotlight initiative was initially launched highlighting eight species most in need of urgent protection; a ninth species was added in 2019. 959 Biological Opinion for the Long-Term Operation of the CVP and SWP with a mean of66 percent hatchery origin spawners over the last generation from 2016 through 2018. The threshold for high risk associated with hatchery influence is 50 percent hatchery origin spawners. The PA increases the population's extinction risk and continues to degrade the PBFs of critical habitat by adding numerous stressors to the species' baseline stress regime, as is generally described in the Integration and Synthesis section of the Opinion. The RPA specifies several actions that will reduce the adverse effects of the proposed action on w inter-run and its critical habitat. The RP A actions specifically address key project-related factors or threats facing the ESU and its critical habitat including: • • • High levels of temperature dependent egg mortality and total mortality in the upper Sacramento River. Reduced spatial, life history and genetic diversity. Low in-river survival of emigrating smolts caused by seasonal operations that reduce river flows in the fall, winter and spring months that expose fish to poor growth condition (reduced access to side-channel and floodplain habitat) and increase fish to high levels of predation. Adverse effects of project operations to winter-run Chinook salmon will be reduced primarily through the following measures: 1) Using supplemental, science-based temperature dependent and egg-to-fry survival objectives that will be used to reducing temperature dependent egg mortality and egg to fry mortality is necessary to avoid an appreciable reduction in survival and recovery of the species by creating management objectives that support population-scale viability for winter-run Chinook salmon below Shasta and Keswick dams. These objectives will help ensure that the single existing population of endangered winter-run Chinook salmon will persist. RPA action SD.1 addresses the abundance and production criteria and may increase growth rate and abundance over time. SD.6 also helps with water temperature management under certain conditions that will protect incubating eggs from certain conditions that require rapid operational flexibility. This RPA action will also address the adverse modification of the PA on spawning and rearing PBFs of critical habitat by improving their biological function. 2) Reinitiating a pilot project to reintroduce winter-run Chinook salmon to their historic habitats upstream from Shasta Dam. RPA action SD.2 addresses the abundance and production criteria, diversity criteria (spatial, genetic and life history) and the growth rate and abundance criteria. This RP A action will also address the adverse modification of the PA on spawning and rearing PBFs of critical habitat by expanding the range of the species to areas where habitat conditions (although not designated as critical habitat) are more favorable to spawning and rearing life stages of the ESU. 3) RPA action SD.3 ensures that the Battle Creek Restoration Program and the Battle Creek winter-run re-introduction program will proceed in a timely fashion and that facilities and monitoring are in place to ensure the program is successful. This Battle Creek program is critical in creating an additional population of winter-run Chinook salmon. This additional population increases the species spatial structure and diversity and should increase growth rate and abundance over time. This RPA action will also address the 960 Biological Opinion for the Long-Term Operation of the CVP and SWP adverse modification of the PA on spawning and rearing PBFs of critical habitat by improving their biological function. 4) RPA action SD.4 for habitat restoration and predation hot-spot removal ensures that winter-run Chinook salmon rearing habitat actions in the lower Sacramento River and Northern Delta will minimize adverse effects of seasonal project operations and low-flow conditions on winter-run Chinook salmon and their critical habitat. These habitat actions will increase the survival and growth rates of individuals that utilize this habitat. These fish are predicted to enter the estuary and ocean with a higher degree of fitness, and therefore, greater resiliency to withstand stochastic events in these later phases of their life history, thereby increasing the viability of the ESU and reducing the likelihood of appreciable reductions in the survival or recovery of the species. This RPA action will also address the adverse modification of the PA on rearing PBFs of critical habitat that occur from seasonally managed low flow conditions by improving the biological function of the rearing and migratory corridor. NMFS believes the PA, as modified by actions in this RP A, would avoid the likelihood of jeopardizing the continued existence of winter-run Chinook salmon or resulting in the destruction or adverse modification of its critical habitat. Central Valley Spring-Run Chinook Salmon and Its Designated Critical Habitat As previously stated in the Status of the Species section, the spring-run ESU is currently likely to become endangered within the foreseeable future due to multiple factors affecting spatial structure, diversity, productivity and abundance. Specific factors include: (I) the ESU currently has only three independent populations. All three of these independent populations are in one diversity group, the Northern Sierra Nevada Diversity Group, and the other diversity groups contain dependent populations; (2) habitat elimination and modification throughout the Central Valley have drastically altered the ESU's spatial structure and diversity; (3) the ESU has a risk associated with catastrophes, especially considering the remaining independent populations' proximity to Mt. Lassen and the probability of a large scale wild fire occurring in those watersheds (Lindley et al. 2007); ( 4) the presence of dams precludes access to historical spawning areas; and (5) for some populations, the genetic diversity of spring-run Chinook salmon has been compromised by hybridization with fall-run Chinook salmon. The effects of the PA on spring-run Chinook salmon are contained in the sections of the opinion on project effects and integration and synthesis. The effects are presented for the Clear Creek population, the mainstem Sacramento River population and for the other populations that are affected by project operations, by diversity group. Ultimately all spring-run Chinook salmon must migrate through the Sacramento River and the Delta, and are affected by Delta operations, particularly low flow conditions related to seasonal operations and exposure to increased export rates in April and May. In the Integration and Synthesis section of this opinion, NMFS described that a species' viability (and conversely extinction risk) is determined by meeting certain VSP criteria for spatial structure, diversity, abundance, and productivity, and more specifically, describes how the PA influences these criteria and affects the likelihood of the species survival and recovery. The RPA actions for CV spring-run Chinook salmon address PA-related effects to these criteria. In addition, NMFS acknowledged the need for the proper functioning of the PBFs that comprise the critical habitat designation. 961 Biological Opinion for the Long-Term Operation of the CVP and SWP The RP A actions specifically address key project-related factors or threats facing the ESU and its critical habitat, including: • • • • Exposure to suboptimal water temperatures during spawning and egg incubation in Clear Creek. Spawning habitat availability, flow conditions, reduced access to riparian habitat and instream cov,e r, loss of natural river morphology and function Low in-river survival of emigrating smolts caused by seasonal operations that reduce river flows in the fall, winter and spring months that expose fish to poor growth condition (reduced access to side-channel and floodplain habitat) and increase fish to high levels of predation. Delayed migration and increased transit times related to Delta entrainment with potential for increased mortality, along with uncertain/poor in-Delta and through-Delta rearing and survival conditions for young-of-year spring-run Chinook salmon in some years and conditions due to both proj,ect related and non-project related stressors. Adverse effects of project operations to CV spring-run Chinook salmon will be reduced primarily through the following measures: 1) RPA action SD.3 ensures that the Battle Creek Restoration Program will proceed in a timely fashion and that facilities and monitoring are in place to ensure the program is successful. The project is critical to improve the resiliency of CV spring-run Chinook salmon to operations effects of the PA and will increases the species spatial structure and diversity and should increase growth rate and abundance over time. This RPA action will also address modification to critical habitat caused by the action on spawning and freshwater rearing and migration PBFs of critical habitat by increasing the amount of habitat on Battle Creek and improving the function of restored habitats. 2) RPA action SD.4 for habitat restoration and predation hot-spot removal ensures that spring-run Chinook salmon rearing habitat actions in the lower Sacramento River and Northern Delta will minimize adverse effects of seasonal project operations and low-flow conditions on spring-run Chinook salmon and its critical habitat. These habitat actions will increase the survival and growth rates of individual CV spring-run Chinook salmon that utilize this habitat. These fish are predicted to enter the estuary and ocean with a higher degree of fitness, and therefore, greater resiliency to withstand stochastic events in these later phases of their life history, thereby increasing the viability of the ESU and reducing the likelihood of appreciable reductions in the survival or recovery of the species. This RPA action will also address modification to critical habitat caused by the action on freshwater rearing and migration PBFs of critical habitat. 3) RPA actions CC.l and CC.2 will enable better forecasting and planning for Clear Creek to provide protective water temperatures for CV spring-run Chinook salmon during holding, spawning, and egg incubation, including evaluation of structural improvements to Whiskeytown Dam to improve cold-water pool availability. The long-term flow and water temperature plan in RPA action CC.3 will help to optimize ecological functions in Clear Creek. These RPA actions will also address modification to critical habitat in Clear Creek caused by the action on freshwater rearing and migration PBFs of critical habitat. 4) The RP A actions for CCV steelhead, DD.l.a and DD.l.b, will also minimize in Delta effects to young-of-year spring-run Chinook salmon. These actions are predicted to 962 Biological Opinion for the Long-Term Operation of the CVP and SWP improve survival for the proportion of these fish that are present in the central and south Delta in April and May, and increase the proportion offish that successfully emigrate past Chipps Island. This RPA action will also address modification to critical habitat caused by the action on freshwater rearing and migration PBFs of critical habitat. NMFS believes the PA, as modified by actions in this RP A, would avoid the likelihood of jeopardizing the continued existence of CV spring-run Chinook salmon or resulting in the destruction or adverse modification of its critical habitat. California Central Valley Steelhead and Its Designated Critical Habitat The PA increases the extinction risk of CCV steelhead and continues to degrade the PBFs of critical habitat by adding numerous stressors to the species' baseline stress regime and reducing the viability of all of the extant CCV steelhead populations, particularly in the Sacramento River, the American River and the San Joaquin Basin. Throughout this opinion, NMFS acknowledged that a species' viability (and conversely extinction risk) is determined by the VSP parameters of spatial structure, div,e rsity, abundance, and productivity. In addition, NMFS acknowledged the need for the proper functioning of the PBFs that comprise the critical habitat designation. The RPA specifies actions will minimize the adverse effects of the PA on individual CCV steelhead, populations and the DPS and bring about the proper functioning of PBFs of its critical habitat. All actions that address CCV steelhead in the RPA are necessary to minimize project effects to the extent where they do not appreciably reduce the likelihood of survival and recovery of the DPS or adversely modify CCV steelhead critical habitat. This analysis summarizes some of the most significant RPA actions that NMFS relied on in its analysis. The RPA actions specifically address key project-related factors or threats facing the CCV steelhead DPS and its critical habitat, as described in the "Objectives" and "Rationale" parts of the actions including: • • • • Spawning habitat availability, flow conditions, reduced access to riparian habitat and instream cover, loss of natural river morphology and function Low in-river survival of emigrating smolts caused by seasonal operations that reduce river flows in the fall, winter and spring months that expose fish to poor growth condition (reduced access to side-channel and floodplain habitat) and increase fish to high levels of predation. Reduced genetic diversity in the American River. Altered hydrodynamics and routing effects in south Delta that reduce through-Delta survival, particularly in April and May to populations comprising the Southern Sierra Diversity Group of the DPS. Adverse effects of project operations to CCV steelhead will be reduced primarily through the following measures: 1) RPA action DD.l for Delta and East-side flow and export action, and HORB and habitat actions, and ED.l for lower San Joaquin habitat restoration, are predicted to create more suitable flow and non-flow related habitat conditions throughout the lower San Joaquin and South Delta that will minimize effects on juvenile CCV steelhead emigrating from the Southern Sierra diversity group and contribute to their growth and survival. The continued existence of this diversity group contributes to the spatial structure and 963 Biological Opinion for the Long-Term Operation of the CVP and SWP therefore viability of the DPS as a whole. This RPA action will also address modification to critical habitat caused by the action on freshwater rearing and migration PBFs of critical habitat. 2) RPA action SD.3 ensures that the Battle Creek Restoration Program will proceed in a timely fashion and that facilities and monitoring are in place to ensure the program is successful. This will help reduce effects to the DPS that occur downstream of Shasta and Keswick dams in the upper Sacramento River that reduce spawning habitat availability, flow conditions, reduced access to riparian habitat and instream cover, loss of natural river morphology and function. The project is critical to improve the resiliency of CCV steelhead to operations effects of the PA and will increases the species spatial structure and diversity and should increase growth rate and abundance over time. This RPA action will also address modification to critical habitat caused by the action on spawning and freshwater rearing and migration PBFs of critical habitat by increasing the amount of habitat on Battle Creek and improving the function of restored habitats. 3) RPA action SD.4.a for habitat ensures that habitat actions in the lower Sacramento River and Northern Delta will minimize adverse effects of seasonal project operations and lowflow conditions CCV steelhead and their critical habitat. These habitat actions will increase the survival and growth rates of individuals that utilize this habitat. These fish are predicted to enter the estuary and ocean with a higher degree of fitness, and therefore, greater resiliency to withstand stochastic events in these later phases of their life history, thereby increasing the viability of the DPS and reducing the likelihood of appreciable reductions in the survival or recovery of the species. This RPA will also address modification to critical habitat caused by the action on freshwater rearing and migration PBFs of critical habitat. 4) The HGMP action (RPA action AR.l) will restore genetic diversity of CCV stcclhcad in the American River which should help improve life-history diversity in the basin. This action will not influence the condition of critical habitat. NMFS believes the P A, as modified by actions in this RPA, would avoid the likelihood of jeopardizing the continued existence of CCV steelhead or resulting in the destruction or adverse modification of its critical habitat. Southern Resident Killer Whales NMFS evaluated effects of the PA on SRKW by evaluating effects on the availability of their preferred prey, Chinook salmon. In this opinion, NMFS determined that the PA increases the extinction risk ofSRKW by reducing Chinook salmon productivity in the Central Valley, especially for non-listed fall-run Chinook salmon, thereby reducing the available Chinook salmon prey resources for SRKW and increasing the risks of reduced survival and reproduction of SRKW individuals. Given the highly endangered status of this population, reduced survival or reproductive potential for individuals of this population increases the extinction risk and limits the recovery potential of the species. The RP A actions specifically address the key project-related factors that are diminishing the productivity of Chinook salmon in the Central Valley, including: • Reduced survival of juvenile Chinook salmon in upstream areas throughout the Central Valley, especially fall-run Chinook salmon, resulting from temperature and flow related 964 Biological Opinion for the Long-Term Operation of the CVP and SWP • • impacts that affect or limit the productivity of available habit for Chinook salmon in the Central Valley. Altered hydrodynamics and routing effects in south Delta that reduce through-Delta survival for all Chinook salmon populations. Increased extinction risks for ESA-Iisted Chinook that could further diminish the productive capacity of the Central Valley and diversity of Chinook salmon prey resources available of SRKW. Adverse effects of project operations to SRKW will be reduced primarily through the following measures: 1) Accelerating the Battle Creek Restoration Program will increase habitat availability for and productivity of winter- and spring-run Chinook, which improves the overall productivity of Chinook salmon in the Central Valley increasing the number of juvenile Chinook salmon that survives to the ocean as potential prey for SRKW. 2) The RP A action for habitat restoration and predation hot-spot removal ensures that Chinook salmon rearing habitat actions in the lower Sacramento River and Northern Delta will minimize adverse effects of seasonal project operations and low-flow conditions on Chinook salmon. These habitat actions will increase the survival and growth rates of individuals that utilize this habitat. These fish are predicted to enter the estuary and ocean with a higher degree of fitness, and therefore, greater resiliency to withstand stochastic events in these later phases oftheir life history, thereby increasing the Chinook salmon prey resources available for SRKW over time. 3) Preparation of an HGMP for fall-run Chinook salmon at Nimbus Fish that evaluate and implement appropriate alternative release strategies and increased hatchery production goals for fall-run Chinook salmon is necessary to reduce operational effects on Southern Residents prey by increasing the number of juvenile Chinook salmon that survives to the ocean as potential prey for SRKW. The HGMP should also improve the genetic diversity and diversity of run timing of Central Valley fall-run Chinook salmon which will decrease the potential for localized prey depletions and thereby provide a more consistent food source for SRKW. 4) The RPA action to use the power bypasses at Keswick Dam and Folsom Dam to meet water temperature objectives helps ensure that all actions necessary to control water temperatures to protect and promote salmon productivity in these rivers are considered. This action will help minimize temperature effects on juvenile Chinook salmon increasing the number of juvenile Chinook salmon that survives to the ocean as potential prey for SRKW. 5) The RPA actions for CCV steelhead in DD.l.a and DD.l.b will also minimize in Delta effects to Chinook salmon young-of-year, including fall-run and CV spring-run Chinook salmon. This action will improve survival for the proportion of these fish that are present in the central and south Delta in April and May, and increase the proportion offish that successfully ,enter the ocean as potential prey for SRKW. 6) The RPA action to develop and implement loss thresholds for all Central Valley Chinook salmon population will address reduced juvenile Chinook salmon survival and overall productivity of Chinook salmon in the Central Valley by ensuring that the effects of Delta Operations on all Central Valley salmon populations are minimized. This action will help increase the available Chinook salmon prey resources for SRKW over time. 965 Biological Opinion for the Long-Term Operation of the CVP and SWP 7) The RPA actions for Delta and East-side flow and export actions along with the habitat actions, are predicted to create more suitable flow and non-flow related habitat conditions throughout the lower San Joaquin and South Delta that will minimize effects on juvenile Chinook salmon. This action will help increase the available Chinook salmon prey resources for SRKW over time. 8) Implementation of all RPA actions for ESA-listed Chinook salmon will allow the PA to proceed without jeopardizing any Chinook salmon ESUs, which will prevent further diminishment of the productive capacity of the Central Valley and the diversity of Chinook salmon prey resources available of SRKW. Because this biological opinion has found jeopardy and destruction or adverse modification of critical habitat, Reclamation is required to notify NMFS of its final decision on the implementation of the RP A. 2.11 Incidental Take Statement Section 9 of the ESA and Federal regulations pursuant to section 4(d) of the ESA prohibit the take of endangered and threatened species, respectively, without a special exemption. "Take" is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to engage in any such conduct. "Harm" is further defined by regulation to include significant habitat modification or degradation that actually kills or injures fish or wildlife by significantly impairing essential behavioral patterns, including breeding, spawning, rearing, migrating, feeding, or sheltering (50 CFR 222.102). "Incidental take" is defined by regulation as takings that result from, but are not the purpose of, carrying out an otherwise lawful activity conducted by the Federal agency or applicant (50 CFR 402.02). Section 7(b)(4) and section 7(o)(2) provide that taking that is incidental to an otherwise lawful agency action is not considered to be prohibited taking under the ESA if that action is performed in compliance with the terms and conditions of this ITS. An ITS is not required for a framework programmatic action, i.e., an action "that approves a framework for the development of future action(s) that are authorized, funded, or carried out at a later time, and any take of a listed species would not occur unless and until those future action(s) are authorized, funded, or carried out and subject to further section 7 consultation" (50 CFR 402.02, 402.14(i)(6)). For a mixed programmatic PA, an ITS is required only for those program actions that are reasonably certain to cause take and are not subject to further section 7 consultation (50 CFR 402.14(i)(6)). A mixed programmatic PAis defined as, "for the purposes of an [ITS], a Federal action that approves action(s) that will not be subject to further section 7 consultation, and also approves a framework for the development of future action(s) that are authorized, funded, or carried out at a later time and any take of a listed species would not occur unless and until those future action(s) are authorized, funded, or carried out and subject to further section 7 consultation" (50 CFR 402.02). However, if an action agency designs a programmatic action or a mixed programmatic action that approves a framework for development of future action(s) that are authorized, funded, or carried out at a later time, and provides adequate information to inform the development of a biological opinion with an ITS related to future actions implemented under the program, NMFS may be able to include an ITS related to such an action if it determines that the action is reasonably certain to cause incidental take of listed species. This Opinion assesses the effects ofthe PA. Based on these assessments, NMFS determined that the PA is reasonably certain to result in incidental take of listed species as 966 Biological Opinion for the Long-Term Operation of the CVP and SWP described in Section 2.11.1 Amount or Extent of Anticipated Take. Incidental take for PA components identified as framework-level, are not included in this ITS (see 2.1.1 and Table 2.111). Table 2.11-1. Programmatic actions considered in the effects and I&S sections at the framework-level, therefore no exemptions from take prohibitions provided in this ITS. Division PA component Lower Intakes near Wilkins Slough Spawning Gravel Injection" Side Channel Habitat Restoration• Shasta-Sacramento River Small Screen Program Adult Rescues (Intervention) Juvenile Trap and Haul (Intervention) Battle Creek Restoration• LSNFH Production (Intervention) Trinity-Clear Creek American Mechanical Channel Maintenance Spawning and Rearing Habitat Restoration• • Gravel augmentation and floodplain wo rk • Cordova Creek Phase II and Carmichael Creek Restoration projects • Maintenance activities at Nimbus Basin, Upper Sailor Bar, and River Bend restoration sites Construction of Spawning and Rearing Habitat" East Side Temperature Management Studyb Lower SJR Habitat Sacramento Deep Water Ship Channel Food Study North Delta Food Subsidies/ Colusa Basin Drain Suisun Marsh Roaring River Distribution System Food Subsidies Study Delta Tidal Habitat Restoration Predator Hot Spot Removal San Joaquin Basin Steelhead Telemetry Studyb .. • Incidental take coverage may already be exempted m separate biological opm10ns b Incidental take ofESA-listed species under NMFS jurisdiction may not occur for these actions, in which case they may proceed without further consultation with NMFS. Under the MMPA "take" means to harass, hunt, capture, or kill, or attempt to harass, hunt, capture, or kill any marine mammal. The definition of harassment includes any act of pursuit, torment, or annoyance which has the potential to injure a marine mammal or marine mammal stock in the wild; or has the potential to disturb a marine mammal stock in the wild by causing disruption of behavioral patterns, including, but not limited to, migration, breathing, nursing, 967 Biological Opinion for the Long-Term Operation of the CVP and SWP breeding, feeding, or sheltering. Under the ESA, "take" is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to engage in any such conduct. Harm is defined by regulation to include significant habitat modification or degradation that actually kills or injures fish or wildlife by significantly impairing essential behavioral patterns, including breeding, spawning, rearing, migrating, feeding, or sheltering (50 CFR 222.1 02). In this Opinion we have identified ESA take in the form of harm to SR.KWs through reduction of their prey. This is an indirect effect. The MMPA definition ofharassment includes any act of pursuit, torment, or annoyance which: (1) has the potential to injure a marine mammal or marine mammal stock in the wild; or (2) has the potential to disturb a marine mammal stock in the wild by causing disruption of behavioral patterns, including, but not limited to, migration, breathing, nursing, breeding, feeding, or sheltering. ESA take in the form of harm due to prey reduction identified in this opinion and subsequent Incidental Take Statement does not take the form of MMPA harassment as described above in this paragraph, and as such there is no corresponding MMPA authorization required for this form of take. 2.11.1 Amount or Extent of Take In the Opinion, NMFS determined that incidental take is reasonably certain to occur as follows: Incidental take of endangered winter-run Chinook salmon, threatened CV spring-run Chinook salmon, threatened CCV steelhead, threatened sDPS green sturgeon, and endangered SRKW will occur as a result of implementing the CVP/SWP operations, as described in Appendix A3 of this Opinion. Reservoir operations are expected to continue to alter the natural hydrological cycle (i.e., releases that are higher in the summer than flows which occurred before the dams were built and releases in the spring which are lower than flows occurring during the spring before the dams were built) in the Sacramento River downstream of Keswick Dam, in Clear Creek downstream of Whiskeytown Dam, in the American River downstream of Folsom Dam, and in the Stanislaus River downstream of New Melones Dam. This ITS uses surrogates to establish the expected level of incidental take due to the P A when direct quantification of take of individuals is not possible to determine. It is not practical to quantify or track the amount or number of individuals that are expected to be incidentally taken per species as a result of the PA due to the variability associated with the response of listed species to the effects ofthe PA, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing injured or dead fish. However, it is possible to estimate the extent of incidental take by designating an ecological surrogate(s), and it is practical to quantify and monitor the surrogate(s) to determine the extent of incidental take that is occurring. This ITS explains the causal link between the surrogate and take of the listed species; and establishes a clear standard for determining when the level of anticipated incidental take is exceeded (the surrogate parameter). Table 2.11.1-1 through Table 2.11 . 1-4, below, describe the amount or extent of take by listed species, life history stage, stressor, and location within the action area. The sections that follow the tables, organized by type of activity within the PA, specify an amount of take where possible (i.e., impingement and entrainment of juveniles, fish salvage estimates), but otherwise, specify a geographic and temporal extent of take. 968 Biological Opinion for the Long-Term Operation of the CVP and SWP Administration of Water Supply Contracts This consultation addresses the long-term operations of the CVP and SWP, including the overall impacts ofthe total volume ofwater diverted from the Central Valley (e.g., higher summer flows, lower spring flows, water temperature, etc.). The volume of water delivered may be reduced from full contract amounts, consistent with the terms of individual contracts. In addition, take from the administration of water transfers is included in CVP/SWP operations for this consultation. However, this consultation does not address ESA section 7(a)(2) compliance for individual water supply contracts, except for the Sacramento River Settlement Contracts. Reclamation and DWR should consult with NMFS separately on their issuance of individual water supply contracts, including analysis of the effects of reduced water quality from agricultural and municipal return flows, contaminants, pesticides, altered aquatic ecosystems leading to the proliferation of non-native introduced species (i.e., warm-water species), or the facilities or activities of parties to agreements with the U.S. that recognize a previous vested water right. 969 Magnitude of E ffect High High Reduced survival probability ( 12% - 15% temperature dependent mortality). Reduced survival probability (5%-6% temperature dependent mortality). Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage Timing (Work Window I ntersection) May - October (May 15 - October 31) May - October (May 15 - October 31) Weight of Evidence 2.11.1.1 Winter-run Chinook Salmon Incidental Take Table Stressor and Life Stage (location) Water Temperature under Tier I management Eggs/Fry (Keswick Dam CCRgauge) Water Temperature under Tier 2 management High: Supported by multiple scientific and technical publications that include quantitative models specific to the region and species. High: Supported by multiple scientific and technical publications that include quantitative models specific to the region and species. Table 2.11.1-1. Winter-run Chinook Salmon Incidental Take Action Component (by division) I (Shasta Summer Cold Water Pool Management) (Shasta Summer Cold Water Pool Management.) Eggs/Fry (Keswick Dam CCR gauge) 970 Type of Incidental Take Lethal: Temperatures higher than 53.5°F would result in reduced survival (mean temperature-dependent mortality of 5 percent [Anderson) and 6 percent [Martin); the standard deviations are +/- 8 percent (Anderson] and+/- 9 percent [Martin)). Lethal: Temperatures higher than 53.5°F would result in reduced survival (mean temperature-dependent mortality of 12 percent (Anderson] and 15 percent [Martin]; the standard deviations are +/- 13 percent [Anderson] and+/- 16 percent [Martin)). Amount or Extent of Winter-Run C hinook Salmon Take Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53 .5°F in Tier I years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier I years the temperat ure target will be 0 53 .5°F at CCR, with acceptable exceedances of no more than 5 consecutive days. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.10.1.3.3 (Upper Sacramento Performance Metrics). • No more than two consecutive years in which winter-run Chinook salmon ETF su rvival is less than 15%, and where measures must be taken towards achieving ETF survival of at least L5% for t he third year, including those measures out! ined in the final PA Section 4. 10.1.4.2 (Conservation Measures). Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53 .5°F in Tier 2 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remai.n consistent with performance metrics described in the Final PA Section 4.1 0. 1.3.3 (Upper Sacramento Performance Metrics). • No more than two consecutive years in which winter-run Chinook salmon, ETF survival is less than 15%, and where measures must be taken to achieve ETF survival of at least 15% for the third Water Temperature under Tier 4 management Eggs/Fry (Keswick Dam CCR gauge) Water Temperature under Tier 3 management Stresso r and Life Stage (location) May - October (May 15 - October 31) May -October (May 15 - October 31) Life Stage T iming (Work W indow Intersection) Higb Higb M agnitude of Effect High: Supported by multiple scientific and technical publications that incJude quantitative models specific to the region and species. High: Supported by multiple scientific and technical publications that incJude quantitative models specific to the region and species. W eight of Evidence Reduced survival probability (79% - 81 % temperature dependent mortality). Reduced survival probability (28%- 34% temperature dependent mortality). Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) (Shasta Summer Cold Water Pool Management.) (Shasta Summer Cold Water Pool Management) Eggs/Fry (Keswick Dam CCR gauge) 971 Type oflncid ent al Take Lethal: Temperatures higher than 53.5°F would result in reduced survival (mean temperature-dependent mortality of 28 percent [Anderson] and 34 percent [Martin); the standard deviations are +/- 25 percent [Anderson] and +/- 31 percent [Martin)). Lethal: Temperatures higher than 53.5°F would result in reduced survival probability (increase in mean temperature-dependent mortality of 79 percent [Anderson] and 8 1 percent [Martin); the standard deviations are +!- 14 percent [Anderson] and+/- 16 percent [Martin)). Amount or Extent of Wi nter-Run C hinook Salmon Take year, including those measures outlined in the final PA Section 4 . 10.1.4.2 (Conservation Measures). Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 53.5°F, in Tier 3 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4. 10.1.3.3 (Upper Sacramento Performance Metrics). • No more than two consecutive years in which winter-run Chinook salmon, ETF survival is less than 15%, and where measures must be taken towards achieving ETF survival of at least 15% for the third year, including those measures outlined in the final PA Section 4.10.1.4.2 (Conservation Measures). Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53.5°F, in Tier 4 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. 0 For Tier 4 years the temperat ure target will be determined in real-time with technical assistance from NMFS and CSFWS. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4. 10.1.3.3 (Upper Sacrame11to Performance Metrics). Juveniles (Upper Sacramento River) To build storage for the subsequent year class, Fall flows are reduced from the high summer flow. This reduction of flows is likely to influence Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function. Stresso r and Life Stage (location) May- October (NA) July- December (October, November) Life Stage T iming (Work W indow Intersection) Medium - High Medium Higb Magnitude of Effect Medium: High level of understanding of the relationship between temperature and egg/fry survival, but limited understanding of the effects of seasonal operations on storage and temperature. Low: Substantial uncertainty with WUA analyses for the juvenile rearing life stage. Quantitative results include WUA analysis. Medium: Supported by select technical publications specific to the region and species. Quantitative results include month-to-month change. W eight of Evidence Decreased survival probability (<2%-6% egg/fry mortality) Decreased growth rate, Reduced survival probability Decreased survival probability, Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) and Winter Refill and Redd Maintenance = ing Pulse Flow Reduced storage caused by spring pulse releases (May 1 - May 15), reduces Reclamation's ability to provide suitable spawning and 972 Type oflncid ent al Take Lethal: Decreased month-tomonth flows resulting in stranding caused by a loss of floodplain inundation and sidechannel habitat. Sublethal: Reduced growth and increased competition and predation related to decreased habitat carrying capacity (WUA) at lower flows Lethal: Summer temperatures higher than 53.5°F would result in increased egg/fry mortality. Amount or Extent of Winter-Run C hinook Salmon Take • No more than two consecutive years in which winter-run Chinook salmon, ETF survival is less than 15%, and where measures must be taken towards achieving ETF survival of at least 15% for the third year, including those measures outlined in the final PA Section 4.10.1.4.2 (Conservation Measures). The extent of i.ncidental take is all juveniles stranded throughout the upper Sacramento River from the Keswick Dam to RBDD that cannot rear or migrate because of lower flows. • July I - March 31: o Releases reduced between sunset and sunrise o Keswick releases > 6,000 cfs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. o Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or I 00 cfs per hour. o Keswick releases between 3,250 cfs and 3,999 cfs; reductions in releases may not exceed I 00 cfs per night. o Variance allowed for flood control releases. In situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. Tn situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects during the emergency reduction in flow. Reclamation may modify the EOS storage levels and associated Keswick flow target with NMFS technical assistance. The extent of incidental take is all eggs or fry exposed to water temperatures greater than 53.5°F as a result of implementing a spring pulse. Expected take would include the marginal difference in temperaturedependent mortality caused by lower in.itial Shasta storage on May I, which is approximately 2% - 6% of eggs/fry in years with a spring pulse. incubation Water Temperatures Stresso r and Life Stage (location) May - October (May I - May 15, and95% WR alevi.n emergence - October 3 1) Life Stage T iming (Work W indow Intersection) Medium- High Magnitude of Effect High: Survivaltemperature relationship supported by multiple scientific and technical publications that include quantitative models specific to the region and species. W eight of Evidence Reduced survival Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) asta Summer Cold Water Pool Management Eggs/Fry (Upper Sacramento River) Water Temperatures. Redds constructed earlier than May 15 would not be protected. Eggs/Fry sti II in redds after the end date of temperature management (10/31, or when 95% a levin have emerged) would also not protected. Eggs/Fry (Keswick Dam CCR gauge) 973 Lethal: Temperatures higher than 53.5°F would result in reduced survival Type oflncid ent al Take The extent of take is described by the number of redds exposed to temperatures in excess of 53.5°F between May I and May 15, as well as the period between the time of 95% WR alevi.n emergence and October 31 or I 00% emergence. Expected take prior to summer temperature management would be I% of winter-run Chinook salmon redds (average proportion of redds constructed prior to May 15). Expected take after summer temperature management would be no greater than 5% of winter-run Chinook salmon redds. Amount or Extent of Winter-Run C hinook Salmon Take Stresso r and Life Stage (location) Flow Conditions Juveniles (Upper mid-Sacramento River) Juvenile migration and rearing October- April (October January) Life Stage T iming (Work W indow Intersection) July - December (December) Low-High Low Medium Magnitude of Effect High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; conclusions supported by modelling results. Low: Substantial uncertainty with WUA analyses for the juvenile rearing life stage. Quantitative results include WUA analysis. Medium: Supported by select technical publications specific to the region and species. Quantitative results include month-to-month change. W eight of Evidence Reduced fitness and/or survival when gates are open Decreased growth rate, Reduced survival probability Decreased survival probability, Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) Minimum flows DCC Gate operations Altered Hydrodynamics downstream of DCC location Juveniles Sacramento River -Delta 974 Type oflncid ent al Take Lethal: Decreased month-tomonth flows resulting in stranding caused by a loss of floodplain inundation and sidechannel habitat. Sublethal: Reduced growth and increased competition and predation related to decreased habitat carrying capacity (WUA) at lower flows Minor to lethal: Increased mortality when gates are open due to changes in routing or transit time through interactions with changes in river flow and tidal influence downstream of DCC location and gate operations Amount or Extent of Winter-Run C hinook Salmon Take Ecological surrogates related to Winter Minimum Flows: The extent of incidental take is all juveniles stranded throughout the upper Sacramento River from the Keswick Dam to RBDD because of lower flows. • July I - March 31: o Releases reduced between sunset and sunrise 0 Keswick releases > 6,000 cfs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. o Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or l 00 cfs per hour. o Keswick releases between 3,2S:O cfs and 3,999 cfs; reductions in releases may not exceed I 00 cfs per night. o Variance allowed for flood control releases. In situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. In situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects during the emergen cy reduction in flow. Reclamation may modify the EOS storage levels and associated Keswick flow target with NMFS technical assistance. Ecological surrogates related to DCC gate operations: (See Section 2. 11.1.6.1) Gates closed Dec-Jan except for up to 2 water quality events in drought conditions of up to 5-days each. Gates open October through November allowin g flow into the Delta interior, except ifKLCI or SCI trigger is exceeded, then gates closed until triggers are no longer exceeded. Stresso r and Life Stage (location) Routing Juveniles Sacramento River- Delta Transit times JuvenilesSacramento River -Delta Altered hydrodynamics in south Delta/ routing Juveniles Sacramento River -Delta Entrainment and loss at the south Delta export facilities Juvenile migration and rearing October- April (October April) Juvenile migration and rearing October- April (October April) Juvenile migration and rearing October- April (OctoberJanuary) Life Stage T iming (Work W indow Intersection) Juvenile migration and rearing October - April (October January) Medium Medium Medium Magnitude of Effect Medium to High - effects of hydrodynamics well studied and modelled. Effects of hydrodynamics on salmonid migrations in south Delta less certain. High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; conclusions supported by modelling results. High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; conclusions supported by modelling results. W eight of Evidence Reduced survival Reduced survival, reduced growth Reduced survival Reduced survival Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) DCC Gate operattons DCC Gate operattons South Delta Exports South Delta Exports Medium - sustained high frequency exposure on small proportion of population High -Numerous studies have evaluated the efficiency of the screening facilities, predation, as well as survival through the facilities 975 Lethal: Increased mortality due to increased migration times with concurrent increased exposure to predators Lethal: increased mortality due to routing into the delta interior with lower survival rates Type oflncid ent al Take Ecological Surrogates related to OMR management that make OMR flows more negative: OMR flows can be more negative than -5,000 cfs prior to January I. OMR Restrictions from - January I through June 30 (specific dates depend on species-specific OMR onset and offramp). OMR limited to no more negative than -5,000 cfs except during Storrn Flex actions, which may make OMR flows substantially more negative, with some exceptioDS as described in Section 2.5.5.8.4.4 Storm related OMR flexibility. Ecological surrogates related to DCC gate operations: (See Section 2.11.1.6.1) Gates open October through November allowing flow into the Delta interior, except ifKLCI or SCI trigger is exceeded, then gates closed until triggers are no longer exceeded. Up to 25 percent of populat·ion ofjuvenile winter run may enter Delta by early December. Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. Ecological surrogates related to DCC gate operations: (See Section 2.1 1.1.6.1) Gates open October through November allowin g flow into the Delta interior, except if KLCI or SCI trigger is exceeded, then gates closed until triggers are no longer exceeded. Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. Approximately 50 percent of annual brood year winterrun juveniles in Delta by end of January. Amount or Extent of Winter-Run C hinook Salmon Take Annual incidental take limit of highest historical loss for wild winter- run Chinook for the period between 20 I 0 and 2018 indexed to the winter-run JPE plus 20 percent ( 1.6 percent of annual JPE). Annual incidental take for hatchery winter-run Chinook salmon is 0.8 percent of hatchery JPE. Sublethal to lethal: Mortality or decrease in condition due to migratory delays in respoDSe to altered hydrodynamics in channels of the south Delta caused by flows more negative than 5,000 cfs. Loss of appropriate migratory cues. Delays increase transit time and exposure to predators, poor water quality, and contaminants. Mortality of fish occurs during the salvage process, resulting in the loss of JuvenilesSacramento River -Delta JuvenilesSacramento River-Delta Routing Increased entrainment and loss at the South Delta Exports facilities AdultsSacramento River - Delta JuvenilesSacramento River -Delta Routing Stresso r and Life Stage (location) Magnitude of Effect W eight of Evidence High - numerous studies have evaluated the potential risk to salmon ids entering the Delta interior and becoming vulnerable to entrainment at the fish salvage facilities. Low Low -sustained population effects on a small to medium proportion of the population present in the Delta Medium - few Chinook salmon observed in regional monitoring efforts in the past. No fish observed behind screens in monitoring efforts. Medium - tagging studies related to straying of Chinook through the DCC when open. Juvenile migration and rearing October- April (October- April) Low -very small proportion of population will be present in Barker Slough, low impacts of diversion volumes on hydrodynamics Juvenile migration and rearing October- April (October January) Juvenile migration and rearing October - April (October - April) Low - screens are designed for delta smelt criteria, few salmonids expected to be present at screen location High - monitoring has few observations of Chinook salmon at this location, multiple studies regarding efficiency of positive barrier fish screens November- June (November January; May 2 1 June 15) Life Stage T iming (Work W indow Intersection) Type oflncid ent al Take Delayed migration, possible reduction of spawning success Minor: Increased straying into the Mokelumne River system when gates are opened for water quality concerns, followed by migratory delays when gates are closed Amount or Extent of Winter-Run C hinook Salmon Take Reduced survival Lethal: Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.11.1.6.2) Diversion up to 175 cfs fish entrained into the facilities Reduced fitness Minor: Increased mortality due to routing into the channels of the Lindsey Slough/ Barker Slough region Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.11. 1.6.2) Diversion up to 175 cfs Ecological surrogates related to DCC gate operations: (See Section 2. 11.1.6.1} Gates open October through November allowin g flow into the Delta interior, except if KLCI or SCI trigger is exceeded, then closed gates are closed. until triggers are no longer exceeded. Gates closed Dec-Jan except gates opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 - June I 5 14 days of closed gates; remainder of days gates are open. See SWP/CVP Salvage operations discussion Minimal decrease in fitness Minor: Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) DCC Gate operations DCC Gate operatiOns North Bay Aqueduct North Bay Aqueduct Entrainment and impingement onto fish screens Juveniles Sacramento River -Delta 976 Stresso r and Life Stage (location) Juvenile migration and rearing October- April (October- April) Juvenile migration and rearing October- April (October - April) Life Stage T iming (Work W indow Intersection) Juvenile migration and rearing October- April (October- April) Low -small numbers of fish are likely to be in the vicinity of the fish screens and intake Low - fish unlikely to be in area of screens during cleaning Low - fish unlikely to be in area of screens during cleaning M agnitude of Effect Low -No reports or studies available Low -No reports or studies available W eight of Evidence Reduced fitness due to delay in migration or i ncreased predation. Mi.nimal decrease in fitness Minimal decrease in fitness Minor to lethal: Delayed migration and increased transit times with potential for increased mortality due to routing into the channel of Rock Slough where predation is likely to be elevated Minor to lethal: Injury or death due to impingement, capture by grappling hooks during weed removal Minor to lethal: Injury or death due to entrainment into dredge or impingement onto fish screens Type oflncid ent al Take Ecological surrogate related to water diversion rate at Rock Slough Pumping Plant: (See Section 2.1 1.1 .6.4) Diversion up to 350 cfs Up to 5 listed juvenile salmonids (which may i.nclude winter-run Chinook salmon) per year- take is likely to be lethal. Up to 5 listed juvenile salmonids (which may include winter-run Chinook salmon) per year - take is likely to be lethal. Amount or Extent of Wi nter-Run C hinook Salmon Take Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) JuvenilesSacramento River -Delta Routing Impingement/ capture during aquatic weed cleaning JuvenilesSacramento River ·Delta Entrainment during sediment cleaning _North Bay North Bay Aqueduct _ Aqueduct Rock Slough water diversions JuvenilesSacramento River -Delta Medium - annual monitoring reports indicate that no fish are entrained through the screens, however some fish are observed in front of the screens, and have been observed in historical monitoring. 977 Stresso r and Life Stage (location) Capture in sampling gear Adults and JuvenilesSacramento River Delta(Cl ifton Court Fore bay) C02 Injections JuvenilesSacramento River-Delta Habitat management Juveniles Sacramento River - De lta Juvenile migration and rearing - Oct April (October - April) Juvenile migration and rearing - Oct April (October- April) Life Stage T iming (Work W indow Intersection) Juvenile migration and rearing October- April (January-April) W eight of Evidence Low Medium - several studies show effectiveness of C02 in removal of predators and sensitivity of smaller fish to C02 exposure Medium - Several reports from previous predator removal studies, literature on sampling methods. Low Medium- several studies have assessed migratory delays at the Suisun Marsh radial gates, Low - infrequent sampling. Study occurs over two to three years of P A duration Magnitude of Effect Sublethal to lethal: Increased vulnerability to injury and predation due to entanglement/entrapm ent in sampling gear Type oflncid ent al Take Over the two-year study Predator Reduction Electrofishing Study: • Incidental take of up to 50 adult or juvenile winterrun Chinook salmon cumulative, with no more than 3 mortalities. Amount or Extent of Winter-Run C hinook Salmon Take Reduced fitness Sublethal to lethal: Small increase in morbidity and mortality due to C02 exposure during predator clean outs of secondary channel Ecological surrogate based on the SMSCG operations: (See Section 2. 11.1.6.6) Operations of C02 injector covered under SWP/CVP operations for salvage and loss (see "CVP/SWP South Delta Exports") as it will be part of standard operations in the future. Over the two-year Predator Fish Relocation Study: • Incidental take of up to 50 adult or j uvenile winterrun Chinook salmon cumulative, with no more than 3 mortalities. Minor reductions to fitness caused by delays • June -September -no more than 60 days of gate closure. • Oct-May - no more than 20 days of gate c losure. • Boat locks arc kept open except as needed for boat transit. • Gate closures only on flood tides Minor: Management of flows entering Suisun Marsh and Roaring River to improve food supplies for Delta smelt, potential temporary migratory delays and blockages. Reduced survival Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) Predator removal studies CVP Improvements Marsh/ Roaring River Food Distribution Studies 978 Stresso r and Life Stage (location) Transit times Juveniles Sacramento River -Delta Stranding following end of transfer releases Egg incubation, juvenile rearing Life Stage T iming (Work W indow Intersection) Juvenile migration and rearing October- April (early May late emigrating fish) Juvenile rearing, holding, and migration upper Sacramento River - July -December (July- November) Fall-Summer Low - installation of barriers occurs at the very tail end of winter-run migratory period, exposure to the barriers is expected to be minimal. Magnitude of Effect Medium - several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of winter-run in the south Delta channels is well documented by salvage records. W eight of Evidence Low Medium- several studies conducted on Chinook salmon stranding in upper Sacramento River. Variable - Beneficial to Medium Low -changes in river flow related to transfers not expected to change river elevations substantially, Type oflncid ent al Take Reduced survival Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to predators Sublethal to lethal Sublethal to lethal Isolation and stranding in side channels and pools following reduction of reservoir releases. Variable Benefits to survival (export reductions) to Reduced Reduced survival due water temperaturerelated effects Reduced survival due to risk of stranding as flows recede Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Componen t (by division) South Delta Agricultural Barriers Transfers Delta Smelt Habitat Action 979 Amount or Extent of Winter-Run C hinook Salmon Take Ecological surrogates related to barrier operations: (See Section 2.11.6.8) Installation of barriers no earlier than May 1. May 16 to May31, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22"C. Sept 15 notch in barrier weirs or flashboard removal Sept 15. No barrier operations between December I and April30. Ecological surrogates related to water transfers Transfers allowed only during the July through November transfer window. Maximum volumes of transferred water restricted to permitted amounts. Implementation of required ramping rates for reduction of releases from Keswick Reservoir to minimize stranding. Take is exempted to the extent that it is covered under the effects of action components described above (export operations, Salinity Control Gate Operations, Seasonal Operations and other Core Water Operations) Biological Opinion for the Long-Term Operation of the CVP and SWP 2.11.1.2 CV Spring-run Chinook Salmon Incidental Take Table Life Stage Timing (Work Wind ow I ntersection) September ISOctober3 1 June !-September 15 June !-September 15 November January Magnitude of Effect High - Medium Medium Medium Low Type of I ncidental Take Amount or Extent of CV Spring.- run Chinook Salmon Take Weight of Evidence Probable Change in Fitness Ecological surrogate is the water temperature The extent of incidental take is spawning habitat to the IGO compliance point exposed to water temperatures at the proposed temperature limit 56°F OAT, with acceptable exceedances of no more than 7 consecutive days, up to 57°F during the fall tempe:rature management season (September 15 to October 31 ). In critical or dry water year types, the extent of incidental take will extend up to 57°F, with acceptable exceedances for the year. Reduced survival and reproductive success. Ecological surrogate is water temperature The extent of incidental take is holdin g habitat to the compliance point that meets the proposed temp erature limit 60°F OAT, with acceptable exceedances o f no more than 7 consecutive days, up to 61 °F DAT during the summer temperature management season (June I to September 15). In critical or dry water year types, the extent of incidental take will extend up to 61°F, with acceptable exceedances for the year. High: data on water temperatures and redd exposure under current conditions, which is the same the proposed action. Sublethal: Adults are exposed to water temperatures resulting in stress, disease, reduced fecundity, and prespawn mortality. Ecological surrogate is flow within migratory habitat The extent of incidental take is migratoryhabitat exposed to minimum base flows in years without full spring pulse flows (critical water year types) Sublethal to lethal: Redds are exposed to water temperatures resulting in temperature dependent mortality of eggs and embryos. Low flow barriers at riffles and cascades may inhibit access to holding locations. Reduced survival and reproductive success. Reduced survival and reproductive success Medium: data on water temperatures and redd exposure under current conditions, which is the same the proposed action. Low Reduced survival The ecological surrogate is flow with.in spawning habitat The extent of incidental take is spawning habitat exposed to flow decreases that result in up to I 0% of redds dewatered before juveniles emerge. Medium: current data on flows required to meet fall water temperatures and dewatering supported by tech.n ical report. Sublethal: Base flow reductions in Critical water year types, and/or following the fall water temperature criteria period, will dewater Table 2.11.1-2. CV Spring-run Chinook Salmon Incidental Take Stressor and Life Stage (location) Water Temperature, Spawning Habitat Availability. Action Component (by division) :<:l£.a r Creek: Water temperature management: Fall Eggslalevins to the IGO compliance point Eggs/aIevins creek-wide Flow conditions Flow Conditions; Passage Impediments Adults migrating creek-wide Adults holding to the IGO compliance point Water Temperature Northwestern California Diversity Group :9£.a r Creek: Water temperature management: Summer Northwestern California Diversity Group Minimum instream base flows Northwestern California Diversity Group Minimum instream base flows. Northwestern California Diversity Group 980 Juveniles/smolts: creek-wide Juveniles/ smelts: creekwide Flow Conditions Flow conditions; Loss of Natural River Morphology and Function Stressor and L ife Stage (location) March - October (May 15 - October 31) AugustDecember (August -October 31) Year round Year round Life Stage Timing (Work Window Intersection) Magnitude of Effect Low Medium High Low Weight of Evidence Low Type of Incidental Take Amount or Extent of CV Spring.- run Chinook Salmon Take The ecological surrogate is flow within juvenile rearing habitat. The extent of incidental take is all juveniles exposed tothe minimum base flows described in the proposed action, in years without channel maintenance flows (40%). redds and cause egglalevin mortality. Reduced growth, survival, and I ife history diversity • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier I years the temperat ure target wi II be 0 53 .5°F at CCR, with acceptable exceedances of no more than 5 consecutive days. • Shasta operations will remain consistent with performance metrics described in the final PA Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53 .5°F or 61 °F (7DADM) in Tier I years, according to the following criteria: Minor: Static flow regime restricts access to rearing habitat and refugia, and does not provide migratory cues. Sublethal: Temperatures in excess of 61 °F 7DADM expected to lead to stress, disease, and bioenergetic depletion. Lethal: Temperatures higher than 53.5°F would cause a decrease in egg survival. Reduced survival Reduced survival probability Sublethal: Flow decreases cause isolation and stranding. Ramping rates wi II reduce the magnitude of effect. High: Supported by multiple scientific and technical publications Reduced reproductive success Medium: current data on species occurrence, and supported by technical publications on flow decreases and stranding Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. The ecological surrogate is the proposed flow ramping rates. • Flow decreases up to 25 cfs per hour, and timed such that the maximum rate of flow decrease occurs primarily during dark hours through the majority of the creek (Section 2.5.3.4.2 Clear Creek Flow Releases). The extent of incidental take is reari ng habitat exposed to reductions in flow during controlled flow decrease from Whiskeytown Reservoir. Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Minimum instream base flows Northwestern California Diversity Group 'C lear Creek: Spring attractionlchanne I maintenance pulse flows, and Minimum instream base flows Eggs/Fry (Keswick Dam BSF gauge) Northwestern California Diversity Group (Shasta Summer Cold Water Pool Management) Water Temperature Basalt and Porous Lava Diversity Group Holding& Spawning Adults (Keswick Dam BSF gauge) 981 March- October (May I 5 - October 31) AugustDecember (August - October 3 I) March - October (May I 5 - October 31) August December (August - October 31) Life Stage T iming (Work W indow Intersection) Weight of Evidence Reduced survival probability Magnitude of Effect High High: Supported by multiple scientific and technical publications Reduced survival probability Low High High: Supported by multiple scientific and technical publications Reduced reproductive success Low Reduced rcproducti ve success High Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Proba ble Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Stressor and L ife Stage (location) Eggs/Fry (Keswick Dam BSF gauge) Action Component (by division) (Shasta Summer Cold Water Pool Management) Holding& Spawning Adults (Keswick Dam BSF gauge) Water Temperature Basalt and Porous Lava Diversity Group Eggs/Fry (Keswick Dam BSF gauge) Water Temperature (Shasta Summer Cold Water Pool Management) Holding& Spawning Adults (Keswick Darn BSF gauge) Water Temperature Basalt and Porous Lava Diversity Group (Shasta Summer 982 Typ e of Incid ental Take Lethal: Temperatures higher than 53.5°F would cause a decrease in egg survival. Sublethal: Temperatures in excess of 61 °F 7DADM expected to lead to stress, disease, and bioenergetic depletion. Lethal: Temperatures higher than 53.5°F would cause a decrease in egg survival. Sublethal: Temperatures in excess of 61 °F 7DADM expected to lead to stress, disease, and bioenergetic depletion. Lethal: Temperatures higher than 53.5°F would Amount o r Extent of CV Spring.- run Ch inook Salmon Take Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53.5°F or 61°F (7DADM) in Tier 2 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the Final PA Section 4. 10.1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management: The extent of incidental take is the spawning habitat that exceeds 53 .5°F or 61 °F (7DADM), in Tier 3 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.10. 1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management: Action Component (by division) Eggs/Fry (Keswick Dam BSF gauge) Stressor and L ife Stage (location) AugustDecember (August -October 31) Life Stage Timing (Work Window Intersection) I Magnitude of Effect I Low High High Weight of Evidence Reduced survival probability Probable Change in Fitness High: Supported by multiple scientific and technical publications Decreased growth rate, Decreased survival probability Reduced survival probability Reduced reproductive success High: Supported by multiple scientific and technical publications specific to the region and species. Quantitative results include WUA analysis and month-tomonth floodplain inundation. Medium: Supported by a limited number of scientific and technical publications specific to the region and species. Quantitative results month-to-month channel inundation (USFWS 2006). Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. I Biological Opinion for the Long-Term Operation of the CVP and SWP Cold Water Pool Management) Basalt and Porous Lava Diversity Group November - April (December February) AugustDecember (October, November) March - October (May IS - October 31) Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural Function I River Morphology and Redds (Upper Sacramento River) Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and lnstream Cover, Loss of Natural River Morphology and Function Holding& Spawning Adults (Keswick Dam BSF gauge) land Winter Refill and Redd Maintenance Basalt and Porous Lava Diversity Group Minimum flows Basalt and Porous Lava Diversity Group Juveniles (Upper mid-Sacramento River 983 I Type of Incidental Take cause a decrease in egg survival. Sublethal: Temperatures in excess of 61 op 7DADM expected to lead to stress, disease, and bioenergetic depletion. Lethal: Decreased month-tomonth flows resulting in possible redd dewatering and decreased floodplain inundation and sidechannel habitat. Sublethal to lethal: Decreased habitat carrying capacity (WUA) at lower flows providing decreased feeding conditions, and increased competition and predation. Decreased month-to-month flows resulting in decreased flood lain inundation I Amount or Extent of CV Spring.- run Chinook Salmon Take The extent of incidental take is the spawning habitat that exceeds 53 .5°F or 61 °F (7DADM), in Tier 4 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier 4 years the temperature target will be 0 determined in real-time with technical assistance from NMFS and CSFWS. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Fall and Winter Refill and Redd Maintenance: The extent of incidental take is all spring-run redds dewatered throughout the upper Sacramento R iver from the Keswick Dam to RBDD because oflower flows. Incidental take of spring-run redds is expected proportional to the dewatering of fall-run redds which are cotemporaneous and more abundant. Dewatering would also occur proportional to the filow reduction such that expected take will be no greater than: • 41% ofredds at 3,250 cfs. • 29% ofredds at 4,000 cfs, • 22% of redds at 4,500 cfs, • 15% of redds at 5,000 cfs The extent of incidental take is all juveniles stranded or delayed throughout the upper Sacramento River from the Keswick Dam to RBDD that cannot rear or migrate because of lower flows. • July 1 - March 31: o Releases reduced between sunset and sunrise o Keswick releases > 6,000 cfs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. JuvenilesSacramento River -Delta Altered hydrodynamics in south De lta/ routing JuvenilesSacramento River -Delta Altered Hydrodynamics downstream of DCC location Stressor and L ife Stage (location) Juvenile migration and rearing December - May (December - May) Juvenile migration and rearing December - May (December January; May 21 May 31) Life Stage Timing (Work Window Intersection) Magnitude of Effect High Medium to High Weight of Evidence High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; conclusions supported by modelling results. Medium to High - effects of hydrodynamics well studied and modelled. Effects of hydrodynamics on salmonid migrations in south Delta less certain. Type of Incidental Take Amount or Extent of CV Spring.- run Chinook Salmon Take Ecological surrogates related to barrier operations (see Section 2.1 1.1.6.1) Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 -June 15 14 days of closed gates; remainder of days gates are open. and side-channel habitat. o Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or I 00 cfs per hour. o Keswick releases between 3,250 efs and 3,999 cfs; reductions in releases may not exceed I 00 cfs per night. o Variance allowed for flood control releases. Reduced fitness and/or survival when gates are open Minor to lethal: Increased mortality when gates are open due to changes in routing or transit time through interactions with changes in river flow and tidal influence downstream of DCC location and gate operations Ecological surrogates related to OMR management that make OMR flows more positive: OMR flows can be more negative than -5,000 cfs prior to January I. OMR Restrictions from - January I through June 30 (specific dates depend on species-specific OMR onset and offramp). OMR limited to no more negative than -5,000 cfs except during Storm Flex actions, which may make OMR flows substantially more negative, with some exceptions. 111 situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. In situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects during the emergency reduction in flow. Reduced survival, reduced growth Sublethal to lethal: Mortality or decreases in condition due to migratory delays in response to altered hydrodynamics in channels of the south Delta. Loss of appropriate migratory cues. Delays increase transit time and exposure to predators, Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) DCC Gate operations Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group South Delta Exports Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and 984 JuvenilesSacramento River - Delta Routing JuvenilesSacramento River -Delta Transit times Juveniles - Delta Entrainment and loss at the south Delta export facilities Stressor and L ife Stage (location) Magnitude of Effect Weight of Evidence Medium to High installation of barriers occurs during SR migratory period, exposure to the barriers is expected to be low for Sacramento River basin SR, high for SJR basin population SR, and phenotypic spring-run from the Stanislaus River. Medium - several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of spring-run in the south Delta channels is well documented by salvage records. Medium to High sustained high frequency exposure on small proportion of population Juvenile migration and rearing December- May (May - early June) Medium to High High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; High - Numerous studies have evaluated the efficiency of the screening facilities, predation, as well as survival through the facilities Juvenile migration and rearing December - May (December Janua.ry, May 21 June15) Juvenile migration and rearing December - May (December - May) Life Stage Timing (Work Window Intersection) Reduced survival Reduced survival Reduced survival Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Southern Sierra Nevada Diversity Group South Delta Exports Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group South Delta Agricultural Barriers Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group DCC Gate operations Populations from Northwestern California Diversity Group, Basalt and 985 Type of Incidental Take poor water quality, and contaminants. Lethal: Mortality of fish occurs during the salvage process, resulting in the loss of fish entrained into the facilities Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to predators Lethal: Increased mortality due to routing into the delta interior with lower survival rates when gates are open. Amount or Extent of CV Spring.- run Chinook Salmon Take OMR flow is restricted to no more negative than -5,000 cfs to protect YOY spring-run Chinook salmon when more than 5 percent of the YOY spring-run population is in the Delta except during Storm Flex operations when OMR flows may be more negative than -5,000 cfs. Take limit of I percent loss of each su rrogate yearling spring-run releases group (CNFH late-fall run Chinook salmon) Ecological surrogates related to barrier operations: (See Section 2.11.1.6.8) 30. Installation of barriers no earlier than May I. May 16 to May 31, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22•c. Sept 15 notch in barrier weirs or flash board removal Sept 15 No barrier operations between December I and April Ecological surrogates related to DCC gate operations: (See Section 2. 11.1 .6.1) Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. Adults Sacramento River- Delta Routing Adults- Delta Transit times JuvenilesSacramento River -Delta Transit times Stressor and L ife Stage (location) January - June (January, May 21 June) Adult migration January - June (May-June) Juvenile migration and rearing December - May (DecemberJanuary, May 21 Junel5) Life Stage T iming (Work W indow Intersection) M agnit ude of Effect Medium to High Medium - installation of barriers occurs during adult SR migratory period, exposure to the barriers is expected to be high for SJR basin population SR and phenotypic spring-run from the Stanislaus River. Low Weight of Evidence conclusions supported by modelling results. High - There are a number of publications regarding the relative survival in various North Delta and Central Delta migratory routes; conclusions supported by modelling results. Medium - several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of spring-run in the south Delta channels is well documented by salvage records. Medium - tagging studies related to straying of Chinook through the DCC when open. Reduced survival Lethal: Increased mortality due to increased migration times with concurrent increased exposure to predators within the Delta interior. Access to Delta interior when the gates are open. Typ e of Incid ental Take Reduced survival Delayed migration, possible reduction of spawning success Minor: Increased straying into the Mokelumne River system when gates are opened, followed by migratory delays when gates are closed for water quality concerns Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to warmer water conditions while moving upriver over barriers Proba ble Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group .DCC Gate operations Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Delta Agricultural Barriers Populations from Southern Sierra Nevada Diversity group DCC Gate operations Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group 986 Amount o r Extent of CV Spring.- run Ch inook Salmon Take May 21 -June 15 14 days of closed gates; remainder of days gates are open. Ecological surrogates related to DCC gate Operations: (See Section 2.11.1.6.1) Gates closed Dee-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 - June 15 14 days of closed gates; remainder of days gates are open. Ecological surrogates related to barrie r operations: (See section 2.11.1.6.8) Installation of barriers no earlier than May 1. May 16 to May31, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22•c. Sept 15 notch in barrier weirs or flash board removal Sept 15 Barriers are removed by November 30 of each year Ecological surrogates related to DCC gate operations: (See Section 2.11 .1.6.1) Gates closed Dee-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 - June 15 14 days of closed gates; remainder of days gates are open. Gates open after June 16 Weight of Evidence High - numerous studies have evaluated the potential risk to salmon ids entering the Delta interior and becoming vulnerable to entrainment at the fish salvage facilities. Magnitude of Effect Low - sustained population effects on a small to medium proportion of the population present in the Delta Medium - few Chinook salmon observed in regional monitoring efforts in the past. No fish observed behind screens in monitoring efforts. Life Stage Timing (Work Window Intersection) Juvenile migration and rearing December- May (December- May) Low- very small proportion of population will be present in Barker Slough, low impacts of diversion volumes on hydrodynamics Stressor and L ife Stage (location) Juvenile migration and rearing December- May (December - May) Low - screens are designed for delta smelt criteria, few salmonids expected to be present at screen location Juvenile migration and rearing December- May (December- May) JuvenilesSacramento River -Delta Routing JuvenilesSacramento River -Delta Entrainment and impingement onto fish screens Juveniles Sacramento River -Delta High - monitoring has few observations of Chinook salmon at this location, multiple studies regarding efficiency of positive barrier fish screens Increased entrainment and loss at the South Delta Exports facilities Reduced survival Sublethal to lethal: Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.11.1.6.2) Diversion up to 175 cfs See SWP/CVP Salvage operations Amount or Extent of CV Spring.- run Chinook Salmon Take Reduced survival Minor: Increased mortality due to routing into the channels of the Lindsey Slough/ Barker Slough region Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.11.1.6.2) Diversion up to 175 cfs Type of Incidental Take Minimal change in fitness Minor: Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. Probable Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) DCC Gate operations Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group North Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group 987 Entrainment during sediment cleaning Stressor and L ife Stage (location) Life Stage T iming (Work W indow Intersection) Juvenile migration and rearing December - May (December - May) Juvenile migration and rearing December- May (December- May) Juvenile migration and rearing December - May (December- May) Juveniles Sacramento River -Delta Impingement/ capture during aquatic weed cleaning JuvenilesSacramento River -Delta Routing JuvenilesSacramento River -Delta Magnitude of Effect Low - fish unlikely to be in area of screens during cleaning Low - fish unlikely to be in area of screens during cleaning Low - small numbers of fish are likely to be in the vicinity of the fish screens and intake Weight of Evidence Low -No reports or studies available Low - No reports or studies available Medium - annual monitoring reports indicate that no fish are entrained through the screens, however some fish are observed in front of the screens, and have been observed in historical monitoring. Minimal change in fitness Minimal change in fitness Sublethal to lethal: Injury or death due to impingement, capture by grappling hooks during weed removal Sublethal to lethal: Injury or death due to entrainment into dredge or impingement onto fish screens Typ e of Incid ental Take Ecological surrogate related to water diversion rate at Rock Slough Pumping Plant: (See Section 2. 11.1.6.4) Diversion up to 350 cfs. Up to 5 listed juvenile salmon ids (which includes CV spring-run Chinook salmon) per year- take is likely to be lethaL Up to 5 listed juvenile salmon ids (which includes CV spring-run Chinook salmon) per year- take is likely to be lethaL Amount o r Extent of CV Spring.- run Ch inook Salmon Take Proba ble Change in Fitness Reduced fitness due to delay in migration or increased predation. Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to routing into the channel of Rock Slough where predation is likely to be elevated Biological Opinion for the Long-Term Operation of the CVP and SWP _North Bay Action Component (by division) _ Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group North Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Rock Slough water diversions Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group 988 capture in sampling gear Stressor and L ife Stage (location) Life Stage T iming (Work W indow Intersection) Adults and juveniles- Delta C02 Injections JuvenilesSacramento River -Delta Temporary change in water flow/water quality (20 days Oct-May, 60 days June-Sept) Adults and juveniles may migrate through the area on their way to spawning grounds or as Adult migration (January - June), Juvenile migration and rearing December - May (December- June) Juvenile migration and rearing December - May (December - May) Adult migration January - June (January- June) Magnitude of Effect Weight of Evidence Medium - Several reports from previous predator removal studies, literature on sampling methods. Low Medium- several studies show effectiveness of C02 in removal of predators and sensitivity of smaller fish to C02 exposure Low - infrequent sampling over two to three years of study Low Medium- data on Chinook salmon migration and rearing in Suisun Marsh is medium, based on a few studies of the Salinity gate operations Typ e of Incid ental Take Sublethal to lethal: Increased vulnerability to injury and mortality due to entanglement/entrapm ent in sampling gear Amount o r Extent of CV Spring.- run Ch inook Salmon Take Over the two-year Predator Reduction Electrofishing Study: • Incidental take of up to 50 juvenile or adult CV spring-run Chinook salmon cumulative, with no more than 5 mortalities. Over the two-year Predator Fish Relocation Study: Operations of C02 injector covered under SWP/CVP operations for salvage and loss. • Reduced fitness Sublethal to lethal: Small increase in morbidity and mortality due to C02 exposure during predator clean outs of secondary channel Ecological surrogate based on the SMSCG operations: (See Section 2. 11.1.6.6) June -September -no more than 60 days of gate closure. Oct-May - no more than 20 days of gate closure. Boat locks are kept open except as needed for boat transit. Gate closures only on flood tides Incidental take of up to 50 juvenile or adult CV spring-run Chinook salmon cumulative, with no more than 5 mortalities. Minimal Minor: During the annual 20 days of periodic operation Oct- May, individual adult spring-run may be delayed in their spawning migration from a few hours to several days. Juveniles may be delayed on their downstream movements by closed Reduced survival Proba ble Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Predator removal studies Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group Improvements Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group Marsh Roaring River Distribution System Food Subsidy Studies Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, 989 Egg incubation, juvenile rearing Stranding following end of transfer releases outmigrating juveniles. Stressor and L ife Stage (location) Fall-Summer Juvenile rearing, holding, and migration upper Sacramento River - November April (November) Life Stage T iming (Work W indow Intersection) Magnitude of Effect Low -changes in river flow related to transfers not expected to change river elevations substantially, Variable- Beneftcial to Medium Weight of Evidence Medium- several studies conducted on Chinook salmon stranding in upper Sacramento River. Low temperaturerelated effects water VariableBenefits to survival (export reductions) to Reduced Reduced survival due Reduced survival due to risk of stranding as flows recede Proba ble Change in Fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Northern Sierra Nevada Diversity Group and Southern Sierra Nevada Diversity Group Transfers Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Delta Smelt Habitat Action 990 Typ e of Incid ental Take Amount o r Extent of CV Spring.- run Ch inook Salmon Take Sublethal to lethal Isolation and stranding in side channels and pools following reduction of reservoir releases. Ecological surrogates related to water transfers: (See Section 2.11.1.6.5) Transfers allowed only July througb November Maximum volumes of water transfers restricted to permitted amounts (See Section 2. 1 l.l.6.S) Implementation of ramping rates for reduction of releases from Keswick Reservoir to minimize stranding. (See Section 2.5.5.6 and Upper Sacramento/ Shasta Water Minimum Flows) gates for several hours while gates are closed on flood tides. Sublethal to lethal Take is exempted to the extent that it is covered under the effects of action components described above (export operations, Salinity Control Gate Operations, Seasonal Operations and other Core Water Operations) Life Stage Timing (Work Window I ntersection) December-March Year round June !-September IS January-June W eight of Evidence Medium Supported by monitoring data on spawning and technical reports on dewatering following flow changes. Magnitud e of Effect Medium Low Low Medium Low Medium Medium: current data on species occurrence, and supported by technical publications on flow decreases and stranding Probable C ha nge in Fitness Typ e of Incidenta l T ake A m ount or Extent of CCV Steelhead Take The ecological surrogate is flow within spawning habitat. The extent of incidental take is spawning habitat exposed to the proposed minimum base flows during controlled flow decreases from Whiskeytown Reservoir i_n critical years. The ecological surrogate is water temperature. The extent of incidental take is rearing habitat to the !GO compliance point exposed to water temperatures above 60°F DAT with acceptable exceedances for up to 7 consecutive days during the temperature management season (June I to September 14). The ecological surrogate is flow within rearing habitat. The extent of incidental take is all juveniles exposed to the minimum base flows described in the proposed action in years no channel maintenance flow occur (40%). Reduced growth. and survival Minor: Exposure to subop timal temperatures cause stress, increased susceptibility to disease, predation, and mortality. Sublethal to lethal: Base flow reductions in Critical water year types, and/or following the fa ll water temperature criteria period will dewater redds and cause egg/a levin mortality. Minor: Static flow regime restricts access to rearing habitat and refugia, and does not provide migratory cues. Reduced survival Sublethal: Flow decreases cause isolation and stranding. Ramping rates will reduce the magnitude of effect. The ecological surrogate is the proposed flow ramping rates: Flow decreases may not exceed 25 cfs per hour and must be timed so the maximum rate of flow decrease occurs primarily during dark hours through the majority of the creek (Section 2.5.3.4.2 Clear Creek Flow Releases). The extent of incidental take is rearing habitat exposed to reductions in flow during controlled flow decreases from Whiskeytown Reserv()ir (Section 2.5.3.4.2 Clear Creek Flow Releases). Reduced growth, su.rvival, and life history diversity Reduced survival and reproductive success Biological Opinion for the Long-Term Operation of the CVP and SWP 2.11.1.3 CCV Steelhead Incidental Take Table Juveniles/ smolts, creekwide Flow Conditions Juvenilesfsmolts upstream of!GO compliance point Juveniles/ smolts: creekwide Water Temperature Flow conditions; Loss of Natural River Morphology and Function Eggs/alevins: creek-wide Flow Conditions Str essor and Life Stage (location) Table 2.11.1-3. CCV Steelhead Incidental Take Action Component ( by division) Diversity G r oup Minimum instream base flows Northwestern California Diversity Group Minimum instream base flows Northwestern California Diversity Group t9£!lf Creek: Water temperature management: summer Northwestern California Diversity Group Q£_ar Creek: Spring attraction/ channel maintenance pulse flows, and Minimum instream base flows Northwestern California Diversity Group 991 Stressor and Life Stage (location) Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and Instrcam Cover, Loss of Natural River Morphology and Function Migrating, Spawning Adults (Upper Sacramento River) January - June (January February) Life Stage T iming (Work Window 1ntersection) AugustDecember (October, November) Magnitude of Effect High High Weight of Evidence Medium: Supported by select technical publications specific to the region and species. Quantitative results include average spawning flows to proposed minimum flows. Medium: Supported by a limited number of scientific and technical publications specific to the region and species. Quantitative results month-to-month channel inundation (USFWS 2006). Fitness Probable Cha nge in Reduced survival probability Reduced survival probability Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup and Winter Refill and Redd Maintenance Basalt and Porous Lava Diversity Group Minimum flows Basalt and Porous Lava Diversity Group Spawning Habitat Availability, Flow Conditions, Loss of Riparian Habitat and Instream Cover, Loss of Natural River Morphology and Function Redds, (Upper mid-Sacramento River) 992 Typ e oflncidental T ake Lethal: Decreased month to month flows resulting in possible dewatering and stranding as decreased floodplain inundation and sidechannel habitat isolated by reduced flows. Lethal: Decreased month to month flows resulting in decreased floodp lain inundation and a temporary loss of spawning habitat leading to steel head redds being dewatered .. Amount or Extent of CCV Steelhead T ake The extent of incidental take is all adults stranded or delayed throughout the upper Sacramento River from the Keswick Dam to RBDD that cannot migrate or spawn because of lower flows. • July I - March 3 1 o Releases reduced between sunset and sunrise o Keswick releases> 6,000 efs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. 0 Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or I 00 cfs per hour. o Keswick releases between 3,250 cfs and 3,999 cfs; reductions in releases may not exceed t 00 cfs per night. o Variance allowed for flood control releases. In situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. In situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects during the emergency reduction in flow. The extent of incidental take is all redds dewatered throughout the upper Sacramento River from the Keswick Dam to RBDD because of lower flows. • July 1 - March 3 1 o Releases reduced between sunset and sunrise o Keswick releases > 6,000 cfs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. 0 Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or I 00 cfs per hour. o Keswick releases between 3,250 cfs and 3,999 cfs; reductions in releases may not exceed I 00 cfs per night. o Variance allowed for flood control releases. Stressor and Life Stage (location) Water Temperature Juveniles (Keswick Dam RBDD) Water Temperature Juveniles (Keswick Dam RBDD) Life Stage T iming (Work Window 1ntersection) January- July (May 15- July) January - July (May 15- July) Magnitude of Effect Medium Low - Medium Weight of Evidence Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Probable Cha nge in Fitness Reduced growth rate, reduced survival Reduced growth rate and survival probability Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup (Shasta Summer Cold Water Pool Management) Basalt and Porous Lava Diversity Group (Shasta Summer Cold Water Pool Management) 993 Typ e oflncidental T ake Sublethal: Temperatures in excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Sublethal: Temperatures in excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Amount or Extent of CCV Steelhead T ake In situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. In situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects duri.n g the emergency reduction in flow. Incidental take of steelhead redds is expected to be proportional to the flow reduction such that expected take wi II be no greater than: • 3 1% of redds at 3,250 cfs. • 22% ofredds at 4,000 cfs, 17% of redds at 4,500 cfs, 12% ofredds at 5,000 cfs • • Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 6 1°F (7DADM) in Tier 1 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. 0 For Tier I years the temperature target will be 53.5°F at CCR, with acceptable exceedances of no more than 5 consecutive days. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4 . 10. 1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 6 1°F (7DADM} in Tier 2 years, according to the following criteria: • Shasta operations will remain consistent with the an.nual Shasta Cold Water Management Plan, (location) Stressor and Life Stage Juveniles (Keswick Dam RBDD) Life Stage T iming (Work Window 1ntersection) January- July (May 15- July) August December (August - October 3 I) January - July (May 15 - July) AugustDecember (August - October 3 I) Magnitude of Effect Low Low Low Low Weight of Evidence Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Fitness Probable Cha nge in Reduced growth, decreased survival Reduced growth rate Reduced growth, decreased survival Reduced growth rate Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup Basalt and Porous Lava Diversity Group Juveniles (Keswick Dam RBDD) Water Temperature (Shasta Summer Cold Water Pool Management) Migrating Adults (Keswick DamRBDD) ::'! Basalt and Porous Lava Diversity Group = r4 (Shasta Summer Cold Water Pool Management) Migrating Adults (Keswick Dam RBDD) Water Temperature Basalt and Porous Lava Diversity Group 994 Typ e oflncidental T ake Sublethal: Temperatures i.n excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Temperatures higher than 68°F (7DADM) would cause increased disease and decreased swimming performance in adults, and increased disease, impaired smoltification, reduced growth, and increased predation for late emigrating juveniles. Sublethal: Temperatures in excess of 61 °F can lead to stress, disease, bioenergetic depletion, or death among rearing Juveniles. Temperatures higher than 68°F (7DADM) would cause increased disease and decreased swimming performance in adults, and increased disease, impaired smoltification, reduced growth, and increased Amount or Extent of CCV Steelhead T ake where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the Final PA Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 6 1°F (7DADM) or 68°F (7DADM) in Tier 3 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 6 1°F (7DADM) or 68°F (7DADM) in Tier 4 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier 4 years the temperature target will 0 be determined i.n real-time with technical assistance from NMFS and USFWS. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Stressor and Life Stage (location) Water temperatures warmer than life stage requirements, particularly occurring upstream of Watt Ave. during June through September Juvenile rearing Primarily upstream of Watt Ave. area Water temperatures warmer than life stage requirements, particularly occurring upstream of Watt Ave. in April and May Embryo incubation Primarily upstream of Watt Ave. area Folsom/Nimbus releases - flow fluctuations Life Stage T iming (Work Window 1ntersection) Year-round (May-October) Late-DecemberMay (Late-December May) Late-DecemberMay (Late-December May) Magnitude of Effect High Medium Medium Weight of Evidence Medium High High Typ e oflncidental T ake Ecological surrogate is temperature: The extent of take is habitat upstream of the Watt A venue Bridge, where water temperature exceeds 65°F between May 15 and October 3 I, which occurs approximately 57 percent of days. Wllen 65°F cannot be met, then temperature would be increased in I degree increments up to 68°F. Amount or Extent of CCV Steelhead T ake Reduced growth; Reduced survival Sublethal: Physiological effects • increased susceptibility to disease (e.g., anal vent inflammation) and predation. Ecological surrogate is temperature: The extent of incidental take is the stretch of the American River where the mean daily water temperature first begins to exceed 54°F, to the downstream extent of steelhead spawning habitat. This is expected to occur in most years during March, April, and May. Probable Cha nge in Fitness Reduced survival Sublethal to lethal: Sublethal effects reduced early life stage viability; direct mortality; restriction of life history diversity (i.e., directional selection against eggs deposited in Mar. and Apr.) predation for late emigrating juveniles. Reduced survival, reduced reproductive success Lethal: Redd dewatering and isolation. Prohibiting successful completion of spawning Redd scour, resulting in egg mortality Ecological surrogate is the frequency and duration of flows that result in redd dewatering, isolation, or redd scour. Extent of incidental take is all embryos exposed to the stressors from redd dewatering flows, which h ave a medium annual frequency (25-75% of years). Extent of take is expected to be limited to releases from Nimbus Dam that are greater than 50,000 cfs during egg incubation (i.e., January through May), Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup Northern Sierra Nevada Diversity Group !American Northern Sierra Nevada Diversity Group Northern Sierra Nevada Diversity Group Spawning and Embryo incubation Primarily 995 Stressor and Life Stage (location) upstream of Watt Ave. area Folsom/Nimbus releases - flow fluctuations; low flows, particularly during late summer and early fall Life Stage T iming (Work Window 1ntersection) Year-round (Ycar-round) January - June (January- June) Late-December early April (Late-December early April) Magnitude of Effect Medium Medium High Weight of Evidence Low High High Amount or Extent of CCV Steelhead T ake Lethal: Fry stranding and juvenile isolation; low flows limiting the availability of quality rearing habitat including predator refuge habitat Ecological surrogate is temperature: The extent of incidental take is the stretch of the American River where the mean daily water temperature first begins to exceed 54°F, during the March through June period of smolt emigration. This is expected to occur in most years. Ecological surrogate is the frequency and duration of flows that result in stranding and isolation, as well as flows insufficient to provide quality rearing habitat. Extent of incidental take is all juveniles exposed to the stressors from strandin g and isolating flows, which have a medium annual frequency (25-75% of years). Typ e oflncidental T ake Reduced survival Sublethal: Physiological effectsreduced ability to successfully complete the smoltification process, increased susceptibility to predation Probable Cha nge in Fitness Reduced growth; Reduced survival Sublethal: Reduced genetic diversity. which occurs approximately once every 5 years (NMFS 2018). Reduced genetic integrity Ecological surrogate is steelhead release location: Extent of incidental take from Nimbus Fish Hatchery, for interim take coverage through 2024, is the release ofjuvenile steelhead downstream of the hatchery, to the Sunrise location (- RM 20). If the release location cannot be met then juvenile steelhead would be released between the Sunrise location and the Discovery Park location. Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup Northern Sierra Nevada Diversity Group Northern Sierra Nevada Diversity Group Juvenile rearing Primarily upstream of Watt Ave. area Water temperatures warmer than life stage requirements, particularly occurring downstream of Watt Ave. during March through June Smolt em igration Throughout entire river Nimbus Hatchery - hatchery 0. mykiss spawning with naturalorigin steelhead Spawning Primarily upstream of Watt Ave. area 996 (location) Stressor and Life Stage Transit times Juveniles Sacramento River -Delta Altered Hydrodynamics downstream of DCC location JuvenilesSacramento River -Delta Routing Adults - Delta Juvenile migration and rearing November - June (NovemberJune) Adult migration July-May (July - January, May 21 -early June) Juvenile migration and rearing November- June (November January, May 2 1 June) Life Stage T iming (Work Window 1ntersection) Juvenile migration and rearing November - June (November January, May2 1 June) High Medium to High- There are a number of publications regarding the relative survival of Chinook salmon in various North Delta and Central Delta migratory routes but not stcelhead; routing and transit time conclusions supported by modelling results. Weight of Evidence High High - There are a number of publications regarding the relative survival of Chinook salmon, but not steclhcad in various North Delta and Central Delta migratory routes; hydrodynamic conclusions supported by modelling and physical testing results. Magnitude of Effect Medium Medium- tagging studies related to straying of Chinook through the DCC when open. Should apply to stcelhead Medium Medium to High- effects of hydrodynamics well studied and modelled. Effects of hydrodynamics on salmonid migrations Fitness Probable Cha nge in Typ e oflncidental T ake Delayed migration, possible reduction of spawning success Reduced fitness and/or su.rvival when gates arc open Sublethal to lethal: Mortality or decreases in condition due to migratory delays in response to altered Minor: Increased straying into the Mokelumne River system when gates arc opened, followed by migratory delays when gates arc closed. Gate operations for water quality concerns Minor to lethal: Increased mortality when gates are open due to changes in routing or transit time through interactions with changes in river flow and tidal influence downstream of DCC location and gate operations Sublethal to lethal: Increased mortality due to increased migration times with concurrent increased exposure to predators Reduced survival, reduced growth Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup :DCC gate operatiOns Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group :DCC gate operattons Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group : DCC Gate operattons Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group South Delta Exports Altered hydrodynamics in south Delta/ routing 997 Amount or Extent of CCV Steelhead Take Ecological surrogates related to DCC gate operations: (See Section 2.11.1.6. 1) Gates open October through November, except if KLCI or SCI trigger is exceeded, then gates are closed until triggers are no longer exceeded. Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 - June 15 14 days of closed gates; remainder of days gates are open. Ecological surrogates related to DCC gate operations: (See Section 2.11.1.6. 1) Gates open October through November, except if KLCI or SCI trigger is exceeded, then gates are closed until triggers arc no longer exceeded. Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21- June 15 14 days of closed gates; remainder of days gates are open. Ecological surrogates related to DCC gate operations: (See Section 2.11.1.6. 1) Gates open October through November, except if KLCI or SCI trigger is exceeded, then gates are closed until triggers arc no longer exceeded. Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5days each. May 21 - June 15 14 days of closed gates; remainder of days gates are open. Gates open June 16 - September 30. Ecological surrogates related to OMR management that make OMR flows more negative: OMR flows more negative than -5,000 cfs prior to January I. Life Stage T iming (Work Window 1ntersection) Magnitude of Effect Weight of Evidence High - Numerous studies have evaluated the efficiency of the screening facilities, predation, as well as survival through the facilities in south Delta less certain . Medium - sustained high frequency exposure on small proportion of population Medium- several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of spring-run in the south Delta channels is well documented by salvage records. Juvenile migration and rearing November- June Juvenile migration and rearingNovember - June (May -June) Medium - installation of barriers occurs during Steelhead migratory period, exposure to the barriers is expected to be low for Sacramento River basin SH, high for SJR basin population SH. Adult migration July -January (south Delta - SJ River population) (July - November) Medium - installation of barriers occurs during adult SH migratory period, exposure to the barriers is expected to be high for SJR basin population SH. Fitness Probable Cha nge in Typ e oflncidental T ake Reduced survival Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to predators when migrating through routes with barriers. hydrodynamiesin chann els of the south Delta. Loss of appropriate migratory cues. Delays increase transit time and exposure to predators, poor water quality, and contami.nants when OMR flows are more negative than -S ,000 cfs... Sublethal to lethal: Mortality of fish occurs during the salvage process, resulting in the loss of fish entrained into the facilities. Reduced survival Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to warmer water conditions while moving upriver over barriers Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP (location) Stressor and Life Stage JuvenilesSacramento River -De lta Entrainment and loss at the south Delta export facilities Action Component ( by division) Diversity G roup Populations from all Diversity Groups South De lta Exports Juveniles - Delta Adults - Delta Transit times Juveniles Sacramento River -Delta Transit times Populations from all Diversity Groups :South Delta Agricultural Barriers Populations from all Diversity Groups but primarily the Southern Sierra Nevada Diversity Group Delta Agricultural Barriers Southern Sierra Nevada Diversity Groups Medium - several studies have indicated that the barriers increase transit time through the south Delta and increase predation risks. Timing of spring-run in the south Delta channels is well documented by salvage records. 998 Amount or Extent of CCV Steelhead T ake OMR restrictions from - January I through June IS (specific dates depend on species-specific OMR onset and offramp). OMR limited to no more negative than -S,OOO cfs except during Storm flex actions with some exceptions December - March: Loss of l,88S steelhead April- June IS: Loss of2,070 steelbead Based on the maximum number offish lost annually between 2010 and 2018 for each time period, plus 20 percent. Ecological surrogates related to barrier operations: (See Section 2.11. 1.6.8) Installation of barriers no earlier than May I. May 16 to May31, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22°C. Sept IS notch in barrier weirs or flashboard removal Sept IS No agricultural barriers operations after Nov 30. Ecological surrogates related to barrier operations: (See Section 2.11.1.6.8) Installation of barriers no earlier than May l. May 16 to May31, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22°C. Sept IS notch in barrier weirs or flash board removal Sept IS No agricultural barriers operations after Nov 30. Stressor and Life Stage (location) Increased entrainment and loss at the South Delta Exports facilities Juveniles· Sacramento River -Delta Routing Juveniles Sacramento River -Delta Entrainment and impingement onto fish screens Juveniles Sacramento River -Delta Entrainment during sediment cleaning JuvenilesSacramento River -Delta Weight of Evidence High - numerous studies have evaluated the potential risk to salmonids entering the Delta interior and becoming vulnerable to entrainment at the fish salvage facilities Magnitude of Effect Low - sustained population effects on a small to medium proportion of the population present in the Delta Medium- few salmonids observed in regional monitoring efforts in the past. No fish observed behind screens in monitoring efforts. Life Stage T iming (Work Window 1ntersection) Juvenile migration and rearing November- June (NovemberJanuary, May2 1 June) Juvenile migration and rearing November- June (NovemberJune) Low - very small proportion of population will be present in Barker Slough, low impacts of diversion volumes on hydrodynamics High - monitoring has few observations of salmonids at this location, multiple studies regarding efficiency of positive barrier fish screens L{)w - No reports or studies available Low - screens are designed for delta smelt criteria, few salmon ids expected to be present at screen location Low- fish unlikely to be in area of screens during cleaning Juvenile migration and rearing November- June (November June) Juvenile migration and rearing November- June (NovemberJune) Probable Cha nge in Reduced survival Lethal: Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.1 1.1.6.2) Diversion up to 175 cfs See SWP/CVP Salvage operations Amount or Extent of CCV Steelhead T ake Reduced survival Minor: Increased mortality due to routing into the channels of the Lindsey Slough/ Barker Slough region Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.11.1.6.2) Diversion up to 175 cfs Typ e oflncidental T ake Minimal change in fitness Minor: Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. Up to 5 listed juvenile salmon ids (which may include CCV steelhead) per year- take is like ly to be lethal. Fitness Minimal change in fitness Sublethal to lethal: Injury or death due to entrainment i.nto dredge or impingement onto fish screens Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup :DCC gate operatiOns Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group : North Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group :North Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group : North Bay Aqueduct Populations from Northwestern California 999 Routing JuvenilesSacramento River -Delta Impingement/ capture during aquatic weed cleaning (location) Stressor and Life Stage Juvenile migration and rearing November- June (November June) Life Stage T iming (Work Window 1ntersection) Weight of Evidence Reduced fitness due to delay in migration or increased predation. Minimal change in fitness Sublethal to lethal: Injury or death due to impingement, capture by grappling hooks during weed removal Typ e oflncidental T ake Medium- annual monitoring reports indicate that no fish are entrained through the screens, however some fish are observed in front of the screens, and have been observed in historical monitoring. Reduced survival Fitness Probable Cha nge in Low- small numbers of fish are likely to be in the vicinity of the fish screens and intake Medium - Several reports from previous predator removal studies, literature on sampling methods. Low - No reports or studies available Low - infrequent sampling Study occurs over two to three years of the PA 's duration Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to routing into the channel of Rock Slough where predation is likely to be elevated Sublethal to lethal: Increased vulnerability to injury and mortality due to entanglementlentrapm ent in sampling gear Low - fish unlikely to be in area of screens during cleaning Magnitude of Effect Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group :North Bay Aqueduct Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Rock Slough water diversions Adult migration: July -May Juvenile migration and rearing November - June (November June) Capture in sampling gear JuvenilesSacramento River-Delta : Predator removal studies Adults and juveniles- Delta Juvenile migration and rearing November - June (January - June Populations from all Diversity Groups Populations from all Diversity Groups 1000 Amount or Extent of CCV Steelhead T ake Up to 5 listed juvenile salmon ids (which may include CCV steelhead) per year- take is like ly to be lethal. Ecological surrogate related to water diversion rate at Rock Slough Pumping Plant (See Section 2.1 1. 1.6.4) Diversion up to 350 cfs Over the two-year Predator Reduction Electrofishing Study: • Incidental take of up to 50 adult or j uvenile CCV steelhead cumulative, with no more than 5 mortalities. Over the two year Predator Fish Relocation Study: • Incidental take of up to 50 adult or juvenile CCV steelhead cumulative, with no more than 5 mortalities. (location) Stressor and Life Stage C02 Injections Juveniles Sacramento River - Delta (TFCF JuvenilesSacramento River -Delta Temporary change in water. flow/water quality (20 days Oct-May, 60 days June-Sept) Adults and juveniles migrating through the Delta. Stranding following end of transfer releases Lack of overbank flow to inundate rearing habitat Life Stage T iming (Work Window 1ntersection) Juvenile migration and rearing - Nov - June (Nov- June) Adult migration (July- May) and juvenile emigration (Nov June). (Nov- June). Juvenile rearing, holding, and migration upper Sacramento River - Year -round (July -November) December- May (year-round, but particularly in May and June) Weight of Evidence Low Medium- several studies show effectiveness of C02 in removal of predators and sensitivity of smaller fish to C02 exposure Magnitude of Effect Low Medium Medium - several studies conducted on Chinook salmon stranding in upper Sacramento River. Low- data on steel head migration and rearing in Suisun Marsh is low Low - changes in river flow related to transfers not expected to change river elevations substantially, Medium to High Amount or Extent of CCV Steelhead T ake Operations of C02 injector covered under SWP/CVP export operations for salvage and loss. Typ e oflncidental T ake Reduced fitness Sublethal to lethal: Small increase in morbidity and mortality due to C02 exposure during predator clean outs of secondary channel Fitness Probable Cha nge in Mi.nimal Ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Ecological surrogates related to water transfers (See Section 2. 11. 1.6.5) Transfers allowed only July through November Maximum volumes of water transfers restricted to permitted amounts. (See Section 2. 11.1.6.5) Implementation of ramping rates for reduction of releases from Keswick Reservoir to minimize stranding. (See Section 2.5.5.6 and Upper Sacramento/ Shasta Water Minimum Flows) Ecological surrogate based on the SMSCG operations: (See Section 2.11. 1.6.6) June - September -no more than 60 days of gate closure. Oct-May - no more than 20 days of gate closure. Boat locks are kept open except as needed for boat transit. Gate closures only on flood tides Reduced survival due to risk of stranding as flows recede Reduced growth rates; Reduced survival Sublethal to lethal: Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indi.rect stress effects, smaller size at time of emigration; Minor: During the annual 70 to 80 days of periodic operation, individual adult steelhead may be delayed in their spawning migration from a few hours to several days. Juveniles may be delayed on their downstream movements by closed gates for several hours while gates are closed on flood tides. Sublethal to lethal: Isolation and stranding in side channels and pools following reduction of reservoir releases. Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup CVP Improvements Populations from all Diversity Groups Marsh Roaring River Distribution System Food Subsidy Studies Populations from all Diversity Groups Transfers Populations from Northwestern California Diversity Group, Basalt and Porous Lava Diversity Group, Northern Sierra Nevada Diversity Group Conditions -.. Southern Sierra Nevada Diversity Group Juvenile rearing Confluence of Stanislaus to Mossdale 1001 Stressor and Life Stage (location) Reduction in rearing habitat complexity due to reduction in channel forming flows _ water temperatures warmer than life history stage requirements, primarily MarchMay Juvenile migration f outmigration Confluence of migration Confluence of Stanislaus to Mossdale Water temperatures warmer than life history stage requirements, primarily in May and June _ - June (year-round) Life Stage Timing (Work Window 1 December-May (flood control and reservoir releases; most likely winter and spring, potentially yearround) Magnitude of Effect Medium to High Medium Weight of Evidence Medium Medium Fitness Probable Change in Type oflncidental Take Sublethal to lethal: Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; survival; Reduced diversity in outrnigration timing Sublethal: Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; Reduced survival; Reduced diversity in outrnigration timing survival Reduced growth rates; Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Conditions Southern Sierra Nevada Diversity Group Conditions Southern Sierra Nevada Diversity Group Southern Sierra Nevada Diversity Group Conditions Southern Sierra Nevada Diversity Group Juvenile out- 1002 Amount or Extent of CCV Steelhead Take The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Joaquin River from the confluence of Stanislaus to Mossdale when this life stage of the listed species is present, with observed water temperatures within the tolerances described in Section 2.1 1.1.5. 1.1. implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). The ecological surrogate is water temperature. Extent of incidental take is the section of the San Joaquin River from the confluence of Stanislaus to Mossdale when this life stage of the listed species is present, with observed water temperatures within the tolerances described in Section 2.1 1.1.5.1 .1. (location) Stressor and Life Stage Confluence of Stanislaus to Mossdale Excessive fines in spawning gravel resulting from lack of overbank flow Egg incubation and emergence Goodwin Dam to Orange B lossom Bridge Water temperatures warmer than life history stage requirements Egg incubation and emergence Goodwin Dam to Orange Blossom Bridge Suboptimal flow Smolt em igration Stanislaus River Lack of overbank flow to inundate rea.ring habitat Juvenile rearing Life Stage T iming (Work Window 1ntersection) December-June (potentially yearround) December-June (year-round) January - June (March-June) Year round (year-round, particularly i.n May and June) Magnitude of Effect High High Medium to High Medium to High Weight of Evidence Medium Medium Medium Medium Reduced survival Reduced survival Sublethal to lethal: Egg mortality, Embryonic deformities Lethal: Egg mortality from lack of interstitial flow; egg mortality from smothering by nest-building activities of other CCV steelhead or fall-run; suppressed growth rates Typ e oflncidental T ake The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). The ecological surrogate is water temperature. Extent of incidental take is the section of the Stanislaus River from Goodwin Dam to OBB when this life stage of the listed species is present, with observed water temperatures within the tolerances described in Section 2.11 . 1.5. 1.1 . The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Excessive fines in spawning habitat may result i.n poor spawning bed conditions, as the proposed frequency of channel mobilizing flows of 5,000 cfs (which will typically occur during flood control releases) may not result in mobilizing flows at higher levels which perform greater geomorphic work. Amount or Extent of CCV Steelhead T ake Fitness Reduced survival; Reduced diversity Sublethal to lethal: Failure to escape river before temperatures rise at lower river reaches and in Delta; thermal stress; misdirection through Delta leading to increased residence time and higher risk of predation The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Probable Cha nge in Reduced growth rates; Reduced survival Sublethal to lethal: Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup East Divisiom Seasonal operations and Stepped Release Plan Southern Sierra Nevada Diversity Group . = Seasonal operations and Stepped Release Plan Southern Sierra Nevada Diversity Group . = Seasonal operations and Stepped Release Plan Southern Sierra Nevada Diversity Group Eastside llim.isl Seasonal operations and Stepped Release Plan 1003 Action Component ( by division) Diversity G roup Southern Sierra Nevada Diversity Group Reduction in rearing habitat complexity due to reduction in channel forming flows Goodwin Dam to Orange B lossom Bridge Life Stage T iming (Work Window 1ntersection) Year round (flood control and reservoir releases; most likely wi.nter and spring, potentially yearround) Year round, with temperature stress likely most acute July-September (June-September) DecemberFebruary (potentially yearround) January - June (year-round) Magnitude of Effect Medium to High Medium to High Medium Low Weight of Evidence Medium Medium to High Medium Medium Typ e oflncidental T ake The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Amount or Extent of CCV Steelhead Take Reduced growth rates; Reduced survival Sublethal to lethal: Reduced food supply; suppressed growth rates; starvation; loss to predation; poor energetics; indirect stress effects, smaller size at time of emigration; The ecological surrogate is water temperature. Extent of incidental take is the section of the Stanislaus River from Goodwin Dam to OBB when this life stage of the listed species is p resent, with observed water temperatures within the tolerances described in Section 2.11 . 1.5. 1.1 . Probable Cha nge in Fitness Reduced growth rates; Reduced survival Sublethal to lethal: Metabolic stress; starvation; loss to predation; indirect stress effects, poor growth; The ecological surrogate is flows. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Excessive fines in spawning habitat may result in poor spawning bed conditions, as the proposed frequency of channel mobilizing flows of 5,000 cfs (which will typically occur during flood control releases) may not result in mobilizing flows at higher levels which perform greater geomorphic work. size at time of emigration; Reduced reproductive success Sublethal: Reduced suitable spawning habitat; For individual: increased energy cost to attempt to "clean" excess fine material from spawning site The ecological surrogate is water temperature. Extent of incidental take is the section of the Stanislaus River from Goodwin Dam to OBB when this life stage of the listed species is p resent, with observed water temperatures withi.n the tolerances described in Section 2.11.1.5.1.1). Reduced diversity Sublethal: Missing triggers to elect anadromous life history; failure to escape river before temperatures rise at lower river reaches Biological Opinion for the Long-Term Operation of the CVP and SWP East Divisiom Seasonal operations and Stepped Release Plan . Southern Sierra Nevada Diversity Group . Stressor and Life Stage (location) Southern Sierra Nevada Diversity Group Juvenile rearing Goodwin Dam to Orange B lossom Bridge End of summer water temperatures warmer than life history stage requirements = Seasonal operations and Stepped Release Plan Juvenile rearing Goodwin Dam to Orange B lossom Bridge Excessive fines in spawning gravel resulting from lack of overbank flow Water temperatures warmer than life history stage requirements (March - June) Spawning Goodwin Dam to Orange B lossom Bridge = Seasonal operations and Stepped Release Plan Southern Sierra Nevada Diversity Group : = Seasonal operations and Stepped Release Plan 1004 (location) Stressor and Life Stage Smoltification and emigration Stanislaus River at mouth Temporary Low DO Barrier Juvenile steel head upstream ofOBB in summer Egg incubation, juvenile rearing Life Stage T iming (Work Window 1ntersection) Juvenile steelhead primarily present upstream of action area (year-round DO requirement, resulting in low DO most often in summer) Fall-Summer Magnitude of Effect Low Variable - Beneficial to Medium Weight of Evidence Medium Low Fitness Probable Cha nge in Variable Benefits to survival (export reductions) to Reduced Reduced survival due water temperaturerelated effects Minimal Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component ( by division) Diversity G roup Southern Sierra Nevada Diversity Group East Divisiom Alteration of Stanislaus River Dissolved Oxygen Requirement (7.0mg!L)31 miles upstream to Orange Blossom Bridge (OBB) Southern Sierra Nevada Diversity Group Delta Smelt Habitat Action 1005 Typ e oflncidental T ake and in Delta; thermal stress; Minor: Juvenile steelhead are primarily present upstream ofOBB, however, few may be migrating through during summer months, and may be exposed to reduced dissolved oxygen. This would be for a short period of time, and a difference of approximately 1-2 mg!L, which may result in delayed outmigration or reduced fitness levels. Sublethal to Lethal Amount or Extent of CCV Steelhead T ake The ecological surrogate is dissolved oxygen concentration. Extent of take is dissolved oxygen 7.0 or higher from Goodwin Dam to OBB. Take is exempted to the extent that it is covered under the effects of action components described above (export operations, Salinity Control Gate Operations, Seasonal Operations and other Core Water Operations) Magnitude of E ffect Medium Low Weight of Evidence Probable C hange in F it ness Reduced reproductive success Reduced reproductive success Biological Opinion for the Long-Term Operation of the CVP and SWP Life Stage Timing (Work W indow Intersection) April - Ju ly (May 15- July), May August (May 15 August) April -July (May 15- July), MayAugust (May 15August) Medium: Supported by multiple scientific and technical publications, however not specific to the region and species. Medium: Supported by multiple scientific and technical publications, however not speci fie to the region and species. 2.11.1.4 sDPS Green Sturgeon Incidental Take Table Water Temperature Spawning Adults, Eggs/Larval, (BSF gaugeHamilton City) Water Temperature Stressor a nd Life Stage (location) Table 2.11.1-4. sDPS Green Sturgeon Incidental Take Action Componen t (by division) (Shasta Summer Cold Water Pool Management) (Shasta Summer Cold Water Pool Management) Spawning Adults, Eggs/Larval, (BSF gauge Hamilton City) 1006 Type oflncidental Take Sublethal: PA temperature ranges from temps associated with abnormal development of eggs and larvae (sublethal) to decrease in egg survival (lethal) in lab studies. Sublethal: PA temperature ranges from temps associated with abnormal development of eggs and larvae (sublethal) to decrease in egg survival (lethal) in lab studies. Amount or Extent of sDP S Green Sturgeon Take Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 63.5°F in Tie r 1 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier I years the temperature target 0 will be 53.5°F at CCR, with acceptable exceedances of no more than 5 consecutive days. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4, 10.1.3.3 (Vpper Sacramento Performance Metrics). Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 63.5°F in Tier 2 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the Final PA Section 4.10.1.3.3 (Upper Sacramento Performance Metrics). Stressor and Life Stage (location) Water Temperature Spawning Adults, Eggs/Larval, (BSF gauge Hamilton City) Water Temperature Spawning Adults, Eggs/Larval, (BSF gaugeHamilton City) Life Stage Timing (Work W indow Intersection) April - Ju ly (May 15- July), MayAugust (May 15 August) April -Ju ly (May 15- July), MayAugust (May 15 August) Magnitude of Effect Low Medium, High Weight of Evidence Medium: Supported by multiple scientific and technical publications, however not speci fie to the region and species. Medium: Supported b y multip le scientific and technical publications, however not speci fie to the region and species. Probable C hange in Fitness Reduced reproductive success, Reduced survival probability Reduced reproductive success Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) (Shasta Summer Cold Water Pool Management) (Shasta Summer Cold Water Pool Management) 1007 Type oflncidental Take Sublethal: PA temperature ranges from temps associated with abnormal development of eggs and larvae (sublethal) to decrease in egg survival (lethal) in lab studies. Sublethal to lethal: PA temperature ranges from temps associated with abnormal development of eggs and larvae (sublethal) to decrease in egg su.rvival (lethal) in lab studies. Amount or Extent of sOPS Green Sturgeon Take Ecological surrogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 63.5°F, or 71.S<>F in Tier 3 years, according to the followi.ng criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4. 10.1.3.3 (Upper Sacramento Performance Metrics). Ecological sunogates related to Shasta Summer Cold Water Pool Management.: The extent of incidental take is the spawning habitat that exceeds 63.SOF, or 71.5<>F in Tier 4 years, according to the following criteria: • Shasta operations will remain consistent with the annual Shasta Cold Water Management Plan, where Reclamation will meet the temperature target with allowable tolerances. For Tier 4 years the temperature target 0 will be determined in real-rime with technical assistance from NMFS and USFWS. • Shasta operations will remain consistent with performance metrics described in the final PA Section 4.10.1.3.3 (Upper Sacramento Performance Metrics). Stressor and Life Stage (location) Flow Conditions, Loss of R ipariian Habitat and lnstream Cover, Loss of Natural River Morphology and Function Adults (Upper Sacramento River) Life Stage Timing (Work W indow Intersection) March - April (little overlap with DecemberFebruary operations) Year round presence (year round presence) Magnitude of Effect Low Medium Weight of Evidence Low: minimal information on flow and habitat requirements for juvenile green sturgeon Medium to High - effects of hydrodynamics well studied and modelled. Effects of hydrodynamics on green sturgeon migrations in South Delta less certain. Probable C hange in Fitness Reduced survival, reduced growth Uncertain: reduced growth rate and survival probability Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Minimum flows CVP/SWP South Delta Exports Altered hydrodynamics in South Delta/ routing Juveniles Sacramento River -Delta 1008 Type oflncidental Take Minor: Decreased flows may reduce access to channel margin and side channel rearing habitats Sublethal to lethal: Mortality or decreases in condition due to migratory delays in response to altered hydrodynamics in channels of the South Delta. Loss of appropriate migratory cues. Delays increase transit time and exposure to predators, poor water quality, and contaminants. Amount or Extent of sOPS Green Sturgeon Take The extent of incidental take is all adults stranded or delayed throughout the upper-middle section of the Sacramento River from the RBDD to Wilkins Slough that cannot migrate because of lower flows. • July I - March 31 o Releases reduced between sunset and sunrise o Keswick releases > 6,000 cfs, reductions in releases may not exceed 15% per night, and no more than 2.5% per hour. 0 Keswick releases 4,000 cfs to 5,999 cfs reductions in releases may not exceed 200 cfs per night, or I 00 cfs per hour. o Keswick releases between 3,250 cfs and 3,999 cfs; reductions in releases may not exceed I 00 cfs per night. o Variance allowed for flood control releases. In situations where Reclamation determines that exceeding these ramping rates would provide a benefit to water storage, a species of concern, or some other benefit, Reclamation may do so with NMFS concurrence. In situations of emergency, Reclamation may exceed these ramping rates, and within two weeks Reclamation will provide to NMFS an assessment of operations and their effects during the emergency reduction in flow. Ecological surrogates related to OMR management that make OMR flows more negative: OMR restrictions from -January I through June 30 (specific dates depend on species-specific OMR onset and offramp). OMR limited to no more negative than -5,000 cfs except during Storm Flex actions, which may make OMR flows substantially more negative, with some exceptions. OMR more negative than -5,000 July through December Action Component (by division) Stressor a nd Life Stage (location) L ife Stage Timing (Work W indow Intersection) Year round presence (Year round presence) Year round presence (May 21- January 30) Year round presence (May21- January 30) Medium - sustained high frequency exposure on small proportion of population Magnitude of Effect Weight of Evidence Medium Medium Low - There is little in formation regarding green sturgeon migratory movements through the DCC Low - There is little information regarding green sturgeon migratory movements through the DCC High Medium - studies have evaluated the effect of screening facilities, and predation on green sturgeon, but not specifically related to loss, as well as survival through at tbe facilities Prob able C ha nge in Fitness Uncertain, minimal negative change in fitness, potential exposure to lower quality rearing habitat Delayed migration, possible reduction of spawning success Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP CVP/SWP South Delta Exports Routing AdultsSacramento River - Delta Routing Juvenil.es Sacramento River -Delta Entrainment and loss at the South Delta export facilities DCC Gate operations - DCC Gate operations JuvenilesSacramento River- Delta 1009 Type oflncidental Take Sublethal to lethal: Mortality of fish occurs during the salvage process, resulting in the loss of fish entrained into the facilities, unknown vulnerability to predation or loss through louvers. Minor: When gates are open movement into and through the Mokelumne River system, increased transit distance to/from western Delta Minor: When gates are open, movement into the Mokelumne River system from the Sacramento River increased routing distance to the western Delta Amount or Extent of sOPS Green Sturgeon Take Cumulative annual salvage of74 sOPS green sturgeon. Ecological surrogates related to DCC gate operations: (See Section 2.11.1.6.1) Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5-days each May 21 - June 15 14 days of closed gates; remainder of days gates are open. Gates open June 16 - November 30 with few exceptions. Ecological surrogates related to DCC gate operations: (See Section 2.1 1.1.6. 1) Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5-days each May 21 -June 15 14 days of closed gates; remainder of days gates are open. Gates open June 16 -November 30 with few exceptions. Stressor a nd Life Stage (location) Transit times JuvenilesSacramento River -Delta Altered Hydrodynamics downstream of DCC location JuvenilesSacramento River -Delta Transit times Juveniles- South Delta Transit times L ife Stage Timing (Work Window Intersection) Year round presence (May 21 • January 30) Year round presence (May 21- January 30) Year round presence (May 21 - January 30) Year round presence (May 1November 30) Magnitude of Effect Medium Medium Medium - installation of barriers occurs every year from ApriVMay through the end of November and blocks off free passage through the three main channels of the South Delta Medium - installation of barriers occurs every year from April/May through the end of November and blocks off free Weight of Evidence Low - There is little information regarding green sturgeon migratory movements through the DCC - Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Low- There is little information regarding green sturgeon migratory movements through the DCC - Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Medium - several studies have indicated that the barriers increase transit time through the South Delta and increase exposure to ambient water quality conditions Medium - several studies have indicated that the barriers increase transit time through the South Delta and increase Prob able C ha nge in Fitness Reduced survival Reduced survival Uncertain, minimal negative change in fitness, potential exposure to lower quality rearing habitat Uncertain, minimal negative change in fitness, potential exposure to lower quality rearing habitat Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) DCC Gate operations DCC Gate operations South Delta Agricultural Barriers South Delta Agricultural Barriers Adults - South Delta 1010 Type oflncidental Take Minor: Increased migration times to western Delta when fish migrate through the delta interior Minor: When gates are closed, riverine reach of Sacramento extends farther downstream, less tidal influence, faster transit times. When gates are opened, more routing into Delta interior Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality due to increased exposure to poor water quality and high water temperatures Sublethal to lethal: Delayed migration and increased transit times with potential for increased mortality Amount or Extent of sOPS Green Sturgeon Take Ecological surrogates related to DCC gate operations: (See Section 2.1 1. 1.6. 1) Gates closed Dec-Jan except for opening for up to 2 water quality events in drought conditions of up to 5 days each May 2 1 -June 15 14 days of closed gates; remainder of days gates are open. Gates open June 16 - November 30 with few exceptions. Ecological surrogates related to DCC gate operations: (See Section 2.1 1. 1.6. 1) Gates closed Dee-Jan except for opening for up to 2 water quality events in drought conditions of up to 5-days each May 2 1 - June 15 14 days of closed gates; remainder of days gates are open. Gates open June 16 -November 30 with few exceptions. Ecological surrogates related to barrier operations: (See Section 2.11.1 .6.8) Installation of barriers no earlier than May I. May 16 to May3 1, tidal flaps on culverts tied open. At least I tidal flap tied open if water temperature < 22°C. No agricultural barriers op_erations a fter Nov 30. Sept 15 notch in barrier weirs or flashboard removal Sept 15. May 16 to May31 , tidal flaps on culverts tied open. Ecological surrogates related to barrier operations: (See Section 2.11.1 .6.8) Installation of barriers no earlier than May I. Stressor a nd Life Stage (location) Exposure to herbicides Adults and juvenilesSacramento River- Delta L ife Stage Timing (Work Window Intersection) Year round presence (June 28 - August 3 1 orwhen ambient water temperatures are greater than 25°C) Year round presence (May 21 - January 30) Magnitude of Effect exposure to ambient water quality conditions Weight of Evidence Medium • several ecotoxicological studies on the herbicides to be used. The majority of the studies are on surrogate fish species. passage through the three main channels of the South Delta Medium Low - sustained population effects on a small to medium proportion of the population present in the Delta Medium - numerous studies have evaluated the potential risk to salmon ids entering the Delta interior and becoming vulnerable to entrainment at the fish salvage facilities. Unknown applicability to green sturgeon Prob able C ha nge in Fitness Reduced survival Reduced survival Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) CCF aquatic weed control DCC Gate operations Increased entrainment and loss at the South Delta Exports facilities Juveniles Sacramento River -Delta 101 1 Type oflncidental Take due to incrcased exposure to poor water quality and high water temperatures Sublethal to lethal: adverse physiological effects (i.e., reduced growth and survival), due to exposure to harmful compounds in the water Sublethal to lethal: Increased mortality of entrained fish at the CVP and SWP fish salvage facilities Amount or Extent of sOPS G reen Sturgeon Take At least I tidal flap tied open if water temperature < 22°C. No agricultural barriers operations after Nov 30. Sept 15 notch in barrier weirs or flashboard removal Sept 15. Ecological surrogates related to the aquatic weed control program: (See Section 2. 11 . 1.6.7.4) Application of herbicides or mechanical weed harvesting between June 28 and August 3 1, inclusive, or when water temperatures exceed 25°C. Herbicide concentrations per label restrictions: Copper based :::;1ppm; endothal based :::; 3ppm; Peroxide based :::: I Oppm. Radial gates closed at least 24 hours prior to herbicide application, opened 12 to 24 hours after application of copper or endothal based herbicides; no hold time for perollide based compounds. CCF drawn down prior to application of herbicides, quickly flushed upon radial gate opening coupled with increased exports. See SWP/CVP Salvage Operations below Stressor and Life Stage (location) Life Stage Timing (Work W indow Intersection) Year round presence (year round presence) Year round presence (year round presence) Year round presence (year round presence) Year round presence (year round presence) Magnitude of Effect Low - screens are designed for delta smelt criteria, few green sturgeon expected to be present at screen location Low - very small proportion of population wi ll be present in Barker Slough, low impacts of diversion volumes on hydrodynamics Low - fish unlikely to be in area of screens during cleaning Low - fish unlikely to be in area of screens during cleaning Weight of Evidence Probable C hange in Fitness Uncertain, minimal change in fitness High - monitoring has few observations of green sturgeon at this location, multiple studies regarding efficiency of positive barrier fish screens Low - There is little information regarding green sturgeon migratory movements through the Delta - Green sturgeon juveniles rear within the waters of the Delta for up to 3 years. Minimal change in fitness Minimal change in fitness Low - No reports or studies available Low - No reports or studies available Uncertain, minimal change in fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) Entrainment and impingement onto fish screens JuvenilesSacramento River -Delta Entrainment during sediment cleaning JuvenilesSacramento River -Delta Routing JuvenilesSacramento River -Delta North Bay Aqueduct North Bay Aqueduct North Bay Aqueduct North Bay Aqueduct Impingement/ capture during aquatic weed cleaning JuvenilesSacramento River -Delta 1012 Type oflncidental Take Minor: Injury and Mortality caused by entrainment and/or impingement on the screens at the North Bay Aqueduct, Barker Slough Pumping Plant intake. Minor: Increased migration times to western Delta Sublethal to lethal: Injury or death due to entrainment into dredge or impingement onto fish screens Sublethal to lethal: Injury or death due to impingement, capture by grappling hooks during weed removal Amount or Extent of sOPS Green Sturgeon Take Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2. 11.1.6.2) Diversion of up to 175 cfs Diversion of up to 175 cfs Ecological surrogate related to water diversion rate at Barker Slough Pumping Plant: (See Section 2.1 1.1.6.2) Up to 2 juvenile sOPS green sturgeon per year take is likely to be lethal Up to 2 juvenile sOPS green sturgeon per year take is likely to be lethal Stressor a nd Life Stage (location) Routing JuvenilesSacramento River -Delta Capture in sampling gear Adults and JuvenilesSacramento River -Delta Temporary change in water flow/ water quality (20 days Oct-May, 60 days June-Sept) L ife Stage Timing (Work Window Intersection) Year round presence (year round presence) Year round presence (January- June) SMSCG ops from October through May coincides with the upstream migration of green sturgeon and late winter and spring downstream juvenile migration. During summer ops, juvenile and adult green sturgeon may be present. Low - small numbers of fish are likely to be in the vicinity of the fish screens and intake Magnitude of Effect Medium - Several reports from previous predator removal studies, literature on sampling methods. Low - No reports or studies available regarding green sturgeon presence in front of the fish screens Weight of Evidence Low Low - data on green sturgeon migration and rearing in Suisun Marsh is low Low- infrequent sampling over two to three years of study Prob able C ha nge in Fitness Minimal Reduced survival Minimal change in fitness Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) CCWD Rock Slough water diversions Predator removal studies Suisun Marsh Roaring River Distribution System Food Subsidy Studies Adults and juveniles may migrate through the area on their way to spawning grounds or as out-migrating juveniles. 1013 Type oflncidental Take Minor: Delayed migration and increased transit times Sublethal to lethal: Increased vulnerability to injury and predation due to entanglement/entrapm ent in sampling gear Minor: During the annual 70 to 80 days of periodic operation, individual adu It green sturgeon may be delayed in their spawning migration from a few hours to several days. Green sturgeon are less affected since they spawn in deep turbulent sections of the upper neaches of the Sacramento River. Amount or Extent of sOPS G r een Sturgeon Take Ecological surrogate related to water diversion rate at Rock Slough Pumping Plant: (See Section 2. 11.1.6.4) Diversion of up to 350 cfs Over the two-year study Predator Reduction Electrofishing Study: • Incidental take of up to 20 adult or juvenile green sturgeon cumulative, with no more than 3 mortalities. Over the two-year Predator Fish Relocation Study: • Incidental take of up to 20 adult o r juvenile green sturgeon cumulative, with no more than 3 mortalities. Ecological surrogate based on the SMSCG operations (See Section 2. 11.1.6.6) June - September - no more than 60 days of gate closure. Oct-May - no more than 20 days of gate closure. Gate closures only on flood tides Boat locks are kept open except as needed for boat transit. Stressor a nd Life Stage (location) Reductions in spring flows and associated temperatures, water quality, water depth, wetland function. Adults and juveniles-- San Joaquin River between the confluence with the Stanislaus River and Mossdale Egg incubation, juvenile rearing L ife Stage Timing (Work Window Intersection) Adults and juveniles present year round, responses to flow and temperaturerelated stressors most likely during winter and spring, when the PA has the most l imiting effect on flows. Fall-Summer Magnitude of Effect Low Variable - Beneficial to Medium Weight of Evidence Low - information available on green sturgeon use of the lower San Joaquin River between Mossdale and the confluence of the Stanislaus River Low Prob able C ha nge in Fitness Variable Benefits to survival (export reductions) to Reduced Reduced survival due water temperaturerelated effects Reduced survival or reduced growth Biological Opinion for the Long-Term Operation of the CVP and SWP Action Component (by division) 1111!1 Conditions Delta Smelt Habitat Action 1014 Type oflncidental Take Sublethal: Decreased survival or growth due to increased exposure to poor water quality and high water temperatures Sublethal to lethal Amount or Extent of sOPS G reen Sturgeon Take The ecological surrogate is flow, the section of the San Joaquin River from the confluence of the Stanislaus River to Mossdale during adult and juvenile migration. The extent of incidental take is that associated with implementation of the SRP minimum flows (as revised by the Stanislaus Watershed Team). Extent of i.ncidental take is all adults and juveniles exposed to the stressors throughout this section of the San Joaquin River from the confluence of the Stanislaus River to Mossdale due to inhibited migration from reduced flows. Take is exempted to the extent that it is covered under the effects of action components described above (export operations, Salinity Control Gate Operations, Seasonal Operations and other Core Water Operations) Biological Opinion for the Long-Term Operation of the CVP and SWP If the ecological surrogates from the above tables are not met and maintained, Reclamation and DWR will be considered to have exceeded their anticipated incidental take levels, thus requiring Reclamation and DWR to coordinate with NMFS within 24 hours, to discuss ways to reduce the amount of incidental take back to anticipated levels. 2.11.1.5 Operation ofCVP and SWP Dams and Reservoirs The following section provides further description of the adverse effects ofthe PA, resulting in varying forms of incidental take. For some PA components and ecological surrogates identified in the tables above, further discuss,i on is warranted, and is included below. 2.11.1.5.1 Water Temperatures and Flows in Clear Creek, and the American River, and Flows in the Sacramento and Stanislaus Rivers The following section provides a summary list of incidental take identified in the tables above due to project operations. Operations of the CVP and SWP reservoirs result in incidental take, including: • dewatering a portion of Sacramento River winter-run, CV spring-run, and CCV steelhead redds, resulting in egg and pre-emergent fry mortality; • poor development of sDPS green sturgeon embryos and larvae when water temperatures exceed suitable levels in the lower reaches of spawning habitat; • mortality ofjuvenile CCV steelhead resulting from high water temperatures (e.g., Clear Creek, American River, Stanislaus River, San Joaquin River); • limited availability and suitability of habitat for juvenile rearing and emigrating winterrun Chinook salmon, CV spring-run Chinook sahnon, and CCV steelhead; • creation of thermal barriers during adult salmonid migration that block or delay access to holding and spawning habitat, increasing risk of mortality due to exposure to suboptimal water temperatures, predation, and poaching; and • restricted window of successful outmigration and thus reduced diversity of outrnigration timing for CV spring-run and CCV steelhead populations on the Stanislaus River. 2.11.1.5.1.1 Incidental Take due to Water Temperatures in the Stanislaus and San Joaquin Rivers The ecological surrogate to define the extent of water temperature-related incidental take in the Stanislaus River is the reach from Goodwin Dam to Orange Blossom Bridge (OBB) during times when rearing juvenile CCV steelhead experience suboptimal water temperatures. The extent of water temperature-related incidental take in the San Joaquin River is the reach from the confluence of the Stanislaus River, downstream to Mossdale when juvenile CCV steelhead rear and emigrate. Incidental take in the form of harm to juvenile CCV steelhead is expected, as a result of PA operations. Suboptimal water temperatures are expected to result in reduced survival during the juvenile life stage. Incidental take is exceeded if the monthly average of measured average daily water temperature exceeds the 75th percentile of modeled monthly average temperature at OBB (for Stanislaus 1015 Biological Opinion for the Long-Term Operation of the CVP and SWP River) and at VER (for San Joaquin River, see Table 2.11.1-1), unless the measured 7DADM water temperatures are less than the EPA criteria for that particular life stage (see Table 2.5.7-11 in the Effects of the Action section). Incidental take is limited to monthly temperature exceedances no more than once every four years, for each month. Temperature exce·edances are likely to occur more frequently during critically dry years, particularly in May and June. Table 2.11.1-5. Table showing OBB and VER 751b Percentile Temperatures (in degrees F) Modeled CALSIM II Temperatures by Month. Stanislaus (OBB) Lower San Joaquin (VER) Jan Feb 50 50 52 55 Mar Apr 55 61 May Jun Jul Aug Sep Oct Nov 58 69 64 76 66 79 65 77 63 74 58 65 56 57 55 65 Dec 52 50 2.11.1.5.3 Downstream Sacramento River Temperatures due to Shasta Reservoir Operations The following section includes additional description of the ecological surrogates defined in the tables above, used to define the amount or extent of temperature related take due to Shasta Reservoir operations. The quantitative modeling of effects that are available are limited to the winter-run Chinook species, and they do not accurately describe the P A. Specific to Shasta temperature management, the foUowing limitations on the available quantitative models make a quantification of take difficult: • • CalSimll modeling, reviewed for the opinion, does not include all components of the PA as described in the June 14, 2019, final PA. HEC-SQ modeling (which relies on the CalSirnii modeling output) reviewed for the opinion does not include all elements of the PA described in the June 14, 2019, final PA. Specifically: o o o • Start and end date/time of temperature management is more variable under the final P A than what is described by modeling (timing and location of redds being less variable). Temperature operations and TCD shutter configuration for Tiers 2 and 3 of summer cold water pool management is not adequately reflected in the modeling due to model limitations. Operational (i.e., temperature) target in Tier 4 of summer cold water pool management is unclear; this affects interpretation of results and whether they describe effects of the PAin Tier 4. Temperature Dependent Mortality results (which are based on the CalSirnii and HEC-5Q modeling outputs) are limited to winter-run Chinook salmon and unavailable for CV spring-run Chinook salmon, CCV steelhead, or sDPS green sturgeon. Instead of a strict quantitative value of take, the ecological surrogate for harm related to Shasta water operations is based on a measure of available habitat for spawning and egg/alevin incubation. The extent of habitat available considered in this opinion is based on annual operations and the following criteria: 1016 Biological Opinion for the Long-Term Operation of the CVP and SWP • Adherence to an annual Shasta Cold Water Management Plan that defines operations within a temperature management tier. The annual Shasta Cold Water Management Plan is a surrogate for available habitat because the plan provides an estimate of achievable conditions in the river during the year. o • • If Reclamation makes a significant deviation from the plan in a way that would reduce the availability of habitat (i.e., higher temperatutres, or shorter duration of suitable temperatures) (i.e., more than 5 consecutive days above the allowable tolerances identified in the plan) or ifReclamation shifts to a warmer tier of Summer Cold Water Pool Management for reasons other than emergencies as identified in the PA, then the ecological surrogate will have been exceeded if NMFS also deems that Reclamation's operations were not consistent with the Shasta specific performance metrics identified in the final PA Section 4.1 0.1.3.3 (Upper Sacramento Performance Metrics). Consistency with operational performance metrics described in BA Section 4.1 0.1 .3.3 (Upper Sacramento Performance Metrics) and/or the Drought and Dry Year Actions. Reclamation proposes a number of performance metrics aimed at assessing whether the range of effects associated with the Summer Co]d Water Pool Management component of the PA are within the range of effects considered. The performance metrics also include provisions for chartering an independent panel consistent with "Chartering of Independent Panels" under the "Governance" section of the PA if recommended by the SRTTG after identifying that a metric is not met. The performance metrics offer an opportunity to collectively assess the effect of operations and whether those effects were adequately considered without triggering reinitiation of consultation. In the event of two consecutive years of poor winter-run Chinook salmon egg-to-fry survival, below 15 percent, measures must be taken to achieve egg-to-fry survival of at least 15 percent for the third year, including those measures outlined in the final PA Section 4.1 0.1.4.2 (Conservation Measures). If egg-to-fry survival appears to be on track to meet 15 percent or better during the third year, then Reclamation may proceed with operations pursuant to the P A. However, if egg-to-fry survival is projected to be less than 15 percent during the third year, then reinitiation of consultation would be likely. 2.11.1.6 Operations in the Delta The following section includes additional description of the ecological surrogates defined in the tables above, used to define the amount or extent of incidental take occurring in the Delta as a result of the PA. Incidental take in the form of death, injury, and harm to juvenile and adult Sacramento River winter-run and CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon is anticipated due to the implementation of the PA components, including the operations of the DCC gates, the BSPP and NBA, the CCWD Rock Slough diversion, the Suisun Marsh Salinity Control Gates, the south Delta agricultural barriers, and the CVP and SWP export facilities in the south Delta. In most cases, the quantification of incidental take will not be possible, and NMFS must use ecological surrogates as a proxy for take. 1017 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.11.1.6.1 DCC Gate Operations Because it is nearly impossible to detect unmarked (i.e., not carrying acoustic tag or other similar detectable device), listed fish entering the mouth of the DCC when the gates are open, an ecological surrogate will be used to establish criteria for incidental take caused by the operations of the DCC radial gates. While individual fish will be present in the action area surrounding the junction of the Sacramento River with the DCC, NMFS cannot, using tlhe best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the operations of the DCC. This is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing injured or dead fish lost to the Delta interior route. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurring. Observations of listed salmonids, both natural and hatchery, entering the DCC route when the gates are open are nearly impossible to achieve. Turbidity in the Sacramento River is frequently a limiting factor in visually observing listed salmonids or sDPS green sturgeon. The clarity of the river water limits visual detection to typically a few feet below the surface, leaving most of the water column obscured from the observer. Acoustic imaging is possible but not practicable, as the targets (acoustic images) frequently lack the details to determine species level determination, and can be obscured by debris and air bubbles in the water, both of which reflect the acoustic beam. Deployment and maintenance ofthe equipment requires considerable effort. However, as mentioned previously, the routing offish into the DCC only occurs wlhen the DCC gates are open. Therefore, the position of the gates is an informative indicator of the potential incidental take of listed fish due to routing into the DCC waterway and subsequently into the Delta interior where loss occurs. When the gates are open, fish can be routed into the interior Delta through the DCC and hydrodynamics downstream of the DCC junction are negatively impacted; when the gates are closed fish are not routed through the DCC into the Delta interior and hydrodynamics below the junction continue to function in a normal way. The incidental take of listed Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon, is associated with the operations the gate, and the operational schedule proposed for the gates will represent the ecological surrogate for take. The most appropriate threshold for incidental take is an ecological surrogate of habitat alteration caused by the opening ofthe radial gates of the DCC that allows Sacramento River water to flow into the DCC and thence into the Delta interior waterways of Snodgrass S1ough and the Mokelumne River system. This flow of water away from the Sacramento River and into the Delta interior facilitates the diversion oflisted fish into the waterways of the interior Delta where survival has been shown to be considerably less than the migratory routes associated with the Sacramento River. Ecological Surrogate: Incidental take is limited to the gate operations pursuant to the June 14, 2019, final P A. 1018 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.11.1.6.2 North Bay Aqueduct I Barker Slough Pumping Plant Since the ability to detect listed fish presence in Barker Slough prior to encountering the fish screen in front ofthe Barker Slough Pumping Plant (BSPP) is nearly impossible, an ecological surrogate will be used to establish criteria for incidental take of the operations of the North Bay Aqueduct (NBA)/ BSPP. While individual fish may be present in the waterway leading up to the fish Screen, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the operations of the NBA/BSPP. This is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annua[ variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing injured or dead fish lost within the waterways leading to the BSPP. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurring. The most appropriate threshold for incidental take is an ecological surrogate of habitat alteration caused by the diversion of water through the BSPP that allows Delta water to flow towards the facility, and potentially causing alterations in fish behavior, such as migratory delays, and increasing the vulnerability of such fish to increased predation through increased exposure time in Barker Slough. Therefore, the ecological surrogate for incidental take of listed winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, and sDPS green sturgeon will be the maximum diversion rate of 175 cfs. 2.11.1.6.3 Incidental Take for North Bay Aqueduct I Barker Slough Pumping Plant Sediment and Weed Control Operations: The removal of sediment that accumulates in front of the screens and within the pumping bays of the BSPP will pose a risk of entrainment. If dredging is used to remove sediment buildup on the aprons in front of the fish screens, there is the potential for incidental take as fish may be entrained into a hydraulic dredge while the sediment is removed. However, since the volume of sediment removed is relatively small compared to many dredging operations, the dredge effluent can be readily observed for the presence of listed unclipped salmonids or sDPS green sturgeon in the sediment containment ponds into which the dredge spoils are discharged. NMFS will set an incidental take limit of 5 unclipped listed salmonids (cumulative) per year, including the potential for winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, to be entrained each year through the use of hydraulic dredging methods in front of the fish screens. The incidental take limit for sDPS green sturgeon will be 2 fish per year. The removal of vegetation that accumulates on the BSPP fish screens has the potential to result in incidental take of listed salmonids and sDPS green sturgeon, as described in the effects section. NMFS will set an incidental take limit of 5 unclipped juvenile listed salmonids (cumulative) per year, including the potential for winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, to be entrapped each year through the use of the aquatic weed removal methods. The incidental take limit for sDPS green sturgeon will be 2 juvenile fish per year. 1019 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.11.1-6. Incidental Take for Sediment Removal and Aquatic Weed Control Action Cumulative Take of Juvenile Sahnonids (WR, SH, SR,) Individuals/year Cumulative Take of Juvenile SDPS Green Sturgeon/ year Sediment Removal 5 2 Weed Removal 5 2 2.11.1.6.4 Contra Costa Water District- Rock Slough Water Diversion Operations Since the ability to detect listed fish presence in Rock Slough prior to encountering the fish screen in front ofthe Rock Slough Head Works is nearly impossible, an ecological surrogate will be used to establish criteria for incidental take of the operations of the Contra Costa Water District (CCWD) Rock Slough Intake. While individual fish may be present in the waterway leading up to the fish screen, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the operations of the CCWD Rock Slough Intake. This is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing injured or dead fish lost within the waterways leading to the CCWD Rock Slough Intake. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with tlhe ability to monitor those surrogates to determine the extent of take that is occurring. The most appropriate threshold for incidental take, is an ecological surrogate of habitat alteration caused by the diversion of water through the Rock Slough Intake's fish screens that allows Delta water to flow towards the faci lity, and potentially causing alterations in fish behavior, such as migratory delays, and increasing the vulnerability of such fish to increased predation through increased exposure time in Rock Slough. The maximum rate of diversion currently permitted is 350 cfs, and is the upper limit of diversion that NMFS assessed in its effects analysis for the CCWD Rock Slough Intake operations in the PA for migratory delays:. Therefore, the ecological surrogate for incidental take of listed winter-run Chinook sahnon, CV spring-run Chinook salmon, CCV steelhead, and sDPS will be the maximum permitted diversion rate of 350 cfs. If diversion of water through the CCWD Rock Slough intake exceeds this rate, then incidental take of listed sahnonids and sDPS green sturgeon will have been exceeded. 2.11.1.6.5 Water Transfers NMFS anticipates that incidental take of listed salmonids and sDPS green sturgeon 11.1pstream of the Delta related to the transfer of water from upstream locations to downstream facilities will be minimal, but some individual fish may be lost due to stranding in side channels or pools as water flows decrease after the completion of the transfer and water recedes from inundated shoreline habitat. Stranding surveys are conducted after flow reductions to scout for locations of stranding, but due to the difficulty in quickly identifying stranding locations, and then quantifying the 1020 Biological Opinion for the Long-Term Operation of the CVP and SWP number of individuals in each stranding location, the results of the surveys are not exact as to the number of fish affected. Stranded fish are captured by seining the side channels and pools, data collected as to the number rescued, species, body length, and potential run classification, and returned to the river as quickly as possible. However, this is a crude assessment of the total number of fish stranded, as not all potential stranding locations are identified, and some fish may be lost to predation prior to being rescued by terrestrial or avian predators, and thus never enumerated. Since the ability to detect the location and spatial distribution of individual listed fish presence in Central Valley waterways is not always possible, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individ11.1als that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the transfer of upstream water to downstream facilities. This is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing injured or dead fish lost within the waterways of the Central Valley containing listed salmonids and sDPS green sturgeon. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurring. The most appropriate threshold for incidental take is an ecological surrogate of habitat alteration (riparian and shoreline habitat inundation) caused by the seasonal timing and volume of water released during the transfers. Incidental take of listed salmonids and sDPS green sturgeon related to the export of the transfer water under this component of the PA will be included under the incidental take limits for the operations of the south Delta export facilities of the SWP and CVP. Ecological Surrogates: Permitted season of water transfers- July 1- November 30. Permitted Volumes of transfers: Table 2.11.1-7. Permitted Volumes of Transfer Water Water year type Maximum Transfer Amount (TAF) Critical Up to 600 Dry (following Critical) Up to 600 Dry (following Dry) Up to 600 All other Years Up to 360 2.11.1.6.6 Suisun Marsh Salinity Control Gate Operations Since the ability to detect listed fish presence in Montezuma Slough prior to encountering the Suisun Marsh Salinity Control Gates (SMSCG) is nearly impossible during the proposed periods of closure, an ecological surrogate will be used to establish criteria for the incidental take of listed salmonids and sDPS green sturgeon during the operations of the SMSCG. While individual 1021 Biological Opinion for the Long-Term Operation of the CVP and SWP fish may be present in the waterway leading up to the gates during periods of closure, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the operations ofthe SMSCG. This is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing delayed, injured, or dead fish lost within the waterways leading to the SMSCG. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the P A that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurring. The most appropriate threshold for incidental take, is an ecological surrogate of habitat alteration caused by the closur,e of the radial gates during flood tides within the periods of operations of the SMSCG, and potentially causing alterations in fish behavior, such as migratory delays, and increasing the vulnerability of such fish to increased predation through increased exposure time in the channel of Montezuma Slough adjacent to the radial gates. Ecological Surrogates: • Incidental take is limited to the operation ofthe SMSCG pursuant to the June 14, 2019, final PA. 2.11.1.6.7 South Delta Export Operations 2.11.1.6.7.1 CVP and SWP Salvage and Loss Incidental Take NMFS and Reclamation held technical discussions in May 2019 and have developed a set ofloss thresholds for natural winter-run Chinook salmon and natural CCV steelhead as Delta performance metrics in the final PA provided on June 14, 2019. Performance targets/loss thresholds provide for review by an independent panel, but do not represent an incidental take limit. The calculations underlying these loss thresholds utilize the loss data from water years 2010 through 2018 for salmonids. The loss thresholds were calculated as 90 percent of the maximum annual historical loss (for salmonids) based on the period between 2010 and 2018. Length at date criteriia are used for run designation in the data for Chinook salmon loss. 2.11.1.6.7.1.1 Winter-run Chinook salmon The cumulative annual loss limit for natural winter-run is 1.6 percent of the JPE [the maximum loss for the period from 2010 to 2018 of 1.30 percent of the JPE, plus a 20 percent allowance to provide a buffer for an occasional higher loss year. 1022 Biological Opinion for the Long-Term Operation of the CVP and SWP Table 2.11.1-8. Natural winter-run loss for the period of December through March (Loss expressed both as percentage of 2 percent of JPE and as a percentage of the JPE). .---- WATIR YEAR WR-SIZED CHINOOK as % of 2% of WRJPI 2010 2011 2012 2013 2014 2015 2016 2017 2018 6.8 64.8 59.3 6 .7 1.3 4.3 Average Dec-]vfarch cumulative loss Mro..imum Dec-March crm111lative loss 90% ofmaximum historical loss 50% of901J,o ofmaximum hisro1ical loss 751J-o of90'?o ofmaximum historical loss 2.8 2.0 13.8 % of2'o ofWR JPE 18.0 64.8 58.3 29.2 43.7 ofVl R JPE 0.36 1.30 1.17 0.58 0.87 The annual incidental take limit for hatchery produced winter-run Chinook salmon from LSNFH released into the upper Sacramento River will be 0.8 percent per year of the estimated hatchery JPE (fish surviving to the Delta) for this specific release location, which is provided in the annual NMFS JPE letter. Similarly, the annual incidental take limit for hatchery produced winter-run Chinook salmon that are released into Battle Creek as part of the reintroduction program will be 0.8 percent per year of the estimated hatchery JPE for this specific release location, which is provided in the annual NMFS JPE letter. 2.11.1.6.7.1.2 CV Spring-run Chinook salmon The annual incidental take limit for natural yearling CV spring-run Chinook salmon emigrating from the tributaries to the Sacramento River is based on an ecological surrogate of hatchery releases of late fall-run Chinook salmon from the CNFH released into Battle Creek. The incidental take limit will be 1 percent of the number of fish released in each surrogate release group. Designation of run by LAD is not sufficiently accurate to determine the exact number of CV spring-run juveniles taken due to the high overlap in sizes with co-occurring fall-run Chinook salmon. However, the take of juvenile spring-run sized fish by LAD is monitored and reported out by the CVP and SWP fish facilities. The annual incidental take limit for natural young-ofyear CV spring-run Chinook salmon emigrating from the tributaries to the Sacramento River is based on an ecological surrogate ofOMR Management pursuant to the June 14,2019, final PA. Furthermore, in determining the extent of incidental take of spring-run Chinook salmon, 1023 Biological Opinion for the Long-Term Operation of the CVP and SWP Reclamation will consider the information in the technical memorandum developed annually by NMFS to ensure that take of Central Valley spring-run Chinook salmon originating from reintroduction to the San Joaquin River is deducted from the incidental take calculation to ensure that the reintroduction does not cause more than a de minimus impact on water supply, additional storage releases, and bypass flows associated with the operations of the CVP and SWP as described in 50 CFR 223.301(b)(5)(ii)(B). 2.11.1.6.7.1.3 CCV Steelhead The cumulative annual loss limit for natural CCV steelhead from December to March is 1,885 [the maximum loss of 1,571 for the period between 2010 and 2018, plus a 20 percent (314 CCV steelhead) allowance to provide a buffer for an occasional higher loss year]. The cumulative annual loss limit for natural CCV steelhead from April to June 15 is 2,070 [the maximum loss of 1,725 for the period of2010 to 2018, plus a 20 percent (345 CCV steelhead) allowance to provide a buffer for an occasional higher loss year]. Table 2.11.1-9. Natura.! steelhead loss for the period of December through March, and April through June 15. " 'a fer Year 2010 2011 2012 2013 20 14 2015 2016 2017 2018 average max 90% ofmax 75% of90% ofmax 50% of90% ofmax Comolatnre loss of anclipped steelhead Dec-l\lar Apr-Ju 15 1571.15 382 929.7 1419.13 740.56 371.81 1013.88 1197.2 58.82 201.69 77.94 61.73 245.92 46.7 113.69 60.12 1127.01 1724.64 663 1571 1414 1061 707 597 1725 1552 1164 776 2.11.1.6.7.1.4 sDPS Green Sturgeon There is no known population estimate for sDPS green sturgeon in order to determine an appropriate level of incidental take and recent salvage has been very low. The incidental take limit is based on the historical salvage considered in the NMFS 2009 opinion and sDPS green sturgeon (expanded) salvage is not expected to exceed 74 juveniles per year. 1024 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.11.1.6.7.2 Predator Reduction Electrofishing Study (PRES) Based on results of previous years of studies, the cumulative two-year incidental take limit for the Predator Reduction Electrofishing Study will be as follows: Table 2.11.1-10. Cumulative Incidental Take for PRES Species Cumulative Incidental Take (juveniles and adults) Lethal Take as Part of Cumulative Incidental Take (juveniles and adults) sDPS Green Sturgeon 20 3 CCV steelhead (unclipped) 50 5 CV spring-run Chinook salmon 50 5 Winter-run Chinook salmon 50 5 • • • No electrofishing will occur ifwater temperatures in CCF are greater than 21°C. Electrofishing may occur in CCF between January I stand June 30th as conditions allow. Incidental take for the PRES does not count towards the incidental take of the SWP and CVP fish salvage facilities. Incidental take will be in the form of harassment, capture, handling, and potentially mortality, occurring during processing. 2.11.1.6.7.3 Predatory Fish Relocation Study (PFRS) Based on previous y,ears of studies with the Predator Reduction Electrofishing Study, the cumulative two-year incidental take limit for the Predatory Fish Relocation Study (PFRS) will be as follows: Table 2.11.1-ll. Cumulative Incidental take for the PFRS Species Cumulative Incidental Take (juveniles and adults) Lethal Take as Part of Cumulative Incidental Take (juveniles and adults) sDPS Green Sturgeon 20 3 CCV steelhead (unclipped) 50 5 CV spring-run Chinook salmon 50 5 Winter-run Chinooik salmon 50 5 • Fish collection methods will be limited to the following types of fishing gear: o o o Beach seine Purse seine Fyke trap 1025 Biological Opinion for the Long-Term Operation of the CVP and SWP o o • • • Hoop trap Traw1 net with skids The PFRS will be conducted between January 1st and June 30th as conditions allow. No fish collection efforts will occur once water temperatures in CCF exceed 21 °C. Incidental take for the PFRS does not count towards the incidental take of the SWP and CVP fish salvage facilities or the PRES. Incidental take will be in the form of harassment, capture, trap, handling, and potentially mortality, occurring during processing. 2.11.1.6.7.4 Aquatic Weed Control and Algal Bloom Management in Clifton Court Forebay Since the ability to detect listed fish presence in CCF prior to application of the proposed herbicides or the use of the mechanical harvester is based on the observation of fish in salvage at the SDFPF, these observations do not allow any precise quantification of the number of fish actually present in CCF at the time of herbicide application or use of the mechanical harvester that may be incidentally taken as a result of the action. Therefore, an ecological surrogate will be used to establish criteria for the incidental take oflisted salmonids and sDPS green sturgeon during the implementation of the CCF aquatic weed and algal bloom management program. While individual fish may be present in the CCF during periods of herbicide applications or use of the mechanical harvester, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of actions related to the CCF aquatic weed and algal bloom management program. This. is due to the variability and uncertainty associated with the response of listed species to the effects of the proposed action, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing physiologically distressed, injured, or dead fish lost within the CCF during the aquatic weed and algal bloom management action. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurnng. The most appropriate threshold for incidental take, is an ecological surrogate of habitat alteration caused by the start date of the application of herbicides to CCF in conjunction with other operational parameters such as the concentration of herbicide in the water column, water temperature in CCF, and the operational status of the radial gates leading into CCF. Ecological surrogates: Herbicides utilized in the aquatic weed and algal bloom management, applied at concentrations per EPA registration label restrictions: • Aquathol K (or other dipotassium salts of endothal based herbicide) - 2-3 parts per million (ppm) target concentration. • Chelated copper based herbicides (copper-ethylenediamine complex and copper sulfate pentahydrate, copper carbonate compounds, or other copper-based herbicides); 1 ppm 1026 Biological Opinion for the Long-Term Operation of the CVP and SWP target concentration for aquatic weeds; 200 parts per billion (ppb) to 1 ppm for algal control. • peroxygen-based algaecides (e.g. PAK 27); 300 ppb to 10.2 ppm as hydrogen peroxide targeted concentration. • Incidental take will be exceeded if application of herbicides or use of the mechanical harvester is done earlier than June 28th or later than August 31 5 \ and the water temperatures are less than 25°C. The exception to this is ifNMFS concurs with DWR's request to apply herbicides or use the mechanical harvester outside the application window due to water temperatures being greater than 25°C. Incidental take will also be exceeded if the concentrations of herbicides applied to CCF exceed the described target concentrations. Furthermore, if the radial gates are not closed at least 24 hours prior to applications of herbicides with the concurrent draw down of CCF water elevation, and reopened less than 12 hours afterwards for endothal or copper based herbicides, then incidental take has been exceeded. The radial gates may be opened immediately after application of peroxide-based algaecides. Finally, incidental take will be exceeded if more than 50 percent of the surface area ofCCF is treated at any one time during herbicide applications. 2.11.1.6.8 South Delta Temporary Agricultural Barriers Since it is impossible to quantify with any precision the number of listed fish present in the channels of Old River, Middle River, and Grantline Canal during installation of the three temporary agricultural barriers and the barriers' subsequent operations, an ecological surrogate will be used to establish criteria for the incidental take of listed salmonids and sDPS green sturgeon during the periods when the temporary agricultural barriers are in place. While individual fish may be present in the waterway leading up to the barriers during periods of installation and closure, NMFS cannot, using the best available information, precisely quantify and track the amount or number of individuals that are expected to be incidentally taken (injured, harmed, killed, etc.) per species as a result of the proposed action component related to the operations of the barriers. This is due to the variability and uncertainty associated with the response of listed species to the effects of the PA, the varying population size of each species, annual variations in the timing of spawning and migration, individual habitat use within the action area, and difficulty in observing delayed, injured, or dead fish lost within the waterways adjacent to the three temporary agricultural barriers. However, it is possible to estimate the extent of incidental take by designating as ecological surrogates, those elements of the PA that are expected to result in incidental take, that are more predictable and/or measurable, with the ability to monitor those surrogates to determine the extent of take that is occurring. The most appropriate threshold for incidental take is an ecological surrogate of habitat alteration caused by the closur,e of the channels by the installation of the barriers and extending through the periods of operations of the barriers. This alteration in the functioning of the channel habitat may potentially cause changes in fish behavior, such as migratory delays, and increases the vulnerability of such fish to predation through increased exposure time to predators residing in waters adjacent to the temporary agricultural barriers. NMFS has described which aspects of the south Delta temporary agricultural barriers will cause incidental take to occur. 1027 Biological Opinion for the Long-Term Operation of the CVP and SWP Incidental take will be exceeded if: • • • • The operation of the barriers occurs earlier than May 1st, or if the barriers are not removed by N ovember 30th of each year. Culverts are installed and operated in such a way as to preclude passage of fish from May 16th to May 301h if DWR has not clearly demonstrated a water elevation situation that would requir,e their closure. If water temperatures are below 22°C, and all of the tidal flap gates are operational at each barrier location without at least one tidal flap at each barrier being tied open to allow fish passage. By September 151h of each year, a notch has not been cut in the weir of Old River at Tracy and Middle River barriers, and the appropriate number of flashboards removed at Grant Line Canal barrier to facilitate upstream movement of Chinook salmon. 2.11.1.7 Southern Resident Killer Whales NMFS anticipates the P A will result in incidental take in the form of harm to SRKW individuals through impairment of foraging behavior through reduced productivity for all Central Valley Chinook salmon populations, including fall-run Chinook salmon, resulting from the adverse effects for Chinook salmon described in Tables 2.11.1- J through 2.1 1.1-4 above and summarized in Section 2.5.8 Southern Resident Killer Whale Effects Analysis. NMFS anticipates that this reduction in the productivity and abundance of Central Valley Chinook salmon will result in some level ofharm to SRKWs, specifically members ofK and L pod (currently 52 individuals), by reducing prey availability and causing impairment in foraging behavior, leading animals to forage for longer periods, travel to alternate locations, and experience nutritional stress and related health effects. These adverse effects increase the probability that SRKW individuals would be subject to reduced survival and reproductive success over time. Currently, we cannot readily observe or quantify impacts to foraging behavior or any changes to health of individual killer whales in the population from the general level of prey reduction that has been described in the proposed action because we do not have the data or metrics needed to monitor and establish relationships between the effects of the PA and individual SRKW health. As a result, we will rely on surrogates ofthe amount or extent of incidental take ofSRKWs as a result of the P A in the form of the extent of effects to Chinook salmon populations relevant to the effects analysis described in Sections 2.5.8 Southern Resident Killer Whale Effects Analysis and 2.7.1 0 Integration and Synthesis for Southern Resident Killer Whales. Specifically, we will rely upon ecological surrogates that are used to describe and monitor the take ofESA-listed salmonids resulting from adverse effects of the proposed action. In Section 2.11 .1.5 Operation ofCVP and SWP Dams and Reservoirs, measures of ecological surrogates are used for describing anticipated temperature-and-flow related effects that diminish the productivity of all Central Valley Chinook populations. Exceedance of the extent of effects as measured by any of these ecological surrogates for effects to Chinook salmon would be viewed as an exceedance ofthe anticipated harm to SRK.Ws. In Section 2.11.1.6 Operations in the Delta, measures of ecological surrogates are used for describing anticipated effects that diminish productivity of all Central Valley Chinook salmon from a number of activities, including the operations of the DCC gates, the BSPP and NBA, the CCWD Rock Slough diversion, the Suisun Marsh Salinity Control Gates, and the south Delta agricultural barriers. 1028 Biological Opinion for the Long-Term Operation of the CVP and SWP Exceedance of the extent of effects as measured by any of these ecological surrogates for effects to Central Valley Chinook salmon would be viewed as an exceedance of the anticipated harm to SRKWs. In Section 2.11.1.6.7 South Delta Export Operations, loss thresholds for natural winterrun Chinook salmon and natural CCV steelhead used as surrogates for incidental take of these ESA-listed species resulting from operation of CVP and SWP export facilities in the south Delta are described. In addition, an ecological surrogate loss threshold for CV spring-run (based on late fall-run Chinook salmon from the CNFH released into Battle Creek) is described. In the absence of a loss threshold specifically for non-listed Central Valley fall-run Chinook salmon populations, or for all Central Valley Chinook salmon, exceedance of the extent of effects as measured by any of the loss threshold surrogates for effects to any Central Valley Chinook salmon would be viewed as an exceedance of the anticipated harm to SRKWs. In addition, because the loss threshold based on the performance measures developed for natural CCV steelhead is expected to benefit Central Valley fall-run Chinook salmon populations by minimizing export impacts on Central Valley fall-run Chinook salmon during their migration through the south Delta, exceedance of this threshold would also be viewed as an exceedance of the anticipated harm to SRKWs. 2.11.2 Effect of the Take In the Opinion, NMFS determined that the amount or extent of anticipated take, coupled with other effects of the PA, is not likely to result in jeopardy to the species or destruction or adverse modification of critical habitat when the reasonable and prudent alternative is implemented. In the accompanying formal biological opinion, NMFS has determined that the anticipated level of incidental take associated with the PA, as modified by the RPA, is not likely to jeopardize the continued existence of winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, sDPS green sturgeon, and SRKWs. 2.11.3 Reasonable and Prudent Measures "Reasonable and prudent measures" are nondiscretionary measures that are necessary or appropriate to minimize the impact of the amount or extent of incidental take (50 CFR 402.02). NMFS believes the following reasonable and prudent measures are necessary and appropriate to minimize take of winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, sDPS green sturgeon and SRKWs .. 1. Reclamation and DWR shall minimize incidental take of listed species during operations of the Shasta Division. 2. Reclamation and DWR shall minimize incidental take of listed species during operations in Clear Creek. 3. Reclamation and DWR shall minimize incidental take of listed species during operations of the American Division. 4. Reclamation and DWR shall minimize incidental take of listed species during operations of the Eastside Division. 1029 Biological Opinion for the Long-Term Operation of the CVP and SWP 5. Reclamation and DWR shall minimjze incidental take of listed species during operations of the Bay-Delta Division. 6. Reclamation and DWR shall minimjze incidental take of Southern Resident killer whales during operations. 7. Reclamation and DWR shall monitor the amount and extent of incidental take described in Section 2.1 as necessary to implement this Opinion. 8. Reclamation shall minimiz·e the incidental take of listed species associated by implementation of the proposed action by supporting the implementation of actions through the Collaborative Planning action component. 9. Sacramento River Settlement Contractor measures. 10. Reclamation and DWR shall coordinate with together and with NMFS to minimjze incidental take of listed species related to coordinated operations. 2.11.4 Terms and Conditions The terms and conditions described below are non-discretionary, and Reclamation and DWR must comply with them in order to implement the RPMs (50 CFR 402.14). Reclamation and DWR have a continuing duty to monitor the impacts of incidental take and must report the progress of the action and its impact on the species as specified in this ITS (50 CFR 402.14). If the entity to whom a term and condition is directed does not comply with the following terms and conditions, protective coverage for the proposed action would likely lapse. Reclamation and DWR must comply or ensure compliance by their contractor(s) with the following terms and conditions, which implement the reasonable and prudent measures described above. NMFS requests that by June 17, 2020, Reclamation provide written notification to NMFS and the State Water Resources Control Board (SWRCB) of any contract that it believes creates a nondiscretionary obligation to deliver water, including the basis for this determination and the quantity of nondiscretionary water delivery required by the contract. For the purposes of this Opinion, NMFS "coordination" with Reclamation and DWR does not mean NMFS concurrence with an action is required under the specified coordination, but rather that NMFS is afforded the opportunity to provide scientific or technical recommendations for Reclamation's consideration on issues for which NMFS has scientific or technical expertise, such as biological issues. Such recommendations would not require changes to Reclamation's Proposed Action, or water and power resources operations and facilities operations pursuant to the Proposed Action. 11. RPM 1: Reclamation and DWR shall minimize incidental take oflisted species during operations of the Shasta Division. 1030 Biological Opinion for the Long-Term Operation of the CVP and SWP a. To minimize the adverse effects of flow fluctuations on listed anadromous fish species spawning, incubation, and juvenile rearing, Reclamation shall implement the following ramping rates. During periods outside of flood control operations and to the extent controllable during flood control operations, Reclamation shaH ramp down releases in the Sacramento River below Keswick Dam from July 1 through March 31 as follows, except as discussed with the SRTTG, including providing an opportunity for technical assistance by NMFS, and for the purposes of providing fish pulse flows that deviate from these levels, or conserving the cold water pool: i. Releases must be reduced between sunset and sunrise; ii. When Keswick releases are 6,000 cfs or greater, decreases may not exceed 15 percent per night. Decreases also may not exceed 2.5 percent in one hour; iii. Foe Keswick releases between 4,000 and 5,999 cfs, decreases may not exceed 200 cfs per night. Decreases also may not exceed 100 cfs per hour; 1v. For Keswick releases between 3,250 and 3,999 cfs, decreases may not exceed 100 cfs per night. v. Variances to these release requirements are allowed under flood control operations. b. Reclamation and DWR shall coordinate with NMFS about forecasted Shasta operations starting with the February forecast, through the April forecast. c. In coordination with NMFS and the SRTTG, Reclamation shall consider technical assistance from NMFS regarding the development of annual temperature management plans, regardless of Shasta storage or tiered temperature management stratum. Reclamation shall submit the final temperature management plan to NMFS by May 20 of each year, as reporting under the opinion. NMFS does not expect Reclamation to seek NMFS concurrence on the plan. In February of each year Reclamation shall create and post a projection of water operations, as described in Appendix C of the BA. In addition, this projection shall include the following: 1. 11. An assessment ofthe performance to date of Shasta Cold Water Pool Management based on expectations outlined in the final PA, Section 4.10.1.3.3 (Upper Sacramento Performance Metrics), which includes: (a) Performance trends to date, frequency of Tiers, range ofTDM within Tiers, and range of egg to fry survival withiin Tiers, (b) Whether convening an independent panel is appropriate based on performance trends to date, and (c) Response to previous independent panel reviews and/or identification of how comments from previous independent panel(s) are being addressed. A forecast oflikely Shasta Cold Water Pool Management Tier and whether Reclamation is proposing to implement the "Anderson approach" to target critical periods in egg and alevin development. d. Reclamation shall implement the Spring Pulse Flow as described in its February 5, 2019, BA. The Spring Pulse Flow, as modified in subsequent PAs (April30, 2019, revised PA, and June 14, 2019, final PA) was not analyzed, discussed, nor agreed upon during 1031 Biological Opinion for the Long-Term Operation of the CVP and SWP multiple consultation meetings between Reclamation and NMFS, nor flagged during Reclamation's multiple review ofNMFS' Shasta Division effects analysis. e. Consistent with the final PA, Reclamation shall develop a stratification model for Shasta Reservoir and evaluate this model for implemention as part of the development of annual temperature management plans. The initial stratification model shall be available for pilot application and evaluation no later than January 1, 2022. At the end of the three-year period starting once the stratification model is available, Reclamation and NMFS shall evaluate and confer on the model's accuracy and utility as a forecasting tool, and Reclamation will to decide whether implementation is appropriate. f. By December 31 of each year, Reclamation shall provide a hindcast of temperaturedependent mortality for winter-run Chinook salmon based on realized temperature management. g. Reclamation shall work with NMFS, USFWS and CDFW to complete a Battle Creek Acceleration Plan (Plan) by December 31, 2020. The plan shan address the Battle Creek Salmon and Steelhead Restoration Program and the Battle Creek Winter-run Chinook Salmon Reintroduction Plan. In the Plan, Reclamation will express a commitment to the Battle Creek Winter-run Chinook Salmon Reintroduction plan. The Plan also shall identify and express Reclamation support implementation of Battle Creek restoration, winter-run Chinook salmon reintroduction and for science actions such as marking and tagging/survival studies. The plan should, at a minimum: 1. Identify a suite of"no-regrets" actions that may be carried out while the disposition of the PG&E hydroelectric project is in process. For the purpose of this opinion, "no regrets" actions are defined as those actions that can move forward on Battle Creek that are not directly tied to future decisions related to the disposition PG&E's hydroelectric license on Battle Creek. n. Support the designing and construction a fish trapping and sorting facility at Coleman National Fish Hatchery iii. Identifiy ongoing monitoring and research needs -- The USFWS partners with the California Department ofFish and Wildlife for much of the monitoring for winter-run Chinook salmon on the Sacramento River. Service efforts include coded-wire tagging and marking Livingston Stone NFH-produced winter-run Chinook salmon, acoustic tagging a subset of those fish, rotary screw trapping at Red Bluff Diversion Dam, and carcass surveys on the mainstem Sacramento River. Reclamation covers the costs for all of the Service efforts, mostly out of the operational funding agreement for Coleman and Livingston Stone NFHs and the Reclamation monitoring agreement with the USFWS Red BluffFish and Wildlife Office. Both of these are long-term agreements with a history of renewal. 1v. Identify Livingston Stone NFH facility improvements necessary to support the Battle Creek Winter-run Chinook Salmon Reintroductin Plan. h. In order to minimize project related impacts to fish growth and survival on the lower Sacramento River, Reclamation shall complete the Fremont and Lisbon Weir Fish Passage Project by 2022 and will report out to NMFS on the progress of meeting project milestones. The anticipated schedule is described below: 1032 Biological Opinion for the Long-Term Operation of the CVP and SWP 1. Implement the Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project , as follows: (a) Summer 2020- Preconstruction vegetation clearing and site preparation begins (b) Summer 2021 - Project construction 11. May 2020- Begin construction on the Agricultural Road Crossing 4 project iii. May 2022 -Begin construction on the Lisbon Weir Fish Passage project 12. RPM 2: Reclamation and DWR shall minimize incidental take of listed species during operations in Clear Creek. a) To minimize incidental take under 60°F daily average water temperature criteria for adult CV spring-run Chinook salmon holding, and 56°F daily average water temperature criteria for CV spring-run Chinook salmon egg and embryo incubation, Reclamation shall, consistent with the proposed action and in consideration of Shasta Cold Pool Management: 1. Continue maintenance of temperature control curtains (Oak Bottom and Spring Creek) in Whiskeytown Reservoir. 11. Through coordination with the Clear Creek Technical Team, consider real-time species information when making decisions regarding operational adjustments. This does not mean that the information will require operations to differ from what is contained in the final PA. b) Reclamation shall expand the Watercourse Engineering model water temperature in Clear Creek to capture the inter-connections of the Trinity-Sacramento river systems, including Whiskeytown Reservoir, to enable better temperature forecasting and planning in Clear Creek. Modeling inputs shall include water temperature impacts from hydropower peaking. c) Reclamation shall continue implementation of a weir annually to separate CV spring-run Chinook salmon and fall-run Chinook salmon during spawning to minimize the effects of redd superimposition and hybridization. d) To minimize the adverse effects of flow fluctuations associated with CVP-controlled water operations on all life stages of listed anadromous fish species in Clear Creek, Reclamation shall: 1. Coordinate flow release schedules with NMFS, USFWS, and CDFW via WOMT or B2IT or a comparable inter-agency fish monitoring group. n. Implement a down ramping rate of no more than 25 cfs per hour for controlled flow decreases from Whiskeytown Reservoir. This ramping rate is operationally feasible, and would reduce stranding risks to juvenile salmonids during controlled flow decreases. To further minimize stranding risk, Reclamation shall time down-ramping so the maximum rate of flow decrease occurs primarily during dark hours through the majority of the creek. 1033 Biological Opinion for the Long-Term Operation of the CVP and SWP 13. RPM 3: Reclamation and DWR shall minimize incidental take of listed species during operations of the American Division. a. Reclamation shall, in coordination with NMFS, USFWS, CDFW, and American River Group (ARG), develop and implement a plan to improve temperatures for all salmonids in the American River, using information from the value engineering report completed under RPA Action 11.3 of the NMFS 2009 Opinion and other relevant information. A draft plan shall be submitted to ARG for review by August 1, 2023. A final plan, incorporating input from ARG and including recommendation for implementation, shall be submitted to NMFS by August 1, 2024. Seasonal operational decisions that affect water temperature and river flows shall be coordinated through the ARG. b. To minimize the adverse effects of flow fluctuations on listed anadromous fish species spawning, incubation, and juvenile rearing, Reclamation shall implement the following ramping rates. During periods outside of flood control operations and to the extent controllable during flood control operations, Reclamation shal[ ramp down releases in the American River below Nimbus Dam as follows, except as discussed with the ARG, including providing an opportunity for technical assistance by NMFS, and for the purposes o f prov1·d mg · fi1sh pu1se flows th at d ev1ate · from th ese leves: 1 Lower American River Daily Rate ofChange (cfiJ) Amo1m.t ofdecrease MJrdmmn change m 24 bJ:s (cfs) per step (elf) 20,000 to 16,000 4,000 1,350 16,000 to 13,000 3,000 1,000 13,000 to 11,000 2,000 700 11,000 to 9,500 1,500 500 9,500 to 8,300 1,200 400 8,300 to 7,300 1,000 350 7,300 to 6,400 900 300 6,400 to 5,650 750 250 5,650 to 5,000 650 250 <5,000 500 100 14. RPM 4: Reclamation and DWR shall minimize incidental take of listed species during operations of the Eastside Division. a. The shift in compliance location from Ripon to Orange Blossom Bridge from June I to September 30 shall not go into effect until NMFS confirms that Reclamation has satisfied both of the following conditions: i. Provide confirmation that a dissolved oxygen gage has been installed and is consistently providing accurate dissolved oxygen data at Orange Blossom Bridge. b. Reclamation shall complete the Final Temperature Management Study by December 31, 2024. 1034 Biological Opinion for the Long-Term Operation of the CVP and SWP c. Reclamation shall provide to NMFS an annual water temperature data set and may provide summary statistics at NMFS request. d. Reclamation shall provide to NMFS an annual report of incidental take associated with monthly temperatures, and provide an assessment of temperature conditions over the year including monthly average data at Orange Blossom. This information could be included in the Stanislaus Watershed Team annual report. e. To minimize the adverse effects of flow fluctuations on listed anadromous fish species spawning, egg incubation, and fry and juvenile rearing, Reclamation shall (during periods outside of flood control operations and to the extent controllable during flood control operations) ramp releases in the Stanislaus River below Goodwin Dam as follows Existing Release Level (cfs) Rate oflncrease (cfs) Rate of Decrease (cfs) at or above 4,500 500 per 4 hours 500 per 4 hours 2,000 to 4,499 500 per 2 hours 500 per 4 hours 500 to 1,999 250 per 2 hours 200 per 4 hours 300 to 499 100 per 2 hours 100 per 4 hours 15. RPM 5: Reclamation and DWR shall minimize incidental take of listed species during operations of the Bay-Delta Division. a. Consistent with the additional Delta measures on habitat restoration in the final PA (Section 4.1 0.5.12.3), Reclamation shall develop and implement a science-based nonnative predator management experiment to reduce the effects of mortality to emigrating juvenile salmonids related to seasonal operations and low flow conditions at key times and locations or "hot spots" in the Bay-Delta. b. Reclamation and DWR shall monitor the salvage of winter-run Chinook salmon, CV spring-run Chinook salmon, fall-run Chinook sa1mon, late fall-run Chinook salmon, sDPS green sturgeon, and CCV steelhead, associated with the operation of the CVP's Jones and SWP's Harvey Banks pumping facilitiies. 1. Reclamation and DWR shall monitor and calculate salvage and loss for winter-run Chinook salmon, CV spring-run Chinook salmon, CV fall-run Chinook salmon, CV late fall-run Chinook salmon, CCV steelhead, and salvage of sDPS green sturgeon at the TFCF and SDFPF. (a) Reclamation and DWR shall prepare and submit to NMFS daily reports from October 1 through June 30 of each water year (or provide data online) regarding the observations of both salmonids and sDPS green sturgeon in the fish salvage facilities. Daily salvage sheets and the operational information needed to calculate salvage and loss shall be provided to NMFS (to a list of recipients updated each water year) or made available online. If, during the period from July 1 to September 30, salmonids and/or sDPS green sturgeon are observed in salvage, Reclamation and/or DWR shall notify NMFS through electronic mail and include 1035 Biological Opinion for the Long-Term Operation of the CVP and SWP the daily salvage sheets and operational information, or direct NMFS to where this information is available online. (b) During the October through June period of each water year, DWR and Reclamation shall prepare and submit to NMFS, DAT and DOSS weekly reports summarizing salvage and loss over the previous week and for the water year to date (or provide data online). (c) No later than December 31, Reclamation and DWR shall submit to NMFS an annual report summarizing salvage and loss over the previous water year (October 1-September 30). n. Reclamation and DWR shall monitor salvage and loss for winter-run Chinook salmon, CV spring-run Chinook salmon, CV fall-run Chinook salmon, CV late fallrun Chinook salmon, and CCV steelhead, and salvage for sDPS of green sturgeon at TFCF and SDFPF. If the estimated rate of salvage or loss approaches the incidental take limit for any of the listed anadromous fish species, Reclamation and DWR shall immediately convene the WOMT to explore additional measures which can be implemented to reduce the rate of take and avoid exceedance of the incidental take limit. iii. Reclamation and DWR shall undertake tissue sampling programs from wild salmonids, and CWT samples from adipose fin-clipped juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead and CV late-fall run Chinook salmon at the TFCF and SDFPF, for genetic analysis or tag removal/reading pursuant to appropriate sampling protocols and statistical power analyses. (a) Reclamaton and DWR shall submit incidental take reports from TFCF and SDFPF by December 31 of each year, to include the genetic results of the tissue samples. (b) Reclamation and DWR shall develop and submit for review and concurrence by NMFS a plan for tissue and whole fish or head processing and storage by December 31,2019. c. Reclamation and DWR shall minimize incidental take through best management practices at the fish facilities: 1. Reclamation and DWR shall develop and submit to NMFS for review within two years of issuance of the biological opinion (July 1, 2021) a protocol that outlines pumping restrictions and loss estimated during salvage disruptions at the TFCF and SDFPF. n. Reclamation and DWR shall standardize salvage, fish handling, and reporting protocols and provide opportunity for technical assistance by NMFS, except when required for structural differences between the fish salvage facilities. Standardized protocols for the SDFPF and TFCF shall be in place before the implementation of the PA. The protocols should also specify training procedures, QNQC of data, and verification of records lby third party inspection. 1036 Biological Opinion for the Long-Term Operation of the CVP and SWP iii. Reclamation shall develop, fund, and implement a plan for long-term improvements to the primary louvers at the TFCF, including methods for cleaning the louvers that do not reduce facility efficiency. A draft plan shall be submitted to NMFS by December 31,2020. Contracting shall be completed by December 31,2030. In the interim period, Reclamation shall develop a loss calculation that incorporates the decrease in louver efficiency during the period of louver cleaning to adjust the estimate of loss during the cleaning process when louvers are removed. This shall be completed within one year of the issuance of this Opinion (July 1, 2020). 1v. In coordination with NMFS, FWS, CDFW, and the relevant technical teams, Reclamation and DWR shall develop and issue by December 31, 2019, a "Delta operations handbook" that provides clarification and detail on the information sources and calculations used to implement the various triggers for Delta operations. d. Reclamation shall incorporate the following terms and conditions related to DCC Gate Operations: 1. In order to streamline the decision process for implementing DCC gate closures based on the Knights Landing Catch Index and the Sacramento Catch indices, the catch indices shall be clarified to mean that greater than 3 fish per day is 3.00 fish and greater, and less than 3 fish is less than 3.00 fish per day. The greater than 5 fish perday is 5.00 fish and greater, and the less than 5 fish per day is less than 5.00 fish. e. Reclamation and DWR shall incorporate the following terms and conditions related to NBA/BSPP operations: 1. Cleaning of sediment from in front of the fish screens shall occur during the summer in-water work window of July 1 through October 31 or if ambient water temperature is greater than 77°F. n. Observers shall be present during sediment cleaning to look for entrained fish in the dredge material discharge as it is pumped into the dredge spoils pit. Any observed fish shall be collected and identified to species. If the species is a salmonid, total body length shall be measured and assigned to race by length at date using the Delta model. Tissue samples shall be collected all wild salmonids, and CWT samples from adipose fin-clipped juvenile winter-run Chinook salmon, CV spring-run Chinook salmon, and CCV steelhead, for genetic analysis or tag removal/reading pursuant to appropriate sampling protocols. iii. All observed sDPS green sturgeon shall be collected. Any living specimens shall be resuscitated if possible, and released away from the BSPP facilities. All dead specimens shall be retained, frozen, and NMFS notified for final disposition. IV. Cleaning of aquatic weeds from in front of the fish screens shall occur during the inwater work window of July 1 through October 31 or when ambient water temperarures are greater than 25°C. v. Observers shall look for any salmonids or sDPS green sturgeon entangled in the weed mass as it is placed in the trucks and as it is dumped in the disposal site area. Any observed fish shall be collected and identified to species. If it is a salmonid, total body length shall be measured and assigned to race by length at date using the Delta model. All observed sDPS green sturgeon shall be collected. Any living specimens shall be resuscitated if possible, and released away from the BSPP facilities. All dead specimens shall be retained and NMFS notified for fmal disposition. 1037 Biological Opinion for the Long-Term Operation of the CVP and SWP vt. An annual report shall be sent to NMFS-CCVO by December 31 of each year for the previous water year's operations. The report shall contain information regarding the dates of sediment removal or vegetation cleaning, the number of observed fish, including the number of salmonids and sDPS green sturgeon, if any, and the final disposition of the fish. [f salmonids are observed, the report shall include the body lengths and run assignments for each fish. f. DWR shall incorporate the following terms and conditions related to the Predator Relocation E lectrofishing Study/ Predatory Fish Relocation Study: 1. The initial "run" of Chinook salmon shall be determined based on length at date criteria if the fish is actually captured and handled prior to release. u. Information shall be collected, to the extent possible, regarding whether the fish have an intact adipose fin or not, and any external signs of sutures or an incision, indicating that it is a special study fish (acoustic tags). iii. For those natural Chinook salmon captured, tissue samples: shall be taken for DNA analysis and archived with CDFW. 1v. All salmonids and sDPS green sturgeon shall be immediately processed and returned to CCF in good health as quickly as possible. v. If salmonids are observed in the electric field of the electrofishing boats, but are not captured, field crews shall note the approximate size and whether there is an adipose fm or not, if possible. vt. When salmonids or sDPS green sturgeon are observed in the electric field, electrofis:hing shall stop in that area, and the boat shall move to another area of the CCF at least 400 yards away from the previous site, and DWR project managers shall be notified immediately. g. DWR shall incorporate the following terms and conditions related to the Aquatic Weed Control Program in CCF: 1. DWR shall provide notification of intent to conduct aquatic weed removal activities to NMFS at least 2 weeks prior to starting, including the types of herbicides intended to be used for that application and the areas that will be treated. n. DWR shall send copies of the water quality monitoring results for the concentration of herbicides in the CCF following treatment to NMFS within I 0 business days of DWR's r,e ceipt of the results. iii. DWR sha ll report to NMFS any fish observed exhibiting unusual behavior or found dead or moribund following herbicide treatment within 10 business days of the incident. All dead specimens shall be retained and NMFS notified for final disposition. h. DWR shall incorporate the following terms and conditions related to South Delta Agricultural Barriers: 1. DWR shall send notice of intent to construct the barriers to NMFS at least 14 days prior to start of construction. This information shall include anticipated start dates and completion dates for each of the barriers. In the fall, DWR shall provide NMFS with the anticipated schedule for removal of the barriers, and notification when the removal has been completed. 11. DWR sha ll provide documentation to NMFS indicating the anticipated schedule for culvert operations, including potential early closures and water elevation conditions, 1038 Biological Opinion for the Long-Term Operation of the CVP and SWP 1. by the completion of barrier installation each season. Updates to barrier operations shall be provided to NMFS on a weekly basis until mid-June. iii. DWR shall develop, in coordination with NMFS, structural improvements or alterations to the south Delta agricultural barriers to allow passage of adult CV spring-run Chinook salmon over the weirs in the spring. This may include notches in the weir, development of "temporary fish ladders" to be installed from May through June to assist passage, or other passage solution. IV. DWR, in coordination with NMFS, shall study the possible development of structures or alterations to the barriers to assist passage of sDPS green sturgeon through the locations of the south Delta agricultural barriers. If a tenable solution is found, DWR shall incorporate it into the design of the south Delta agricultural barriers. Reclamation and DWR shall confer with NMFS prior to making decisions to use storage releases for the Delta Smelt Summer-Fall Habitat action. The purpose of conferring is to avoid or minimize the potential for the action to reduce Shasta storage conditions necessary to for winter-run Chinook temperature management. 16. RPM 6: Reclamation and DWR shall minimize incidental take of Southern Resident killer whales during operations. a. Reclamation shall continue to support the USFWS' study of alternative release sites for Coleman NFH produced fall-run Chinook salmon for the next 2 years to determine if trucking to an alternative release site can increase juvenile survival to the ocean and adult returns to the Sacramento River without unacceptable levels of straying. b. Reclamation shall coordinate with the American River fish and water agencies to carefully consider protections for fall-run Chinook salmon while implementing the 2017 Flow Management Standard Releases and "Planning Minimum" for the American River. 7. RPM 7: Reclamation and DWR shall monitor the amount and extent of incidental take described in Section 2.1 as necessary to implement this Opinion. a. Reclamation and DWR shall monitor the amount and extent of incidental take through the continued use of monitoring programs described in Appendix C of the BA and summarized below, which NMFS expects will continue without interruption. Reclamation and DWR also shall update Appendix C to describe how these monitoring programs will be used to monitor the amount and extent of take, how they will be applied to CVP and SWP water operation decision making and how they will be used for validation and effectiveness monitoring of Collaborative Planning actions. 1. Clear Creek (a) Adult Spring Chinook Escapement Monitoring in Clear Creek: video weir; snorkel surveys; life history sample collection (carcass) (b) Juvenile Spring-Run and Steelhead Production Monitoring in Clear Creek: rotary screw traps (c) Adult Steelhead and Late-fall Chinook Escapement Monitoring in Clear Creek: video weir and kayak redd counts (d) Operation of Clear Creek segregation weir (to separate fall and spring run Chinook salmon during spawning). 1039 Biological Opinion for the Long-Term Operation of the CVP and SWP 1. (e) Clear Creek habitat surveys. Sacramento River (a) Red Bluff Diversion Dam Rotary Screw Trap Juvenile Monitoring Project: juvenile estimates for all Chinook salmon runs, lamprey, and sturgeon. Currently covered under an ESA Section IO(a)(l)(a) permit held by USFWS. (b) Juvenile Salmon Delta Emigration Real Time Monitoring: Sacramento and Chipps Trawl for salmonids. Currently covered under an ESA Section lO(a)(l)(a) permit held by USFWS. Listed as compliance for the NMFS 2009 opinion in the IEP Workplan. (c) Lower Sacramento River Juvenile Salmon and Steelhead Monitoring Project: rotary screw trapping at Knights landing. Currently covered under an ESA Section lO(a)(l)(a) permit held by CDFW. Listed as compliance for the NMFS 2009 opinion in the IEP Workplan. (d) Winter-run Chinook Salmon Escapement Monitoring: Carcass surveys (e) Spring, Fall, and Late-fall Chinook Salmon and Steelhead Escapement Monitoring in the Upper Sacramento River Basin: carcass surveys, aerial and wading redd surveys; video weirs, snorkel surveys in mainstem and major tributaries. Life history sample collection (carcass). (f) Upper Sacramento River Habitat Restoration Monitoring Project: project effectiveness surveys at habitat improvement projects (snorkel; video; electrofish; seine). Inclusion of steelhead at Red Bluff Diversion Dam screw trapping- 0. mykiss counts are reported monthly. n. American River (a) American River Chinook Salmon and Steelhead Escapement Estimation: carcass surveys, aerial and wading redd surveys. iii. Stanislaus River (a) Stanislaus River Chinook Salmon and Steelhead Escapement Estimation: carcass surveys, weir counts, and redd surveys. IV. San Joaquin (a) Mossdale Spring Trawl: trawl for juvenile steelhead and Chinook salmon. Currently covered under an ESA Section lO(a)(l)(a) permit held by USFWS. Listed as compliance for the NMFS 2009 opinion in IEP Workplan. v. Hatchery (a) Genetic Analyses of California Salmonid Populations: Parentage Based Tagging (PBT) of salmonids in California Hatchery Programs. v1. Delta (a) Fish Salvage Operations: Tracy and Skinner: daily salvage and loss; operational conditions, tissue sample collection. Tissue collection currently covered under an ESA Section 1O(a)(l)(a) permit held by Reclamation. Included in IEP Workplan (b) Delta Juvenile Salmon Monitoring (DJFMP seines and trawls). Currently covered under an ESA Section lO(a)(l)(a) permit held by USFWS. Salmonid components listed as compliance for the NMFS 2009 opinion in IEP Workplan 1040 Biological Opinion for the Long-Term Operation of the CVP and SWP (c) Fall Midwater Trawl: Delta, Deep water shipping channel, and San Pablo BayCurrently covered under an ESA Section 1O(a)(l )(a) permit held by CDFW. Included in IEP Workplan. (d) Spring Kodiak Trawl- Currently covered under an ESA Section lO(a)(l)(a) permit held by CDFW. Included in IEP Workplan. (e) Estuarine and Marine Fish Abundance and Distribution Survey (Bay Study)Currently covered under an ESA Section lO(a)(l)(a) permit held by CDFW. Included in IEP Workplan. (f) Tidal Wetland Monitoring Studies- Listed as compliance for the NMFS 2009 opinion in IEP Workplan. vii. Multi Division (a) Genetic Identification of Salmonids to Inform Central Valley Project Operations and Bay-Delta Monitoring: For verifying winter and spring run. Sampling at fish facilities and monitoring programs to help with juvenile estimates; and larval fish ID at fish facilities. Tissue collection covered under Section 10(a)(l )(a) permit held by Reclamation. Included in IEP WorkplanOperation of Thermograph Stations- no take coverage necessary-USGS. Included in IEP Workplan (b) Enhanced Acoustic Tagging, Analysis, and Real-time Monitoring: Sacramento River through Delta for salmonids and sturgeon. (c) Funding or studies beyond collection of data (ototlith/scale collection). Genetics may be covered for all monitoring. (d) Adult sturgeon population estimates- covered under Section I 0(a)(l )(a) permit held by CDFW. Included in IEP Workplan. b. Reclamation and DWR shall work with NMFS, USFWS, CDFW and the IEP Biotelemetry Project Work Team to review, consolidate, and accommodate researcher requests related to special handling of salvaged fish (e.g., release of ad-clipped sutured fish; checking for acoustic tags) unless not practicable. Reclamation and DWR shall respond to such consolidated requests at least annually to assist with planning for future years, and any denial of accommodation shall be explained in writing. c. Reclamation shall continue to support and develop SacPAS. 8. RPM 8: Reclamation shall miinimize the incidental take of listed species associated by implementation of the proposed action by supporting the implementation of actions through the Collaborative Planning action component. to review the past year's a. Reclamation shall convene an annual Director's collaborative planning actions and coordinate on outyear planning. 9. RPM 9; Sacramento River Settlement Contractor measures a. The Sacramento Settlement Contractors drafted for adoption a resolution for activities involving recovery projects, actions related to annual operations, and engagement in 1041 Biological Opinion for the Long-Term Operation of the CVP and SWP ongoing science partnership. The SRS Contractors, in coordination with NMFS, shall continue to pursue activities in accordance with this resolution. 10. RPM 10: Reclamation and DWR shall coordinate with together and with NMFS to minimize incidental take of listed species related to coordinated operations. a. Reclamation and DWR shall continue to integrate the Feather River Operations Group (FROG) into other CVP and SWP fishery monitoring groups. 2.12 Conservation Recommendations Section 7(a)(l) of the ESA directs Federal agencies to use their authorities to further the purposes of the ESA by carrying out conservation programs for the benefit of the threatened and endangered species. Specifically, conservation recommendations are suggestions regarding discretionary measures to minimize or avoid adverse effects of a proposed action on listed species or critical habitat or regarding the development of information (50 CFR 402.02 2007). NMFS understands and expects that these projects will be partially or wholly funded by public funding sources such as the CVPIA program, the PCSRF/FRGP NOAA funds for salmon recovery and or State bond funds (e.g. Prop 1) in addition to PWA funds and other non-state and federal sources. NMFS further understands that each of these funding programs have their own processes, and expects Reclamation, DWR and local sponsors to compete for these funds. Furthermore, NMFS understands that PWAs will apply for funds, and if funded, implement several projects on this list. 1. Reclamation and DWR should use the recovery plans for Central Valley Salmonids (National Marine Fisheries Service 2014b) and sDPS North American Green Sturgeon (National Marine Fisheries Service 2018g) to help identify and prioritize restoration and other Collaborative Planning actions that address the underlying processes that limit fish recovery by identifying high priority actions in the action area. 2. Reclamation should consider the following list of Restoration, Technology, Science and Monitoring actions when implementing the Collaborative Planniing and Scheduling components of the P A. Restoration and Technology a. Reclamation, in coordination with the Clear Creek Technical Team, should identify and implement projects to restore the creek channel to one that is more responsive to the decreased magnitude high flow releases. Examples: lowering floodplains, removal of encroached riparian vegetation, creation of braided channels, all which improve would improve connectivity with the lower magnitude flows, increasing and improving the amount and quality of spawning and rearing habitat. This is intended to minimize impacts of controlled channel maintenance pulse flow releases, which are not high enough in magnitude and frequency to provide geomorphic processes that support connectivity and stream function in the current channel configuration, which thereby decreases optimal habitat for salmonids. b. Spawning Habitat Keswick to Red Bluff Diversion Dam; Objective- Annually place 40,000 to 55,000 tons of gravel at the Keswick and/or Salt Creek injection site(s). Create 1042 Biological Opinion for the Long-Term Operation of the CVP and SWP c. d. e. f. g. h. t. J. at least three site-specific gravel restoration projects upstream of Bonnyview Bridge by the end of2024. Rearing Habitat Red Bluff Diversion Dam to Verona 1. Enhance at least 2,000 acres of floodplain habitat in the Sutter Bypass. 11. Provide fish passage and floodplain habitat at Tisdale Weir within 5 years and Colusa Weir within 10 years. 111. Inventory historic oxbows and design fish passage and floodplain projects within 5 years and implement projects within 10 years. Support fish passage improvements on Mill and Deer creeks. Support Nigiri North: Floodplain restoration in the lower Sutter Bypass. Reclamation should coordinate with NMFS on the planning and implementation of Delta Smelt Habitat Actions to maximize opportunity for multi-species benefits. For the purpose of this term and condition, coordination is not meant to infer NMFS concurrence with an action, but rather that NMFS is afforded the opportunity to provide scientific or technical recommendations for Reclamation's consideration. In additional to the 8,000 acres of the Delta Smelt Habitat Action, Reclamation and DWR should actively support the restoration of an additional 3,000 acres of tidal habitat for improved rearing and reduced reverse tidal flows in critical migratory channels. Reclamation and DWR should support the following Lower San Joaquin River Habitat Projects consistent with the Collaborative Planning Action described in the final PA (Section 4.12.3). 1. Restoration of floodplain access and San Luis National Wildlife Refuge 11. Franks tract or other San Joaquin corridor specific restoration actions in the southern Delta llt. Sturgeon Bend Floodplain Restoration iv. Durham Ferry State Recreation Area floodplain restoration Reclamation and DWR should support the following physical and non-physical barrier projects. 1. Non-physical exclusion barrier at Georgiana Slough consistent with DWR's prior pilot study results. ii. DWR Salmon Protection and Technology Study at Steamboat and Sutter Sloughs. Pursuant to the USFWS June 19, 2019 Letter providing an update on four efforts that the USFWS has been engaged in regarding Coleman and Livingston Stone National Fish Hatcheries and their ·c ontribution to the management and restoration of Chinook salmon in the Sacramento River and Battle Creek (Appendix C), Reclamation should work with USFWS to: Secure an emergency/alternate water supply when Shasta and Keswick reservoirs reach elevations below the current penstock, or acquire (either purchase or rent) water chillers to ensure that adequate water temperatures are provided during critical wint·e r-run Chinook salmon life stages (e.g., adult holding, egg incubation, and juvenile rearing). 1. Support the findings of a multi-agency teamed that concluded the need to expand by 8 to 10 circular tanks to raise an additional 350,000 fish if the hatchery were to engage in the same drought operations they did in the recent drought. Increasing the capacity 1043 Biological Opinion for the Long-Term Operation of the CVP and SWP n. iii. 1v. v. of Livingston Stone NFH would require expanding to the west side of the hatchery road, additional piping to that side of the property, and additional water. Coordinate with USFWS to evaluate the need for modifications or improvements to Keswick Dam Fish Trap and Elevator, or operational adjustments to reduce the likelihood of injure or death to adult fish entering or attempting to enter the trap. Coordinate with USFWS to investigate the feasibility of installing an alternative winter-run fish collection facility on the south side of the Sacramento River at the ACID fish ladder. The study should begin in in January 2020. If the results of the investigation determine that a collection facility would be technically and economically feasible, Reclamation should install such a facility within 2 years of the recommendation. Coordinate with the USFWS on the need to install a drum screen to remove solids from the hatcheries effluent. The purpose of the drum screen would be to provide more flexibility to use medicated feed to prevent disease. Support the construction of a fish sorting facility at the Coleman National Fish Hatchery Science and Monitoring k. Fund science actions such as marking and tagging/survival studies for Battle Creek Reintroduction, spring pulse flow actions and for studying alternative release strategies for Coleman NFH fall-run. 1. Fund science, model development and monitoring; experimental design (with validation monitoring) for spring pulse flows and Anderson approach prior to operations. m. Reclamation and DWR, in coordination with NMFS, FWS, and CDFW, should develop, fund, and implement an updated plan for life cycle model development. n. Reclamation should update and recalibrate models to use recent data, especially that of the recent drought, to strengthen their ongoing application base for the purpose of minimizing the effect of take. Models that would benefit from recalibration include: i. Loss-density method ii. Delta Passage Model iii. lOS model iv. SWFSC Central Valley Winter-Run Chinook Life Cycle Model o. In order to reduce uncertainties regarding the mechanisms and extent oftake in the form ofjuvenile salmonid behavioral modifications to hydrodynamic changes in the south Delta that are associated with water operations, Reclamation and DWR should, in close coordination with NMFS, using the Collaborative Science and Adaptive Management Program (CSAMP) and IEP processes: 1. Implement the recommendations of the CAMT 2017 workplan for salmonids (Collaborative Adaptive Management Team 2017). As part of this workplan, Reclamation and DWR should fund continued development of enhanced particle tracking modeling that is sensitive to realistic changes in south Delta operations, analyze existing data, and conduct experiments to assist in model development. u. Develop an adaptive management approach with a sound experimental design to test key alternative hypotheses (e.g., exports are important in additional to inflow in some circumstances in influencing juvenile salmon behavior, etc.). This experimental approach should build on lessons learned from VAMP, the six-year steelhead study, 1044 Biological Opinion for the Long-Term Operation of the CVP and SWP and the CSAMP/CAMT gap analysis report and recent Delta salrnonid research workshop (that occurred on May 22, 2018). The study design would likely need to test both more restrictive and less restrictive approaches to the current RPA, given low survivals in the South Delta. A power analysis should be conducted to determine the sample size necessary in order to detect the results we are looking for. This experimental operational approach could be paired with habitat restoration and or predator management actions/studies in the Delta and on the main stern San Joaquin River. p. Reclamation should consult with NMFS and CDFW to study, develop and implement an eight-year science-based predator hotspot management experiment. f. The draft experimental design should be developed and submitted to NMFS for review by December 31, 2021. The plan should include proposed actions and locations and a funding and implementation strategy. g. NMFS WCR and NMFS SWFSC should be consulted on the experimental design, including the objectives, scope, locations, timing, questions/hypotheses, and methods. h. A final plan should be completed by June 1, 2022. 1. Actions may be taken as soon as possible but should begin no later than July 2022. J. Reports summarizing the effectiveness of the experiment are due by July 2025, and Ju ly 2030. q. To improve the understanding of salrnonid life-history in Clear Creek, and determine if salrnonids produced in Clear Creek are successfully returning, Reclamation should develop genetic and otolith studies in coordination with the NMFS, CDFW, and USFWS, and provide funding. This information would help relate flow, temperature, and habitat restoration management actions to populations. The studies should also include non-listed fall-run Chinook salmon, which are prey for SRKW. 3. Reclamation and DWR should pilot some alternative techniques to quantify incidental take of listed anadrornous salrnonid species at the Federal and State export facilities, including at least one option developed under Term and Condition 2(a) of the 2009 NMFS Opinion. a. In coordination with NMFS, Reclamation should design an initial pilot project to use existing alternative techniques, for implementation beginning October 1, 2020. During the pilot, official take should be based on the current estimation methods. Reclamation should continue to work cooperatively with other State and Federal agencies, private landowners, governments, and local watershed groups to identify opportunities for cooperative analysis and funding to support salrnonid and sturgeon habitat restoration projects within the Sacramento River Basin, Delta, and San Joaquin River Basin. Reclamation and DWR should make (or continue to make) all monitoring data collected under implementation of this opinion publicly available in order to facilitate integration with concurrent ecological monitoring efforts related to anadrornous fish in the California Central Valley. The SacPAS website is an excellent example of how this is already being achieved for key monitoring data. Reclamation and DWR should post interpretive signs and artwork characterizing local species and ecological function of nearby aquatic systems. 1045 Biological Opinion for the Long-Term Operation of the CVP and SWP 2.13 Reinitiation of Consultation This concludes formal consultation for the Reinitiation of Consultation on the Coordinated Longterm Operation of the Central Valley Project and State Water Project. This opinion shall take effect after Reclamation signs a record of decision under the National Environmental Policy Act, and shall supersede the NMFS Biological Opinion on the Long-term Operations of the Central Valley Project and State Water Project (2009, as amended in 2011) at that time. As 50 CFR 402.16 states, reinitiation of formal consultation is required where discretionary Federal agency involvement or control over the action has been retained or is authorized by law and if: (1) The amount or extent of incidental taking specified in the ITS is exceeded, (2) new information reveals effects of the agency action that may affect listed species or critical habitat in a manner or to an extent not considered in this opinion, (3) the agency action is subsequently modified in a manner that causes an effect on the listed species or critical habitat that was not considered in this opinion, or (4) a new species is listed or critical habitat designated that may be affected by the action. The following provide specific reinitiation of consultation triggers pursuant to implementation of the proposed action. 1. Limitations of Analysis regarding Shasta Dam Raise: As discussed in the effects analysis in this Opinion, Shasta Dam raise project as operated to the criteria in this PA is expected to have significant effects that have not been analyzed in this opinion. These include: a. additional adverse effects to all juvenile salmonids due to reduced flood plain and channel margin habitats at certain times of years and locations that have not been analyzed, including reduced inundation ofYolo Bypass; b. likely, but not assured, additional beneficial effects to winter-run Chinook salmon eggs due to reduced temperature dependent mortality in some years; c. reduced inflow to delta in winter and spring and higher Delta inflow in summer and fall, d. reoperation of reservoirs and delta pumps to deliver the newly stored water. Therefore, NMFS expects that this consultation will need to be reinitiated prior to Shasta Dam raise operations. 2. Limitations of Analysis regarding water contracts: NMFS was informed by Reclamation as part of this consultation that the CalSimii modeling in the BA is based on historic use patterns of contractual water use. In some cases, this is significantly less than contractual water obligations listed in the P A. NMFS has only analyzed the contractual deliveries as modeled. Therefore, any significant changes to these patterns would likely trigger reinitiation of consultation. 1046 Biological Opinion for the Long-Term Operation of the CVP and SWP 3 DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW The Data Quality Act (DQA) specifies three components contributing to the quality of a document. They are utility, integrity, and objectivity. This section ofthe opinion addresses these DQA components, documents compliance with the DQA, and certifies that this opinion has undergone pre-dissemination review. 3.1 Utility Utility principally refers to ensuring that the information contained in this consultation is helpful, serviceable, and beneficial to the intended users. The intended users of this Opinion are Reclamation and DWR (through the coordinated operations of the SWP with the CVP). Other interested users could include DWR, public water agencies, commercial and recreational fishing interests, environmental organizations, agricultural interests, and residents in California's Central Valley. An electronic copy of this Opinion was provided to Reclamation. The format and naming adheres to conventional standards for style. 3.2 Integrity This consultation was completed on a computer system managed by NMFS in accordance with relevant information technology security policies and standards set out in Appendix III, 'Security of Automated Information Resources,' Office of Management and Budget Circular A-130; the Computer Security Act; and the Government Information Security Reform Act. 3.3 Objectivity Information Product Category: Natural Resource Plan Standards: Within the limitations of the aggressive consultation schedule imposed by the October 19,2018, White House Memorandum on "Promoting the Reliable Supply and Delivery of Water in the West", this consultation and supporting documents are clear, concise, complete, and unbiased; and were developed using commonly accepted scientific research methods. They adhere to published standards including the NMFS ESA Consultation Handbook, ESA regulations, 50 CFR 402.01 et seq. Best Available Information: Within the limitations of the aggressive consultation schedule imposed by the October 19, 2018 White House Memorandum on "Promoting the Reliable Supply and Delivery of Water in the West," this consultation and supporting documents use the best available information, as referenced in the References section. The analyses in this Opinion contain more background on information sources and quality. Referencing: All supporting materials, information, data and analyses are properly referenced, consistent with standard scientific referencing style. Review Process: This consultation was drafted by NMFS staff with training in ESA, and reviewed (albeit on an accelerated schedule) in accordance with West Coast Region ESA quality control and assurance processes. 1047 Biological Opinion for the Long-Term Operation of the CVP and SWP 4 REFERENCES 50 CFR 402.02. 2007. Status of the Species. National Marine Fisheries Service, pp. 815-817. 50 CFR 402.14. 1986. 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