Urban Ecosystems
https://doi.org/10.1007/s11252-020-01020-3

Chicago’s fish assemblage over ~30 years – more fish and more
native species
Austin Happel 1

&

Dustin Gallagher 2

# Springer Science+Business Media, LLC, part of Springer Nature 2020

Abstract
How fish assemblages change over time in highly-modified urban rivers, where physical and chemical properties rarely mimic
non-urban systems, has sparsely been documented. Data have been collected on fishes within the boundaries of the Chicago
Metropolitan area routinely since the mid-1980’s. Representing fish assemblages in one of the largest cities of America, this
dataset offers the ability to investigate and track changes in assemblage composition in an urbanized river. To this end, multivariate modelling, as well as various visualization techniques, were used to assess and describe compositional changes in the fish
assemblage of Chicago’s waterways. In general, there were gradual enhancements in the fish assemblages of Chicago’s waterways throughout the years studied, which are characterized by more fish, of which more are native species. Small-bodied native
fishes (Cyprinidae), game fishes (Centrarchidae), as well as catfish (Ictaluridae) have increased in relative abundance, whereas
several invasive fish species exhibited declines. Exponential growth of Banded Killifish (Fundulus diaphanous) relative abundance appears to continue from previously noted range expansions. As Chicago and other cities move towards supporting
fishable waterways, interest may lay in investigating population vital rates and habitat or water quality factors affecting them
in heavily urbanized settings.
Keywords Chicago . Fish assemblage . Community . Urban River . Electrofishing

Introduction
When studied over long periods of time, the composition of
species at a location may be classified as continually shifting,
changing in sudden steps, returning to a state prior to some
disturbance, or resisting change (Holling 1973; Connell and
Sousa 1983). Fish assemblages within stream systems
experiencing natural disturbances (i.e., droughts or floods)
are thought to return to some pre-disturbance state in the absence of human disturbance (Matthews et al. 2013). Whereas
in human disturbed riverine systems fish assemblages appear
to be temporally dynamic, often reflecting directional change

* Austin Happel
ahappel@sheddaquarium.org
Dustin Gallagher
gallagherd@mwrd.org
1

Daniel P. Haerther Center for Conservation and Research, John G.
Shedd Aquarium, Chicago, IL, USA

2

Metropolitan Water Reclamation District Greater Chicago, Stickney,
Chicago, IL, USA

rather than a return to some previous composition (Pyron et al.
2006; Whitten et al. 2018; DeBoer et al. 2019).
However, many rivers upon which urban centers have developed have experienced landscape level physical and chemical alterations to the point that they may be considered novel
ecosystems, rather than something disturbed from a previous
natural state (Francis 2014). Modifications such as channelization, dams, and levees alter flow regimes as well as reduce
physical habitat variability in order to reduce flooding and
increase navigability (Gurnell et al. 2007). Such physical alterations compound upon effects of urban and industrial effluents affecting water quality, together leading to reduced ecosystem function and biodiversity (Walsh et al. 2005; Booth
et al. 2016). Consequently, urban rivers often simultaneously
represent highly valuable resources and highly degraded ecosystems compared to non-urban systems (Vörösmarty et al.
2010; Everard and Moggridge 2012). While regulations like
the Clean Water Act seek to abate water quality issues, the
level of engineering (e.g., sheet pile walls), maintenance (e.g.,
removal of debris), and barge traffic often preclude restoration
or rehabilitation efforts (Francis 2009). The hard structure
construction of urban waterways, combined with water quality issues make the ecosystem un-like typically studied

 Urban Ecosyst

riverine systems and their associated communities.
Considering highly-modified urban rivers as novel ecosystems would suggest enhancement of biotic communities is to
be expected in the years and decades following the Clean
Water Act, rather than restoration or rehabilitation, however
published works are lacking and thus temporal patterns in fish
assemblages remain difficult to predict.
The Chicago area waterway system (CAWS) is composed
of 78 miles of modified waterways, 75% of which is manmade, and the remaining 25% have been dredged,
reconfigured, or rerouted (Greenberg 2004; Solzman 2006;
LimnoTech 2010; Hill 2019). Charged with managing
Chicago’s wastewater treatment and stormwater management,
the Metropolitan Water Reclamation District of Greater
Chicago (MWRD) has monitored biotic and abiotic aspects
of the CAWS since early on in its history and developed a
more comprehensive program in the 1970’s, coinciding with
the enactment of the Clean Water Act. On the Illinois River,
downstream of the CAWS, improvements in both water quality and in-turn fish assemblages have been noted since the
enactment of the Clean Water Act (Pegg and McClelland
2004; McClelland et al. 2012; Parker et al. 2016; GibsonReinemer et al. 2017b). It is unknown whether fish assemblages in heavily-modified urbanized river systems such as
the CAWS have exhibited similar positive changes since passage of the Clean Water Act, but this information is needed to
assess its ecological impacts.
Fish communities of the CAWS have been monitored at
various locations since the late 1970’s by MWRD, several
locations have been monitored nearly every year since the
mid-1980s. Such monitoring efforts, done by electrofishing
both sides of the waterway, identify and enumerate fishes
found to help MWRD assess the general condition of the
CAWS and its inhabitants. Although data is publicly available
(http://geohub.mwrd.org/), changes in the fish assemblage
throughout the history of the dataset, and the CAWS, have
yet to be assessed and described outside of internal reports
available from MWRD. To this end, goals were to test for
changes in the fish assemblage since 1985 as well as provide
visualizations of such changes. It was hypothesized that fish
communities would exhibit gradual directional changes,
going from a degraded community to one of improvement,
realized through increases in species richness as well as
changes in native species relative abundances (CPUEs).

Methods
Study area description
The CAWS consists of two rivers (Chicago River and Calumet
River) whose flows have been reversed, connected by two manmade canals (Chicago Sanitary and Ship Canal and the Cal-Sag

Channel), which all eventually flow south to the Illinois River. An
additional constructed canal, the North Shore Channel, supplies
water, via discretionary flow, from Lake Michigan aiding the flow
of water through the channel through the northern Chicago communities towards downtown (Illinois Coastal Management
Program 2011). Other inlets from Lake Michigan are located on
the Chicago River (Chicago River Control Works) and the
Calumet River (T.J. O’Brien Lock and Dam) help to maintain
adequate flows and water levels in the CAWS. The CAWS includes outflows from four wastewater treatment plants (Terrence
J. O’Brien, Stickney, Lemont, and Calumet), one of them the
world’s largest (MWRD 2019), as well as a combined sewer
overflow system which releases untreated wastewater into the
surface waterways when the tunnel and reservoir sewer system
is overwhelmed by heavy rainstorms. The system is generally
described as slow flowing, non-wadable, lotic waters with vertical
steel walls or near vertical banks, soft fine sediment, and little
submerged habitat (LimnoTech 2010). Overall the system stands
as an engineering marvel and its history is well summarized well
by L. Hill (2019) and Olson and Morton (2017).
Numerous actions have been taken by MWRD over the
years to improve water quality of the system, including the
building of five Sidestream Elevated Pool Aeration (SEPA)
stations in the Cal-Sag Channel (3), The Little Calumet River
(1), and Calumet River (1) (Butts et al. 1999), an instream
aeration station in each of the North Shore Channel and the
North Branch Chicago River (Melching 2018), improved nitrification and disinfection practices, as well as continued construction of the Tunnel And Reservoir Plan (known as: TARP)
which greatly reduces combine sewer overflow events. Such
actions were, and continue to be, taken toward reaching the
general goal of having fishable and swimmable waters, a mandate by the Clean Water Act (Karr and Dudley 1981).

Program description
Electrofishing sampling has been carried out by MWRD personnel in the Chicago Area Waterways since 1974, although a
fully expanded, comprehensive program did not begin until
1985. Several locations were chosen to collect water quality
data as part of an Ambient Water Quality Monitoring
(AWQM) program, and to coincide with such data, electrofishing has been conducted to collect fish community information at the same locations. Initially, Alternating Current
(AC) electrofishing was used until the agency transferred to
pulsed-Direct Current (DC; generally, 120 pulses sec−1
targeting 12–14 amps) electrofishing at the start of 2001.
At each location, each river bank (where applicable) was
sampled for 400 m separately, and effort (timed in seconds)
was recorded. Fish were netted, identified, length and weight
were recorded, and fish were returned to the waterway. When
both banks were sampled, each “haul” was kept separate and
treated as a separate sample for the location, after both “hauls”

 Urban Ecosyst

were completed fish were returned to the waterway to avoid
recaptures. Catch per unit effort (CPUE) was standardized to
the number fish caught per 30 min of sampling for each “haul”
at each site. Sampling of fish communities occurred in July,
August and September, sometimes more than once in a year,
whereas data were not available for other years (e.g., 2008,
2014, and 2015).
In total, the data set included 58 species, including one
group for hybridized sunfish (Lepomis spp.), which summarized an additional 6 “species”, since whether these represented F1, or some other generation, was unknown (Table 1).
Species were classified into tolerance levels 1 being tolerant,
2 being neutral, and 3 being intolerant in accordance with
Grabarkiewicz and Davis (2008) and Poff and Allan (1995),
some species were not located in either source and thus remain
as “NA” herein. Species are also categorized by being native
or invasive (including simply non-native species) in accordance with Laird and Page (2011) and IL-DNR (2018).

Data selection and treatment
Nine AWQM sites were chosen for this analysis, ones which
were most comprehensively sampled throughout the 34-yr
period of interest. Sites in close proximity were lumped together leading to six waterways of interest (Fig. 1). Of note,
AWQM station 37 is just downstream of the confluence of the
North Shore Channel and the North Branch of the Chicago
River although it is lumped under the general waterway
“North Shore Channel” herein, along with two other locations
which were 3.2 km apart. Two sites on the Chicago Sanitary
and Ship Canal (shortened to “Sanitary-Ship Canal” in figures
and tables) were 5 km apart and were used together to represent this waterway. The Calumet River AWQM station (#55)
is on the Lake Michigan side of the O’Brien lock and dam (at
130th street bridge), meaning it is heavily influence by both
Lake Calumet and Lake Michigan compared to other locations
included herein which are all “inside” the lock and dam system of the CAWS. One sampling location was used to represent each of the Calumet Saganashkee Channel (shortened to
“Cal-Sag Channel” throughout manuscript), Little Calumet
River, and Lockport Lock and Dam (shortened to “Lockport
Dam” in figures and tables) (Fig. 1).
Data were separated by the two types of electrofishing,
leading to a 1985–2000 AC dataset and a 2001–2018 DC
dataset. This separation was done to remove the effect different electrofishing currents may have on fish community data
(McClelland et al. 2013).

Data analysis
All analyses were conducted using R (v3.6.3) programming
(R Development Core Team 2020). We used generalized linear models (GLMs) to test the effects of year, waterway, and

their interactions on richness and abundance of native and
invasive species. We used negative binomial distributions in
models to account for mean-variance relationships and
overdispersion. We also included sampling effort (measured
in the seconds; log transformed) as an offset to account for
variation in effort across samples. Separate models were constructed for richness and abundance of native and invasive
species, for the 1985–2000 AC dataset and a 2001–2018 DC
dataset. We used χ2 test statistics to assess significance and
differences among waterways were assessed using TukeyKramer post hoc tests.
We used a multivariate GLM with a negative binomial
distribution to assess the effects of year and waterway on the
fish assemblage using the manyglm function (“mvabund”
package; Wang et al. 2012, 2020). The predictor variables
are fit to each species as GLMs and a resampling procedure
(PIT-trap resampling; Warton et al. 2017) used to assess the
significance of assemblage-level effects, as well as adjusted Pvalues for effects of each species. We used multivariate Wald
χ2 test statistic to evaluate compositional differences and species level differences, with 9999 sampling iterations. We used
the Tukey-Kramer method to compare expected marginal
means and trends (i.e., interactions) among waterways for
each species with the emmeans and emtrends functions
(“emmeans” package; Lenth et al. 2018) .
We used non-metric multidimensional scaling (nMDS) to
visualize community-level changes across years and among
waterways. Data were transformed into catch per unit effort
(CPUE) and standardized to 30-min of effort. We performed
nMDS on the 1985–2000 AC and 2001–2018 DC datasets
separately using the metaMDS function (“vegan” package;
Oksanen et al. 2019; Oksanen 2013, 2019), which automatically transforms raw data using a square-root transformation
followed by Wisconsin standardization prior to calculating
Bray-Curtis distances between samples. We averaged nMDS
scores to yearly means for each waterway to illustrate differences in assemblage level changes over years among waterways. Faceting was used to separate each waterway, avoiding
overlap in their points.

Results
The dataset consisted of a total of 456 sampling events in
which a total of 53,917 fish were caught across the 58 species
(hybrid Lepomids counted as 1 species total; Table 1). The
species captured the most during all of the sampling events
included Gizzard Shad Dorosoma cepedianum (total catch
16,845), Bluntnose Minnow Pimephales notatus (5294),
Common Carp Cyprinus carpio (4740), Goldfish Carassius
auratus (3665), Pumpkinseed Lepomis gibbosus (3204),
Fathead Minnow Pimephales promelas (3156), Bluegill
Lepomis macrochirus (2543), and Largemouth Bass

 Urban Ecosyst
Table 1

Species found within the CAWS dataset used in this analysis of compositional changes from 1985 through 2018

Species

Tolerance

Native/
Invasive

Years Found

AC

DC

Alewife (Alosa pseudoharengus)
Banded Killifish (Fundulus diaphanus)
Black Buffalo (Ictiobus niger)
Black Bullhead (Ameiurus melas)

NA
NA
NA
1

I
N
N
N

15
4
6
21

122
–
–
136

41
728
28
34

Black Crappie (Pomoxis nigromaculatus)
Blackstripe Topminnow (Fundulus notatus)
Bluegill (Lepomis macrochirus)
Bluntnose Minnow (Pimephales notatus)
Brook Silverside (Labidesthes sicculus)
Brook Stickleback (Culaea inconstans)
Brown Bullhead (Ameiurus nebulosus)
Common Carp (Cyprinus carpio)
Carp x Goldfish (C. carpio X C. auratus)
Central Mudminnow (Umbra limi)
Channel Catfish (Ictalurus punctatus)
Chinook Salmon (Oncorhynchus tshawytscha)
Creek Chub (Semotilus atromaculatus)
Emerald Shiner (Notropis atherinoides)
Fathead Minnow (Pimephales promelas)
Flathead catfish (Pylodictis olivaris)
Freshwater Drum (Aplodinotus grunniens)
Gizzard Shad (Dorosoma cepedianum)

2
NA
1
1
3
3
1
1
NA
1
2
NA
1
2
1
2
2
1

N
N
N
N
N
N
N
I
I
N
N
I
N
N
N
N
N
N

22
5
30
30
6
6
3
31
25
9
18
1
7
25
24
1
17
31

31
–
481
2625
–
45
–
2141
373
6
5
–
2
821
3084
–
4
4992

40
13
2062
2669
54
–
4
2599
17
7
92
1
9
1056
81
1
51
11,853

Golden Shiner (Notemigonus crysoleucas)
Goldfish (Carassius auratus)
Grass Carp (Ctenopharyngodon idella)
Grass Pickerel (Esox americanus vermiculatus)

1
NA
NA

N
I
I

30
30
1

966
3286
–

1112
379
1

Green Sunfish (Lepomis cyanellus)
Hybrid Lepomids
Largemouth Bass (Micropterus salmoides)
Longnose Dace (Rhinichthys cataractae)
Mimic Shiner (Notropis volucellus)
Mosquitofish (Gambusia affinis)
Nile Tilapia (Oreochromis niloticus)
Ninespine Stickleback (Pungitius pungitius)
Northern Pike (Esox lucius)
Orangespotted Sunfish (Lepomis humilis)
Oriental Weatherfish (Misgurnus anguillicaudatus)
Pumpkinseed (Lepomis gibbosus)
Quillback (Carpiodes cyprinus)
Rainbow Smelt (Osmerus mordax)
Rainbow Trout (Oncorhynchus mykiss)

2
1
NA
2
3
3
NA
NA
NA
3
1
NA
2
2
NA
3

N
N
N
N
N
N
I
I
N
N
N
I
N
N
I
I

4
31
18
31
1
2
12
1
1
3
12
10
29
5
3
1

2
474
18
617
1
–
–
5
1
–
31
5
200
1
8
1

3
781
11
1667
–
4
1768
–
–
3
4
78
3004
5
–
–

Rock Bass (Ambloplites rupestris)
Round Goby (Neogobius melanostomus)
Sand Shiner (Notropis stramineus)
Skipjack Herring (Alosa chrysochloris)
Smallmouth Bass (Micropterus dolomieu)
Smallmouth Buffalo (Ictiobus bubalus)
Spotfin Shiner (Cyprinella spiloptera)

3
NA
2
NA
3
2
1

N
I
N
N
N
N
N

18
14
3
2
17
3
15

24
4
–
–
34
–
–

295
116
9
4
293
4
378

 Urban Ecosyst
Table 1 (continued)
Species

Tolerance

Native/
Invasive

Years Found

AC

DC

Spottail Shiner (Notropis hudsonius)
Tadpole Madtom (Noturus gyrinus)
Threadfin Shad (Dorosoma petenense)
White Bass (Morone chrysops)
White Crappie (Pomoxis annularis)
White Perch (Morone americana)
White Sucker (Catostomus commersoni)
Yellow Bass (Morone mississippiensis)

3
2
NA
2
1
NA
1
NA

N
N
N
N
N
I
N
N

16
1
1
2
5
17
24
11

156
–
–
–
–
135
51
3

16
1
1
3
7
107
298
43

Yellow Bullhead (Ameiurus natalis)
Yellow Perch (Perca flavescens)

2
2

N
N

18
15

5
708

375
103

Tolerance values reported by Poff and Allan (1995) and Grabarkiewicz and Davis (2008), or if unavailable (“NA”), as well as native or invasive status
(Laird and Page 2011; IL-DNR 2018), and the number of individuals caught in the years AC fishing was used (1985–2000) and DC fishing was used
(2001–2018)

Micropterus salmoides (2284) (Table 1). By occurrence in
sampling events, the top six species were Common Carp
(present in 401 surveys), Gizzard Shad (354), Largemouth
Bass (252), Goldfish (241), Bluegill (241), and Green
Sunfish Lepomis cyanellus (237).
Native species richness increased across years in both
1985–2000 and 2001–2018 periods (χ2 = 13.10, P < 0.001;
χ2 = 37.22, P < 0.001). Native species richness was also different among waterways (χ2 = 110.67, P < 0.001; χ2 = 65.04,
P < 0.001), there were no significant interaction effects (χ2 =
7.90, P = 0.16; χ2 = 8.78, P = 0.12). For the 1985–2000 period, native species richness was significantly higher in the
Calumet River than other waterways, the North Shore
Channel was second highest compared to others, and all other
waterways were not significantly different from each other
(Fig. 2). For the 2001–2018 period, differences in native species richness among waterways were less distinct with a gradient in differences richness, with Little Calumet River and
Calumet River having similar but higher richness than others
and Lockport Lock and Dam had the lowest (Fig. 2).
Invasive species richness exhibited no significant change
across years nor among waterways in the 1985–2001 dataset
(χ2 = 0.0008, P = 0.98; χ2 = 3.62, P = 0.60 respectively).
Similarly, there were not changes in invasive species richness
across years in the 2001–2018 dataset (χ2 = 0.073, P = 0.79)
but there were differences among waterways (χ2 = 24.927,
P < 0.001), primarily with there being fewer invasive species
at Lockport Lock and Dam, compared to the Little Calumet
River, Chicago Sanitary and Ship Canal, and Cal-Sag channel
(Fig. 2).
Interactions between years and waterways existed for native species abundance (CPUEs) in both 1985–2000 and
2001–2018 periods (χ2 = 10.02, P = 0.075; χ2 = 14.23, P =
0.014; respectively, Fig. 3). Between 1985 and 2001 a

significant positive trend was noted in the Chicago Sanitary
and Ship Canal as well as a negative trend in the Calumet
River, whereas the other waterways were not significantly
different from either of these trends (Fig. 3). In the 2001–
2018 period, a significant positive trend was noted at the
Lockport Lock and Dam. No trends were noted for the
North Shore Channel and the Chicago Sanitary and Ship
Canal, significantly different from Lockport Lock and Dam,
whereas the other waterways were not significantly different
from either of these two groups (Fig. 3).
For both the 1985–2000 and 2001–2018 periods, invasive
species abundance (CPUEs) was affected by differences
among waterways (χ 2 = 88.46, P < 0.001; χ 2 = 112.35,
P < 0.001; respectively), more so than trends in years (χ2 =
29.79, P < 0.001; χ2 = 3.74, P = 0.053; respectively), there
was no evidence of significant interactions (χ2 = 7.79, P =
0.17; χ2 = 7.38, P = 0.19; respectively). Higher CPUEs were
found in the Chicago Sanitary and Ship Canal compared to
others and lower CPUEs in the Calumet River, Cal-Sag
Channel and at Lockport Lock and Dam in the 1985–2000
period. In the 2001–2018 period, invasive species CPUE was
higher in the Chicago Sanitary and Ship Canal and Little
Calumet River compared to others, which were not different
from each other.
Multivariate GLMs indicated that how assemblages
changed over years was different among waterways for
each 1985–2000 and 2001–2018 period (interactions;
χ2 = 17.72, P < 0.001; χ2 = 19.74, P < 0.001). Effects of
year (χ2 = 20.57, P < 0.001; χ2 = 21.16, P < 0.001) and
waterway (χ2 = 34.14, P = 0.002; χ2 = 39.35, P = 0.003)
were also significant for both datasets. Species specific
outputs indicated multiple species exhibited trends across
years (Table 2), different CPUES among waterways
(Tables 2 and 3), as well as different trends across years

 Urban Ecosyst
Fig. 1 A subset of the locations in
the Chicago Area Waterways
sampled by MWRD since the
mid-1980’s, from which fish
community data is summarized
herein. Specific sampling sites in
close proximity were grouped
into the main waterway of
interest, signified by sharing
symbols and colors

Lockport Lock
and Dam

among waterways (Tables 2 and 4), leading to the assemblage level interaction. Faceting nMDS scores by waterways
illustrated how changes across years differed among waterways (Figs. 4 and 5). For both nMDS plots, data scores for
samples from the Calumet River were located more positively
on nMDS1, and for the 2001–2018 period more positively on
nMDS2, compared to other waterways. This is likely due to
larger CPUEs of several species in Calumet River compared
to other locations (Table 3). All waterways exhibited a trend
across 1985–2001 from lower to higher values on nMDS2
(Fig. 4), which can be attributed to the loss of Brook
Stickleback Culaea inconstans, Black Bullhead Ameiurus
melas, Common Carp-Goldfish hybrids, Goldfish, and
Fathead Minnows concomitant with increases in Gizzard
Shad and Largemouth Bass (Tables 1 and 4). Changes in the

fish community across 2001–2018 were visible as diagonal
trend in nMDS scores from the top left to the bottom right of
the nMDS plot (Fig. 5). For the 2001–2018 period, changes in
the fish community in the Cal-Sag Channel were not as evident compared to Lockport Lock and Dam and the Chicago
Sanitary and Ship Canal.
General trends for 10 species of interest are shown in
Fig. 6, selected for their importance as sport fish (Bluegill,
Green Sunfish, Largemouth Bass, and Pumpkinseed), being
an invasive species (Common Carp), having high abundance
(Bluntnose Minnow and Gizzard Shad), or a species with
large changes in CPUE (Banded Killifish Fundulus
diaphanus, Golden Shiner Notemigonus crysoleucas, and
Yellow Bullhead Ameiurus natalis), as well as generally all
having significant trend outputs in Table 2.

 Urban Ecosyst

Fig. 2 Changes in native and invasive species richness in six waterways
within the Chicago Area Waterways from 1985 to 2018. Negative
binomial regression used separately for the period of 1985–2000 and
2001–2018 due to different fishing gears being used, and included sampling time as an offset. To reduce clutter, yearly averages are plotted for
each waterway. We refer readers to the text for discussion of significant
differences among waterways

Fig. 3 Changes in catches (log scale) of native and invasive fishes in six
waterways within the Chicago Area Waterways from 1985 to 2018.
Negative binomial regression used separately for the period of 1985–
2000 and 2001–2018 due to different fishing gears being used and included sampling time as an offset. To reduce clutter, yearly averages are
plotted for each waterway. We refer readers to the text for discussion of
significant differences among waterways

Discussion

data collection, suggesting gradual enhancements rather than
stepwise changes or reversion to previous states.
Changes in species richness seem to be influenced by new
occurrences of native species, rather than newly invasive populations. Invasive fishes such as Common Carp, Goldfish, and
Oriental Weatherfish Misgurnus anguillicaudatus have been
found throughout the 34 years of the data series. Round Goby
Neogobius melanostomus were first documented in 1994 and
continue to be routinely found, and there were single instances
of Nile Tilapia Oreochromis niloticus (1999) and Grass Carp
Ctenopharyngodon idella (2001) being found in the CAWS.
Instead, evidence is provided that native fishes such as Mimic
Shiner Notropis volucellus, Sand Shiner Notropis stramineus,
Smallmouth Buffalo Ictiobus bubalus, Tadpole Madtom
Noturus gyrinus, Threadfin Shad Dorosoma petenense, and
White Crappie Pomoxis annularis have returned to the system, although abundances appear to remain low and could be

The fish assemblage of the Chicago Area Waterway System
presently has increased species richness and abundance compared to the 1980’s, and those changes are due to native species. On average, between 13 and 16 native species were
found during a 30-min electrofishing trip on the CAWS in
2018, compared to < 3 species in 1985. A total of 19 new
species were found since 2001, of which only Mosquitofish
Gambusia affinis represented an invasive species with a sizable population (> 10 individuals). Conversely, six species
were captured prior to 2001 but not in recent years, the largest
decline being native Brook Stickleback. Several native and
sportfish species exhibited increases in CPUEs, suggesting
improvements to the ecosystem of the CAWS from previous
years. Ordination plots (nMDS) illustrated significant directional changes in fish assemblages over the entire period of

 Urban Ecosyst
Table 2 Outputs of regressions testing for changes in species catches over the years for time periods of 1985–2000 and 2001–2018, where AC and DC
electrofishing were used respectively
1985–2000 AC

2001–2018 DC

Species

Yr

Wwy Inter. Tr. Yr

Alewife

NS **

NS

NS NS

NS

Banded Killifish
Black Buffalo
Black Bullhead
Black Crappie
Blackstripe Topminnow
Bluegill
Bluntnose Minnow
Brook Silverside
Brook Stickleback
Brown Bullhead
Common Carp
Carp X Goldfish
Central Mudminnow
Channel Catfish
Chinook Salmon
Creek Chub
Emerald Shiner
Fathead Minnow

NS
NS
NS
NS
NS
***
**
NS
**
NS
NS
**
NS
NS
NS
NS
NS
***

NS
NS
***
NS
NS
***
***
NS
NS
NS
***
***
NS
NS
NS
NS
NS
***

NS
NS
NS
NS
NS
***
**
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
***

***
NS
NS
NS
NS
***
NS
*
NS
NS
NS
NS
NS
***
NS
NS
NS
NS

***
NS
NS
NS
NS
***
***
**
NS
NS
***
NS
NS
NS
NS
NS
***
NS

NS
NS
NS
NS
NS
*
NS
NS
NS
NS
***
NS
NS
*
NS
NS
NS
NS

Flathead Catfish
Freshwater Drum
Gizzard Shad
Golden Shiner
Goldfish
Grass Carp
Grass Pickerel
Green Sunfish
Hybrid Sunfish
Largemouth Bass

NS
NS
*
***
***
NS
NS
NS
NS

NS
NS
***
***
***
NS
NS
***
NS

NS
NS
***
NS
**
NS
NS
NS
NS

NS
NS
NS
**
NS
NS
NS
***
NS

NS
NS
NS
***
***
NS
NS
***
NS

NS
NS
**
NS
NS
NS
NS
***
NS

*** ***

***

NS ***

NS

+
+
–

–

–

+
–
–

+

1985–2000 AC

Wwy Inter. Tr. Species

+

+
+

–

+

–
+

+

Yr

2001–2018 DC

Wwy Inter. Tr. Yr

Wwy Inter. Tr.

Longnose Dace

NS NS

NS

NS NS

NS

Mimic Shiner
Mosquitofish
Nile Tilapia
Ninespine Stickleback
Northern Pike
Orangespotted Sunfish
Oriental Weatherfish
Pumpkinseed
Quillback
Rainbow Smelt
Rainbow Trout
Rock Bass
Round Goby
Sand Shiner
Skipjack Herring
Smallmouth Bass
Smallmouth Buffalo
Spotfin Shiner

NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
**
NS
NS
NS
***
NS
NS

NS
NS
NS
NS
NS
NS
NS
***
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS

NS
NS
NS
NS
NS
**
NS
*
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS

NS
**
NS
NS
NS
NS
***
***
NS
NS
NS
NS
NS
NS
NS
NS
NS
**

NS
**
NS
NS
NS
NS
NS
***
NS
NS
NS
***
***
NS
NS
***
NS
***

NS
NS
NS
NS
NS
NS
NS
**
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS

Spottail Shiner
Tadpole Madtom
Threadfin Shad
White Bass
White Crappie
White Perch
White Sucker
Yellow Bass
Yellow Bullhead

**
NS
NS
NS
NS
NS
NS
NS
NS

NS
NS
NS
NS
NS
NS
NS
NS
NS

NS
NS
NS
NS
NS
NS
NS
NS
NS

–

NS
NS
NS
NS
NS
NS
NS
NS
**

NS
NS
NS
NS
NS
***
***
NS
***

NS
NS
NS
NS
NS
NS
*
NS
NS

+

Yellow Perch

*** NS

NS

–

**

NS

NS

+

–
–

+

+

+

+
+

+

+

Negative binomial regressions included year (Yr), waterway (Wwy), and their interaction effects (Inter.) with sampling time as an offset. Significance
denoted with: NS = non-significant, * = < 0.1, ** = < 0.05, and *** = < 0.01. The general trend (Tr.) of the effect for year (i.e, the general direction of
change) is denoted using “+” for increases and “-“ for decreases in catches. Species with significant results are bolded

considered rare. Similarly, increases in species richness since
the mid-1970’s were shown to be due to increases in sportfish
and native richness indices downstream of Chicago on the
Illinois River (Gibson-Reinemer et al. 2017b) as well as several other midwestern riverine systems (Mapes et al. 2015;
Holloway et al. 2018; Pyron et al. 2019). Parker et al. (2016)
provide evidence that the improvements in fish assemblages
downstream of Chicago were associated with reductions in
sewage-related variables (e.g. ammonia and fecal-coliform
bacteria). The results of studies downstream (e.g., Parker
et al. 2016, 2018; Gibson-Reinemer et al. 2017b), together
with ours suggest that reduced sewage effluents within the

Chicago area and improvements in wastewater treatment have
had impacts on the fish community locally (within Chicago)
as well as further downstream.
Changes in species-specific relative abundances (as judged
by CPUE) do not offer strong inferences on changes in water
quality. For example, many of the species that increased in
abundance (e.g., Banded Killifish, Bluegill, Green Sunfish,
Pumpkinseed, Yellow Bullhead, etc.) are considered either
neutral to or tolerant of pollution (Poff and Allan 1995;
Grabarkiewicz and Davis 2008). In seeming contrast, a report
on the more natural (e.g., not fully channelized, riparian areas
remain, not manually cleared of debris) Des Plaines River,

 Urban Ecosyst
Table 3
Table 2

Expected marginal mean CPUEs (unit of effort = 30 min) for each waterway for species indicated to have significantly different CPUEs in
1985–2000 AC

Species

Cal-Sag Channel

Calumet River

Little Calumet River

Lockport Dam

North Shore Channel

Sanitary-Ship Canal

Alewife

0.02(ab)

0.02(b)

0.01(ab)

NA

0.96(a)

0.10(b)

Black Bullhead
Bluegill
Bluntnose Minnow
Common Carp
Carp X Goldfish
Fathead Minnow
Gizzard Shad
Golden Shiner
Goldfish
Largemouth Bass
Green Sunfish
Pumpkinseed

NA
1.62(a)
14.1o(a)
2.12(c)
0.07(c)
<0.01 (ab)
27.0(a)
0.21(b)
0.19(d)
6.39(a)
1.48(ab)
2.30(a)

0.07(b)
0.38(b)
0.77(b)
6.02(b)
0.49(b)
0.24(b)
20.90(a)
1.17(b)
6.75(ab)
0.12(c)
0.20(cd)
0.13(bc)

NA
0.18(bc)
0.80(b)
5.56(b)
0.38(bc)
0.02(ab)
16.50(ab)
0.14(b)
2.45(bc)
0.72(bc)
0.69(bc)
NA

0.84(a)
1.89(a)
7.00(a)
2.34(c)
1.75(a)
7.88(a)
4.49(bc)
5.97(a)
6.88(ab)
0.67(b)
2.61(a)
0.43(b)

0.17(b)
0.05(c)
8.53(a)
14.70(a)
0.78(b)
0.66(b)
3.39(c)
0.35(b)
9.32(a)
0.46(bc)
0.07(d)
0.09(c)

Banded Killifish
Bluegill
Bluntnose Minnow
Brook Silverside
Common Carp

0.01(ab)
0.41(b)
1.28(b)
5.48(b)
0.43(bc)
<0.01(ab)
9.42(abc)
<0.01(ab)
1.77(c)
0.28(bc)
0.25(cd)
0.03(bc)
2001–2018 DC
<0.01(ab)
2.00(c)
15.00(bc)
0.07(b)
13.70(bc)

0.38(a)
7.65(ab)
61.20(a)
1.10(a)
7.95(c)

<0.01 (ab)
20.30(a)
5.65(cd)
<0.01 (ab)
25.30(ab)

<0.01(ab)
2.15(c)
1.47(d)
NA
2.56(d)

<0.01 (ab)
10.00(ab)
2.48(d)
NA
15.40(abc)

<0.01 (b)
7.93(b)
20.30(b)
NA
24.10(a)

Emerald Shiner
Golden Shiner
Goldfish
Green Sunfish
Largemouth Bass
Mosquitofish
Pumpkinseed
Rock Bass
Round Goby
Smallmouth Bass
Spotfin Shiner
White Perch
White Sucker
Yellow Bullhead

13.60(a)
2.05(b)
0.51(bc)
4.86(a)
11.50(b)
NA
0.83(c)
NA
0.35(bc)
0.05(b)
0.85(bc)
0.53(ab)
NA
1.05(b)

16.80(a)
0.17(c)
0.042(bc)
2.19(abc)
30.10(a)
NA
6.46(b)
7.95(a)
2.73(a)
15.70(a)
0.82(bc)
0.33(b)
2.22(b)
<0.01 (ab)

8.35(ab)
8.91(a)
12.40(a)
1.76(bc)
26.80(a)
NA
30.30(a)
NA
1.42(ab)
0.04(b)
0.30(c)
3.82(a)
7.74(a)
4.82(a)

1.93(abc)
0.50(bc)
0.01(abc)
5.95(a)
1.63(c)
0.45(b)
4.84(b)
NA
<0.01(abc)
<0.01(ab)
0.10(c)
NA
NA
0.64(b)

0.17(c)
13.80(a)
0.06(c)
1.00(c)
9.25(b)
NA
7.53(b)
0.19(b)
0.05(c)
NA
5.96(a)
0.02(b)
1.93(b)
0.43(b)

1.50(bc)
6.62(a)
1.48(b)
3.85(ab)
0.89(c)
26.60(a)
30.60(a)
NA
0.07(c)
NA
2.53(ab)
0.15(b)
<0.01(b)
3.76(a)

Those sharing letters are not significantly different (Tukey-Kramer). NA represents that this species was not found in this waterway and thus its CPUE
cannot be estimated

which flanks the CAWS, indicated moderate decreases in proportions of tolerant species, increases in neutral species, and
relatively minor increases in intolerant species over the same
time period (Pescitelli and Widloe 2018). Increases in intolerant species linked to water quality improvements have been
documented in in rivers in Illinois (Illinois River; Parker et al.
2018), Indiana (West Fork of the Wabash; Holloway et al.
2018), Ohio (the Scioto and Cuyahoga Rivers; Rahel 2010),
and Texas (Trinity River; Perkin and Bonner 2016). In a

watershed in Kansas, Whitney et al. (2019) found that species
intolerant to pollution did not change in abundance and in fact
species considered tolerant increased in abundance after water
quality improvements. Similarly, although water quality
downstream of the CAWS has improved over recent decades
(Parker et al. 2016, 2018), there were no notably large increases in intolerant species within the CAWS. It is important
to note that water quality is not a factor in isolation, and that
fish populations respond to habitat factors beyond just water

 Urban Ecosyst
Table 4 Expected marginal trends across years (i.e., multiplicative rate of change in CPUE) for each waterway for species indicated to have
significantly different CPUEs in Table 2
1985–2000 AC
Species

Cal-Sag Channel

Bluegill

0.993(ab)

Bluntnose Minnow
Fathead Minnow
Gizzard Shad
Goldfish
Largemouth Bass
Orangespotted Sunfish
Pumpkinseed

1.1(ab)
2.81(ab)
1.02(b)
0.724(ab)
1.3(ab)
0.729(ab)
0.993(ab)
2001–2018 DC
1.17(abc)
0.99(a)
1.54(a)
1.11(a)
1.03(b)
1.15(ab)
NA

Bluegill
Common Carp
Channel Catfish
Gizzard Shad
Green Sunfish
Pumpkinseed
White Sucker

Calumet River

Little Calumet River

Lockport Dam

North Shore Channel

Sanitary-Ship Canal

0.899(b)

0.853(b)

1.01(ab)

1.22(a)

1.02(ab)

0.813(b)
0.0974(ab)
0.939(b)
1.03(a)
1.03(b)
0.476(b)
0.848(b)

1.06(ab)
0.781(a)
0.983(b)
0.754(ab)
1.68(a)
NA
1.26(ab)

1.04(ab)
0.634(ab)
1.03(b)
0.939(a)
1.38(a)
NA
NA

0.898(b)
0.425(b)
1.44(a)
0.807(ab)
1.39(a)
1.09(a)
1.15(a)

1.11(a)
1.19(a)
1.22(ab)
0.69(b)
1.36(a)
NA
1.33(a)

1.11(c)
0.962(a)
NA
1.05(ab)
1.07(b)
1.15(a)
0.998(b)

1.39(ab)
0.731(b)
0.844(c)
1.13(a)
1.37(a)
1.26(a)
NA

1.17(abc)
0.975(a)
1.07(bc)
0.925(b)
1.03(b)
0.975(b)
1.28(a)

1.32(a)
0.989(a)
1.12(ab)
0.935(b)
1.08(b)
1.09(ab)
1.83(ab)

1.11(bc)
0.947(a)
201(abc)
0.871(b)
1.2(ab)
1.26(a)
0.915(b)

Values <1 indicate decreases in abundance, whereas values >1 indicate increases in CPUEs. Those sharing letters are not significantly different (TukeyKramer). NA represents that this species was not found in this waterway and thus its CPUE cannot be estimated

quality (i.e., canopy cover, riparian areas, local land use,
overwinter habitat, etc.; Raibley et al. 1997; Sawyer et al.
2004). To this point, a study by LimnoTech (2010) indicated
that in the early 2000’s, habitat quality was more important to
predicting fish community indices within the CAWS than
dissolved oxygen (a single proxy of many for water quality).
Our evidence of few to no populations of pollution-intolerant
species increasing in abundance (except Smallmouth Bass
Micropterus dolomieu and Rock Bass Ambloplites rupestris)
compared to other species, combined with the habitat studies
mentioned suggests that both water quality as well as habitat
remain as limiting factors in the CAWS.
The seemingly exponential increase in Banded Killifish
relative abundance is of interest to regional biologists as the
species is listed as state-threatened in Illinois (IESPB 2015,
2019). Although classified by MWRD as one species, both
Western (F. diaphanus menona) and Eastern (F. diaphanus
diaphanus) subspecies of Banded Killifish occur in the area
and appear to readily hybridize (Willink et al. 2018). It has
been suggested that Eastern Banded Killifish populations have
migrated from Lake Michigan into the CAWS system as several Banded Killifish of unknown subspecies appeared in
seine surveys of Illinois beaches in 2001 (Willink et al.
2018). Banded Killifish first appeared in the CAWS in
2010 at SEPA station 1, near our Calumet River location, at
which they did not appear until 2012, and were later found in
other parts of the CAWS. Causative agents for the exponential

population growth of the Banded Killifish in the CAWS remains uncertain. It has been suggested that the Eastern subspecies is more tolerant to pollution and has less strict vegetative demands for spawning (Trautman 1981), and thus the
Eastern subspecies (or hybrids) may be able to take advantage
of degraded habitats the Western subspecies once utilized.
Decreases in Common Carp have been shown throughout
the Illinois River as well as along the upper Mississippi
(Gibson-Reinemer et al. 2017a). Such declines, believed to
have begun in the 1960’s, were thought to be due to disease
as other possibilities (i.e., water quality, predation, competition) had little or contradicting support. We note that Common
Carp populations in the CAWS declined in 2001–2018, especially at the Lockport Lock and Dam sampling site compared
to other waterways included herein. Declines were not noted
between 1985 and 2000 and populations throughout the
CAWS appeared steady during this period. Whether a similar
lack of recruitment is experienced by this population as those
described by Gibson-Reinemer et al. (2017a) is unclear and
may be of further research interest given the spatial differences
in noted declines in the CAWS compared to across the
Mississippi River drainage.
Switching from AC to DC electrofishing changes which
species are susceptible to electrofishing (McClelland et al.
2013). Some species in the CAWS were caught only with
one type of electrical current and within that gear type did
not have significant changes in abundance suggesting that

 Urban Ecosyst
Fig. 4 Changes in fish
communities of six Chicago
waterways between 1985 and
2000 visualized using nMDS,
faceted for each waterway to
reduce overlap. Points represent
yearly averaged nMDS scores for
each waterway. nMDS scores
based on Bray-Curtis similarities
among square-root transformed
and Wisconsin double standardized fish CPUE data

switching gears did affect which species were susceptible to
the gear. Although not formally tested, Brook Stickleback and
Spotfin Shiner Cyprinella spiloptera each occurred for multiple years under a single electrofishing regime (6 AC-years and
15 DC-years respectively). A comparative study conducted on
the Illinois River suggests that biomass captured as well as
species richness are increased with DC electrofishing over AC
electrofishing (McClelland et al. 2013). As gear-related differences in species richness were expected, we chose to separate
data by the time periods the different electrofishing types were
used. Within the recent DC (2001–2018) period of sampling
there were larger increases in species richness than in the AC
(1985–2000) period, offering evidence that the CAWS is
home to a greater diversity of fishes now than any period
included in the study.
The uniqueness of the Calumet River sampling location
was evident in both the 1985–2000 and 2001–2018 nMDS
ordinations. This sampling location is proximal to Lake

Calumet, which hosts a fish community routinely targeted
by tournament anglers (anglers-dream.com). Lake Calumet
is a heavily modified lake that is largely shallow but has
several man-made slips that are deep enough for barge traffic.
Some slips within the CAWS have been shown to host more
diverse fish communities than the mainstem of the waterways
(Gallagher and Wasik 2018), and slips potentially act as refuges for fishes during poor water quality events (Gaulke et al.
2015). Slips have also been known to have higher abundances
of Largemouth Bass than encountered in the CAWS proper
(Gallagher and Wasik 2018). This sampling location routinely
received higher index of biotic integrity scores, than others
included herein, when assessed by MWRD biologists
(Gallagher et al. 2014). When compared to other waterways
herein, the diverse fish community at this location, as well as
increases in sportfish here, offers evidence that habitat availability may be a larger limiting factor within other areas of the
CAWS at this point in time.

 Urban Ecosyst
Fig. 5 Changes in fish
communities of six Chicago
waterways between 2001 and
2018 visualized using nMDS,
faceted for each waterway to
reduce overlap. Points represent
yearly averaged nMDS scores for
each waterway. nMDS scores
based on Bray-Curtis similarities
among square-root transformed
and Wisconsin double standardized fish CPUE data

Given the level of engineering performed to construct and
maintain CAWS, and other working rivers, future fish-habitat
enhancements likely need to be creative compared to traditional restoration activities (Francis 2009). Any in-river habitat improvements must preserve the functionality of the river
as a shipping conduit, and thus also be able to withstand the
hydrodynamics caused by barge traffic. Large woody debris is
well known for a number of benefits in riverine systems
(Larson et al. 2001; Gurnell et al. 2005), however to maintain
navigability, would need to be attached to and flush with
existing artificial structures. For example, timber fenders
added to Deptford Creek in London has supported new plant
communities on sheet pile, typically void of vegetation
(Francis and Hoggart 2008). Riprap (i.e., mixed composition
rock piles) used to stabilized channelized banks has been
shown to increase abundances of fish species over bare mud
banks (White et al. 2010). Protection from current and wave

action has been trialed by creating planted wetlands along the
banks behind existing sheet pile walls, allowing a diversity of
aquatic and riparian plants to grow (Weber et al. 2012), which
may potentially act as nursery areas for fishes. Floating
enhancements such as docks and pontoons or less anthropocentric methods like artificial floating wetlands provide shelter, shade, and spawning possibilities (Schanze et al. 2004).
Despite reports and presentations of such creative enhancements, published outputs of their effectiveness in enhancing
fish communities remain sparse and more evidence is needed
to support such tools in urban river management.
In conclusion, directional improvements have occurred in
the fish assemblages of the Chicago Area Waterway System.
Although a pristine riverine community for comparison is
unavailable, nor data from prior to Chicago’s development,
management and policy actions have likely elicited the noted
enhancements toward including more native species, typically

 Urban Ecosyst

Fig. 6 Changes in selected species’ CPUEs (30 min electrofishing; log+1
transformed) in six waterways within the Chicago Area Waterways from
1985 to 2018. Negative binomial regressions used separately for the
periods of 1985–2000 and 2001–2018 due to different fishing gears being

used, and included sampling time as an offset. To reduce clutter, yearly
mean CPUEs for each waterway are displayed as points instead of all of
the data

thought of as signals of less degraded systems. Continued
improvements to water infrastructure and increased attention
to submerged or in-water habitat quality is likely needed to
further aide fish assemblages in similar highly-modified urban
rivers. Beyond the assessment of assemblage-level changes, our
understanding of urban rivers as their own subset of ecosystem

is sparse (Francis 2012). As Chicago and other urban centers
strive to support fishable waterways (a general condition of The
Clean Water Act; Karr and Dudley 1981), interests may lay in
investigating water quality and habitat variables affecting population vital rates, food web structures, and life history characteristic variations within such urban ecosystems.

 Urban Ecosyst
Acknowledgments We wish to thank the numerous biologists and staff at
MWRD who worked throughout the years to collect this data, in particular: Jennifer Wasik, Thomas Minarik, Justin Vick, and Patrick Kennedy
offered initial conversation, comments, and help with navigating and
cleaning the database. We thank the creative and constructive feedback
provided by two anonymous reviewers which improved the presentation
of the manuscript.

References
Booth DB, Roy AH, Smith B, Capps KA (2016) Global perspectives on
the urban stream syndrome. Freshw Sci 35:412–420
Butts TA, Shackleford DB, Bergerhouse TR (1999) Evaluation of
reaeration efficiencies of sidestream elevated pool aeration (SEPA)
stations. ISWS contract rep CR-653
Connell JH, Sousa WP (1983) On the evidence needed to judge ecological stability or persistence. Am Nat 121:789–824
DeBoer JA, Thoms MC, Casper AF, Delong MD (2019) The response of
fish diversity in a highly modified large river system to multiple
anthropogenic stressors. J Geophys Res Biogeosci 124:384–404.
https://doi.org/10.1029/2018JG004930
Everard M, Moggridge HL (2012) Rediscovering the value of urban
rivers. Urban Ecosyst 15:293–314. https://doi.org/10.1007/s11252011-0174-7
Francis RA (2009) Perspectives on the potential for reconciliation ecology in urban riverscapes. CAB Rev Perspect Agric Vet Sci Nutr Nat
Resour 4:1–20
Francis RA (2012) Positioning urban rivers within urban ecology. Urban
Ecosyst 15:285–291
Francis RA (2014) Urban rivers: novel ecosystems, new challenges.
Wiley Interdiscip Rev Water 1:19–29
Francis RA, Hoggart SPG (2008) Waste not, want not: the need to utilize
existing artificial structures for habitat improvement along urban
rivers. Restor Ecol 16:373–381
Gallagher D, Wasik J (2018) Report No. 18–24 Assessment of South
Branch Chicago River slips using biological sampling, habitat, sediment chemistry, and dissolved oxygen profiling data between 2013
and 2015. Chicago
Gallagher DW, Kollias NJ, Vick JA, et al (2014) Report no. 14-55 ambient water quality monitoring in the Chicago, calumet, and Des
Plaines river systems: a summary of biological sampling, and habitat
assessments during 2012. Chicago
Gaulke GL, Wolfe JR, Bradley DL et al (2015) Behavioral and physiological responses of largemouth bass to rain-induced reductions in
dissolved oxygen in an urban system. Trans Am Fish Soc 144:927–
941
Gibson-Reinemer DK, Chick JH, VanMiddlesworth TD et al (2017a)
Widespread and enduring demographic collapse of invasive common carp (Cyprinus carpio) in the upper Mississippi River system.
Biol Invasions 19:1905–1916
Gibson-Reinemer DK, Sparks RE, Parker JL, DeBoer JA, Fritts MW,
McClelland MA, Chick JH, Casper AF (2017b) Ecological recovery
of a river fish assemblage following the implementation of the clean
water act. Bioscience 67:957–970
Grabarkiewicz JD, Davis WS (2008) An introduction to freshwater fishes
as biological indicators. EPA-260-R-08-016. U.S. environmental
protection Angecy; Office of Environmental Information; Office
of Information Analysis and Access; National Service Center for
Environmental Publications (NSCEP), Washington, D.C.
Greenberg J (2004) A natural history of the Chicago region. University of
Chicago Press, Chicago
Gurnell A, Tockner K, Edwards P, Petts G (2005) Effects of deposited
wood on biocomplexity of river corridors. Front Ecol Environ 3:
377–382

Gurnell A, Lee M, Souch C (2007) Urban rivers: hydrology, geomorphology, ecology and opportunities for change. Geogr Compass 1:
1118–1137
Hill L (2019) The Chicago River: a natural and unnatural history.
Southern Illinois University Press, Carbondale
Holling CS (1973) Resilience and stability of ecological systems. Annu
Rev Ecol Syst 4:1–23
Holloway D, Doll J, Shields R (2018) The temporal effects of heavy
metal contamination on the fish community of the west fork White
River, Delaware County, Indiana, USA. Environ Monit Assess 190:
695
IESPB (2015) Checklist of endangered and threatened. In: October.
http://www.dnr.state.il.us/espb/index.htm. Accessed 7 Nov 2019
IESPB (2019) Minutes of 183rd meeting of the Illinois endangered species protection board. https://www2.illinois.gov/dnr/ESPB/
Documents/Minutes/183 ESPB minutes.Pdf. Accessed 27 Dec 2019
IL-DNR (2018) Exotic species in Illinois. Illinois Department of Natural
Resources. https://www.dnr.illinois.gov/education/Pages/
ExoticsHome.aspx. Accessed 7 Nov 2019
Illinois Coastal Management Program (2011) Illinois Coastal
Management Program Issue Paper: Chicago River and North
Shore Channel Corridors. http://www.chicagoareawaterways.org/
documents/CAWS-UAA-DRAFT-REPORT.pdf. Accessed 30
Dec 2019
Karr JR, Dudley DR (1981) Ecological perspective on water quality
goals. Environ Manag 5:55–68
Laird CA, Page LM (2011) Non-native fishes inhabiting the streams and
lakes of Illinois. Illinois Nat Hist Surv Bull 35:1–51. https://doi.org/
10.5962/bhl.title.50306
Larson MG, Booth DB, Morley SA (2001) Effectiveness of large woody
debris in stream rehabilitation projects in urban basins. Ecol Eng 18:
211–226
Lenth R, Singmann H, Love J (2018) Emmeans: estimated marginal
means, aka least-squares means. R package “emmeans” version
1.4.5
LimnoTech (2010) Chicago area waterway system habitat evaluation and
improvement study: habitat evaluation report. Ann Arbor, MI. URL:
https://mwrd.org/sites/default/files/documents/Habitat_
Improvement_Report_FINAL_1-4-10.pdf
Mapes RL, DuFour MR, Pritt JJ, Mayer CM (2015) Larval fish assemblage recovery: a reflection of environmental change in a large degraded river. Restor Ecol 23:85–93
Matthews WJ, Marsh-Matthews E, Cashner RC, Gelwick F (2013)
Disturbance and trajectory of change in a stream fish community
over four decades. Oecologia 173:955–969. https://doi.org/10.1007/
s00442-013-2646-3
McClelland MA, Sass GG, Cook TR et al (2012) The long-term Illinois
River fish population monitoring program. Fisheries 37:340–350.
https://doi.org/10.1080/03632415.2012.704815
McClelland MA, Irons KS, Sass GG et al (2013) A comparison of two
electrofishing programmes used to monitor fish on the Illinois River,
Illinois, USA. River Res Appl 29:125–133. https://doi.org/10.1002/
rra.1590
Melching CS (2018) Application of a water quality model for determining instream aeration station location and operational rules: a case
study. Water Sci Eng 11:8–16. https://doi.org/10.1016/j.wse.2017.
09.005
MWRD (2019) Stickney water reclamation plant, Metropolitan Water
Reclamation District of Greater Chicago Fact Sheet
Oksanen J (2013) Multivariate analysis of ecological communities in R:
vegan tutorial. R Packag version 17 1–43
Oksanen J (2019) Vegan: an introduction to ordination. https://cran.rproject.org/web/packages/vegan/vignettes/intro-vegan.pdf
Oksanen J, Blanchet FG, Friendly M, et al (2019) “The vegan package.”
Community ecology package. R Package Version 2.5–6. https://
CRAN.R-project.org/package=vegan

 Urban Ecosyst
Olson KR, Morton LW (2017) Chicago’s 132-year effort to provide safe
drinking water. J Soil Water Conserv 72:19A–25A. https://doi.org/
10.2489/jswc.72.2.19A
Parker J, Epifanio J, Casper A, Cao Y (2016) The effects of improved
water quality on fish assemblages in a heavily modified large river
system. River Res Appl 32:992–1007. https://doi.org/10.1002/rra.
2917
Parker J, Cao Y, Sass GG, Epifanio J (2018) Large river fish functional
diversity responses to improved water quality over a 28 year period.
Ecol Indic 88:322–331. https://doi.org/10.1016/j.ecolind.2018.01.
035
Pegg MA, McClelland MA (2004) Spatial and temporal patterns in fish
communities along the Illinois River. Ecol Freshw Fish 13:125–135.
https://doi.org/10.1111/j.1600-0633.2004.00046.x
Perkin JS, Bonner TH (2016) Historical changes in fish assemblage composition following water quality improvement in the mainstem
Trinity River of Texas. River Res Appl 32:85–99. https://doi.org/
10.1002/rra.2852
Pescitelli S, Widloe T (2018) Current Status of Fish Assemblages and the
Sport Fishery in the Des Plaines River Watershed–Changes over 44
years of Basin Surveys. https://www.ifishillinois.org/ssr/2018_Des_
Plaines_River_Basin_Report_FINAL.pdf. Accessed 6 Nov 2019
Poff NL, Allan JD (1995) Functional Organization of Stream Fish
Assemblages in relation to hydrological variability. Ecology 76:
606–627. https://doi.org/10.2307/1941217
Pyron M, Lauer TE, Gammon JR (2006) Stability of the Wabash River
fish assemblages from 1974 to 1998. Freshw Biol 51:1789–1797.
https://doi.org/10.1111/j.1365-2427.2006.01609.x
Pyron M, Mims MC, Minder MM, Shields RC, Chodkowski N, Artz CC
(2019) Long-term fish assemblages of the Ohio River: Altered trophic abundances with hydrologic alterations and land use modifications PLoS One 14:. https://doi.org/10.1371/journal.pone.0211848
R Development Core Team (2020) R: A language and environment for
statistical computing. Version 3.6.3. R Foundation for Statistical
Computing, Vienna, Austria. Https://www.R-project.org/
Rahel F (2010) Homogenization, differentiation, and the widespread alteration of fish faunas. Am Fish Soc Symp 73:311–326
Raibley PT, Irons KS, O’Hara TM et al (1997) Winter habitats used by
largemouth bass in the Illinois River, a large river-floodplain ecosystem. North Am J Fish Manag 17:401–412. https://doi.org/10.
1577/1548-8675(1997)017<0401:whublb>2.3.co;2
Sawyer JA, Stewart PM, Mullen MM, Simon TP, Bennett HH (2004)
Influence of habitat, water quality, and land use on macro-

invertebrate and fish assemblages of a southeastern coastal plain
watershed, USA. Aquat Ecosyst Health Manag 7:85–99. https://
doi.org/10.1080/14634980490281353
Schanze J, Olfert A, Tourbier JT, et al (2004) Existing urban river rehabilitation schemes
Solzman DM (2006) The Chicago River: an illustrated history and guide
to the river and its waterways. University of Chicago, Chicago
Trautman MB (1981) The fishes of Ohio Ohio State University Press.
Columbus, Ohio
Vörösmarty CJ, McIntyre PB, Gessner MO et al (2010) Global threats to
human water security and river biodiversity. Nature 467:555–561.
https://doi.org/10.1038/nature09440
Walsh CJ, Roy AH, Feminella JW, Cottingham PD, Groffman PM,
Morgan RP II (2005) The urban stream syndrome: current knowledge and the search for a cure. J North Am Benthol Soc 24:706–723.
https://doi.org/10.1899/04-028.1
Wang YI, Naumann U, Wright ST, Warton DI (2012) Mvabund–an R
package for model-based analysis of multivariate abundance data.
Methods Ecol Evol 3:471–474
Wang Y, Naumann U, Wright S, et al (2020) Mvabund: statistical
methods for Analysing multivariate abundance data. R package
‘mvabund’ version 4.1.3
Warton DI, Thibaut L, Wang YA (2017) The PIT-trap—A “model-free”
bootstrap procedure for inference about regression models with discrete, multivariate responses. PLoS One 12:e0181790
Weber A, Lautenbach S, Wolter C (2012) Improvement of aquatic vegetation in urban waterways using protected artificial shallows. Ecol
Eng 42:160–167. https://doi.org/10.1016/j.ecoleng.2012.01.007
White K, Gerken J, Paukert C, Makinster A (2010) Fish community
structure in natural and engineered habitats in the Kansas River.
River Res Appl 26:797–805
Whitney JE, Holloway JA, Scholes DT, King AD (2019) Long-term
change of fish communities in a polluted watershed: does cleaner
water “act” on fishes? Trans Am Fish Soc 148:191–206. https://doi.
org/10.1002/tafs.10130
Whitten AL, Gibson-Reinemer DK, MacArthur R et al (2018) Tracking
the trajectory of change in large river fish communities over 50 Y.
Am Nat 180:25–36. https://doi.org/10.1674/0003-0031-180.1.98
Willink PW, Widloe TA, Santucci VJ et al (2018) Rapid expansion of
banded killifish Fundulus diaphanus across northern Illinois: dramatic recovery or invasive species? Am Midl Nat 179:179–190.
https://doi.org/10.1674/0003-0031-179.2.179