U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2020–5035

Prepared in cooperation with the Milwaukee Metropolitan Sewerage District

Ecological Status of Aquatic Communities in Selected 

Streams in the Milwaukee Metropolitan Sewerage District 

Planning Area of Wisconsin, 2004–13
Cover. Photograph showing the Milwaukee River at Milwaukee, Wisconsin (U.S. Geological Survey 

station 04087000), looking upstream from the falls near the U.S. Geological Survey streamgage in 

Estabrook Park, taken by Michelle Nott, U.S. Geological Survey, June 23, 2007.
Ecological Status of Aquatic Communities 

in Selected Streams in the Milwaukee 

Metropolitan Sewerage District Planning 

Area of Wisconsin, 2004–13

By Barbara C. Scudder Eikenberry, Michelle A. Nott, Jana S. Stewart, Daniel J. 

Sullivan, David A. Alvarez, Amanda H. Bell, and Faith A. Fitzpatrick

Prepared in cooperation with the Milwaukee Metropolitan Sewerage District

Scientific Investigations Report 2020–5035

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DAVID BERNHARDT, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2020

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Suggested citation:

Scudder Eikenberry, B.C., Nott, M.A., Stewart, J.S., Sullivan, D.J., Alvarez, D.A., Bell, A.H., and Fitzpatrick, F.A., 2020, 

Ecological status of aquatic communities in selected streams in the Milwaukee Metropolitan Sewerage District 

planning area of Wisconsin, 2004–13: U.S. Geological Survey Scientific Investigations Report 2020–5035, 84 p., 

https://doi.org/ 10.3133/ sir20205035.

Associated data for this publication: 

Scudder Eikenberry, B.C., Nott, M.A., Stewart, J.S., Sullivan, D.J., Fitzpatrick, F.A., Bell, A.H., and Olds, H.T., 2020, 

Aquatic community and environmental data for 14 rivers and streams in the Milwaukee Metropolitan Sewerage 

District Planning Area, 2004–13: U.S. Geological Survey data release, https://doi.org/10.5066/P9FWMODL.

U.S. Geological Survey, 2016, USGS water data for the Nation: U.S. Geological Survey National Water Information 

System database, https://doi.org/10.5066/F7P55KJN.

ISSN 2328-0328 (online)
iii

Acknowledgments

Funding was provided by the Milwaukee Metropolitan Sewerage District (MMSD) with 

Cooperative Matching Funds by the U.S. Geological Survey (USGS). We thank MMSD employees 

Chris Magruder, Matt Magruder, Beth Sauer, and Eric Waldmer. Additional thanks to Beth Sauer 

for providing MMSD water-quality data summaries for ecological sampling years 2004–13.

The Academy of Natural Sciences in Philadelphia, under the supervision of Don Charles and 

Frank Acker, identified and counted algal taxa. The Aquatic Biomonitoring Laboratory at the 

University of Wisconsin-Stevens Point (Stevens Point, Wisconsin), under the supervision of 

Stanley Szcztyko and Jeffrey Dimick, identified and counted invertebrate taxa. Semipermeable 

membrane device dialyses and extract preparations were done by Terri Spencer with EST Labs, 

St. Joseph, Missouri; the USGS Columbia Environmental Research Center completed Microtox 

and Fluoroscan tests on extracts; David R. Johnson and Choo Yaw Ang completed cytochromeP450 reporter gene system toxicity tests on semipermeable membrane device extracts at the 

U.S. Army Corps of Engineers, Engineer Research and Development Center—Waterways 

Experiment Station in Vicksburg, Mississippi.

Many USGS employees assisted with data collection over the years, including Austin K. 

Baldwin, Cheryl A. Buchwald, Nicolas H. Buer, Dean Burdett, Daniel J. Burns, Rebecca B. 

Carvin, Mitchell A. Harris, Jennifer L. Hogan, Krista A. Hood, Ryan T. Jirik, Leah E. Kammel, 

James L. Kennedy, Bernard N. Lenz, S. Bridgett Manteufel, Kassidy T. Mapel, Hayley T. Olds, 

Mark L. Olson, Kevin D. Richards, Laura L. Rozamulski, David A. Saad, Denis P. Scanlan, Jeffery 

J. Steuer, Judith C. Thomas, Rebecca H. Woll, and Benjamin M. Young. Kassidy T. Mapel 

also assisted with compilation of water-quality data, and Hayley T. Olds also computed light 

extinction coefficients. Daren M. Carlisle computed additional invertebrate metrics. Jessica L. 

Thompson computed annual discharge metrics from USGS streamgage data. Sara B. Levin and 

Edward G. Dobrowolski provided technical comments, and Janet M. Carter provided technical 

and editorial comments on an earlier version of the report.

v

Contents

Acknowledgments........................................................................................................................................iii

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................2

Study Areas............................................................................................................................................3

Methods...........................................................................................................................................................6

Data Collection ......................................................................................................................................7

Data Analysis.........................................................................................................................................8

Assessment of Aquatic Communities in Relation to Stream Condition ..............................................10

Comparative Bioassessment across Sampled Streams ..............................................................10

Algae............................................................................................................................................10

Invertebrates ..............................................................................................................................26

Fish ...............................................................................................................................................27

Comparative Bioassessment among Algae, Invertebrates, and Fish ........................................49

Physical and Chemical Stressors at Sampled Sites .....................................................................49

Toxicity and Chemical Assessment with Passive Sampling Devices ...............................49

Relations between Biological Metrics and Environmental Stressors ..............................52

Algae ...................................................................................................................................52

Invertebrates .....................................................................................................................64

Fish ......................................................................................................................................65

Summary Bioassessments of Individual Streams .........................................................................66

Milwaukee River near Cedarburg ...........................................................................................66

Lincoln Creek ..............................................................................................................................67

Milwaukee River at Milwaukee ...............................................................................................68

Willow Creek...............................................................................................................................69

Menomonee River at Menomonee Falls ................................................................................70

Little Menomonee River ............................................................................................................70

Underwood Creek ......................................................................................................................71

Honey Creek................................................................................................................................72

Menomonee River at Wauwatosa ..........................................................................................73

Kinnickinnic River ......................................................................................................................74

Oak Creek ....................................................................................................................................74

Root River at Greenfield ............................................................................................................75

Root River near Franklin ...........................................................................................................76

Jewel Creek ................................................................................................................................77

Summary and Conclusions .........................................................................................................................77

References Cited..........................................................................................................................................79
vi

Figures

1. Map showing sites where biological assessments were completed in 2004–13 

in the Milwaukee Metropolitan Sewerage District planning area of Wisconsin ..............4

2. Multidimensional scaling ordination plot for algal assemblages collected at 

14 sites in the Milwaukee area, Wisconsin, 2004–13 ...........................................................11

3. Bar plots showing selected algal metrics for each of 14 stream sites in the 

Milwaukee area, Wisconsin, 2004–13 .....................................................................................21

4. Map showing pollution-sensitive diatom algae scores at 14 stream sites in the 

Milwaukee area, Wisconsin, 2004–13 .....................................................................................25

5. Multidimensional scaling ordination plot for invertebrate assemblages 

collected at 14 sites in the Milwaukee area, Wisconsin, 2004–13 .....................................32

6. Bar plots showing selected invertebrate metrics for each of the 14 stream sites 

in the Milwaukee area, Wisconsin, 2004–13 ..........................................................................33

7. Map showing invertebrate Hilsenhoff Biotic Index scores, modified to limit the 

number of individuals per taxon to 10 for index computation, for fall samples 

at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning 

area, Wisconsin, 2004–13 ..........................................................................................................37

8. Multidimensional scaling ordination plot for fish assemblages collected at 14 

sites in the Milwaukee area, Wisconsin, 2004–13 ................................................................43

9. Bar plots showing selected fish metrics for each of the 14 stream sites in the 

Milwaukee area, Wisconsin, 2004–13 .....................................................................................44

10. Map showing fish Index of Biotic Integrity scores for fall samples at 14 stream 

sites in the Milwaukee Metropolitan Sewerage District planning area, 

Wisconsin, 2004–13 ....................................................................................................................48

11. Graphs showing relations between algal metrics and environmental metrics for 

14 streams in the Milwaukee area, Wisconsin, 2004–13 .....................................................54

12. Graphs showing relations between invertebrate metrics and environmental 

metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13 .................................58

13. Graphs showing relations between fish metrics and environmental metrics for 

14 streams in the Milwaukee area, Wisconsin, 2004–13 .....................................................61

Tables

1. U.S. Geological Survey stream sites where biological assessments were 

completed in 2004–13 in the Milwaukee Metropolitan Sewerage District 

planning area of Wisconsin, showing drainage area .............................................................5

2. Algal-assemblage information from surveys completed in 2004, 2007, 2010, 

and 2013 at 14 stream sites in the Milwaukee Metropolitan Sewerage District 

planning area, Wisconsin ..........................................................................................................12

3. Comparison of algal-assemblage data at 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area, Wisconsin, 2004–13 ................................17

4. Water-quality ratings for the invertebrate Hilsenhoff Biotic Index and 

macroinvertebrate Index of Biotic Integrity for streams .....................................................27

5. Comparison of invertebrate-assemblage data at 14 stream sites in the 

Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–13 ...........28
vii

6. Scores and ratings for the fish Index of Biotic Integrity for warmwater streams ...........38

7. Comparison of fish-assemblage data at 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area, Wisconsin, 2004–13 ................................39

8. Mean trophic-level rankings and aggregate bioassessment rankings for 

14 stream sites in the Milwaukee area, Wisconsin, 2013 and 2004 ...................................50

9. Results for toxicity tests and selected chemical analyses of passive sampling 

devices deployed at 10 of 14 sites in the Milwaukee area, Wisconsin, 2004–13 .............51

10. Summary of environmental metrics correlated to metrics for algae, 

invertebrates, and (or) fish in streams of the Milwaukee Metropolitan 

Sewerage District planning area of Wisconsin, 2004–13 ....................................................64

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

inch (in) 2.54 centimeter (cm)

inch (in) 25.4 millimeter (mm)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2)

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

International System of Units to U.S. customary units

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in)

meter (m) 3.281 foot (ft)

liter (L) 1.057 quart (qt)

liter (L) 0.2642 gallon (gal)

Area

square centimeter (cm2) 0.001076 square foot (ft2)

square centimeter (cm2) 0.1550 square inch (ft2)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as 

°F = (1.8 × °C) + 32.
viii

Supplemental Information

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm 

at 25 °C).

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L), 

micrograms per liter (μg/L), or nanograms per liter (ng/L).

A water year is the 12-month period from October 1 to September 30 and is designated 

by the year in which it ends; for example, water year 2015 was from October 1, 2014, to 

September 30, 2015.

Abbreviations

BOD5 biological oxygen demand, 5 day

CFU colony forming units

DO dissolved oxygen

EPA U.S. Environmental Protection Agency

EPT Ephemeroptera-Plecoptera-Trichoptera invertebrate taxa

HBI Hilsenhoff Biotic Index

HBI–10 Hilsenhoff Biotic Index, modified to limit the number of individuals per taxon to 10 for 

index computation (also known as the 10-Max BI)

IBI Index of Biotic Integrity

MDS multidimensional scaling

mIBI macroinvertebrate Index of Biotic Integrity

MMSD Milwaukee Metropolitan Sewerage District

NAWQA National Water-Quality Assessment

NLCD National Land Cover Database

P450RGS cytochrome-P450 reporter gene system toxicity test

PAH polycyclic aromatic hydrocarbon compound

PBDE polybrominated diphenyl ether compound

PCB polychlorinated biphenyl compound

SPMD semipermeable membrane device

TEQ toxic equivalent related to an SPMD extract

TU50 toxicity unit related to an SPMD extract concentration causing a 50-percent 

reduction in bacterial light production

USGS U.S. Geological Survey
Ecological Status of Aquatic Communities in Selected 

Streams in the Milwaukee Metropolitan Sewerage 

District Planning Area of Wisconsin, 2004–13

By Barbara C. Scudder Eikenberry, Michelle A. Nott, Jana S. Stewart, Daniel J. Sullivan, David A. Alvarez, 

Amanda H. Bell, and Faith A. Fitzpatrick

Abstract

A total of 14 wadable streams in urban or urbanizing 

watersheds near Milwaukee, Wisconsin, were sampled in 

2004, 2007, 2010, and 2013 to assess the ecological status 

of aquatic communities (biota), including benthic algae and 

invertebrates, and fish. To assess temporal variation, additional community sampling was also done at a subset of three 

sites in 2011 and 2012. Relative abundances of each type of 

organism were used to calculate biological metrics, such as 

richness and diversity, percentages of intolerant and tolerant 

organisms, and indexes of biotic integrity for invertebrates and 

fish. Selected environmental (physical and chemical) data in 

the streams were collected to evaluate potential relations to 

the biota and the ecological health of the stream. Physical and 

chemical data included land use/land cover, stream discharge 

from U.S. Geological Survey (USGS) streamgages (except 

at 2 creeks that were not gaged), stream habitat, microhabitat 

at invertebrate collection locations, water quality (except at 

2 creeks that were not gaged), field measurements of several 

water-quality constituents, measures of benthic algal biomass, and toxicity and chemical tests on extracts from passive 

samplers deployed at a subset of 6 sites. Relative abundances 

of organisms and biological metrics were compared among 

sampling years and with environmental metrics to evaluate 

the ecological status of these streams and determine primary 

stressors on the aquatic communities, with the aim of helping 

resource managers understand and work toward improving 

the ecological health of these and other urban and urbanizing 

rivers in the study area.

Biological metrics for most sites indicated some level 

of diminished ecological status when compared across all sampled sites and when compared with rating scales for selected 

metrics. The least degraded sites among all those sampled—

indicated by aggregate bioassessments for algae, invertebrates, 

and fish metrics and in order starting with the best overall 

condition—were the Milwaukee River near Cedarburg, 

Menomonee River at Menomonee Falls, Jewel Creek, and 

Milwaukee River at Milwaukee. The most degraded sites were 

Menomonee River at Wauwatosa, Root River at Greenfield, 

Lincoln Creek, and the Kinnickinnic River. Differences in 

aggregate bioassessments indicate that aquatic communities at 

the Menomonee River at Wauwatosa site and the Root River 

at Greenfield site were worse in 2013 than in 2004; however, 

Oak Creek and Honey Creek sites were better. In 2013, several 

sites had less than 30-percent pollution-sensitive diatoms 

indicating degraded algal assemblages. Invertebrate metrics 

for most of the 14 sites in 2013 were lower than in 2004 and 

indicate that invertebrate assemblages at most sampled sites 

were more degraded in 2013. Tolerant fish taxa made up 

more than 40 percent of assemblages at most sites and nearly 

100 percent of assemblages at four sites. At times, in some 

smaller streams, too few fish were captured to compute an 

Index of Biotic Integrity with confidence, and invertebrates 

provided a better means for assessing the ecological status and 

water quality. With these few exceptions, the use of all three 

groups of biota provided the most robust assessments at the 

14 sites in 2004–13.

Physical and chemical stressors were correlated to 

adverse effects on aquatic biota at the sampled streams. 

Passive samplers were deployed at a subset of six sites in 

2013. Microtox results indicated there was little or no toxicity at the Milwaukee River near Cedarburg site and at the Oak 

Creek site, slight toxicity at the Lincoln Creek and Honey 

Creek sites, and moderate toxicity at the Milwaukee River at 

Milwaukee site and the Little Menomonee River site; however, based on cytochrome-P450 reporter gene system toxicity 

tests, potential toxicity from hydrophobic organic contaminants was measured at all six sites. For all 14 sites, physical and chemical stressors related to urbanization correlated 

with biological metrics for algae, invertebrates, and fish. 

Most stressors for aquatic biota reflected an urban signature. 

Stressors related to ecological condition in our study were 

chemical and physical, such as developed land, impervious 

surface in the watershed, urban land in a buffer area around the 

stream (a 100-foot [30-meter]-wide area on each side of the 

stream, and maximum instantaneous discharge normalized by 

drainage area (a measure of flood and scour effects). Chemical 

stressors included low waterborne concentrations of dissolved 
2 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

oxygen and high concentrations of chloride, zinc and other 

metals, nutrients (nitrite and phosphorus), and fecal coliform 

bacteria.

Although algae, invertebrates, and fish did not always 

demonstrate a significant response to the same stressors, 

higher abundances of high total phosphorus-indicator diatoms, 

lower ratings for invertebrate biotic integrity indexes and percentages of mayflies-stoneflies-caddisflies, and lower values 

for fish biotic integrity indexes underscored possible adverse 

effects of even low levels of developed land. Developed land 

is typically associated with more rapid runoff, which washes 

chemicals from impervious surfaces into area waterways and 

degrades stream habitat for aquatic communities. However, 

with respect to at least chloride from road salt, diatoms tolerant to dissolved salts were significantly lower with as little as 

1-percent mixed forest in the watershed. Lower percentages 

of urban land in the stream buffer correlated with healthier 

aquatic assemblages of algae, invertebrates, and fish. The 

assessment of algal, invertebrate, and fish assemblages 

coupled with physical and chemical data were highly useful 

in evaluating the ecological status of aquatic communities at 

the 14 sites and for determining environmental stressors that 

may be contributing to reduced stream condition. Some of the 

stressors could potentially be removed or lessened with stream 

rehabilitation or changes in watershed management.

Introduction

With increasing urbanization in many areas of the 

United States and elsewhere, the resulting changes in 

stream discharge, water quality, and habitat can degrade 

streams and resident aquatic biota including algae, invertebrates, and fish (Paul and Meyer, 2001; Walsh and others, 

2005; U.S. Environmental Protection Agency, 1997, 2006; 

Southeastern Wisconsin Regional Planning Commission and 

others, 2007; Coles and others, 2009, 2012; Richards and others, 2010). Streams in different areas of the country may not 

respond in the same way to the same environmental stressors 

because of underlying differences in watershed size, land use/

land cover, agricultural practices, soil chemistry, and topography (Buck and others, 2004; Coles and others, 2012). For this 

reason, long-term (years or even decades long) monitoring of 

the biological, chemical, and physical characteristics of stream 

sites provides a means to assess the relative importance of different stressors on the aquatic communities of selected streams 

in relation to local climate, soils, and other key environmental 

settings.

Multiple lines of evidence provided by biological, chemical, and physical data are critical in developing an understanding of how different land uses can adversely affect aquatic 

communities and how such effects might be mitigated through 

watershed management actions. An evaluation of the environmental stressors affecting aquatic communities requires 

monitoring of constituents in sufficient detail and frequency to 

be able to relate differences in constituents to differences in the 

aquatic communities. As land surfaces become urbanized, they 

are covered by less pervious surfaces such as developed open 

spaces and are more affected by impervious surfaces such as 

rooftops and paved areas, including roads, driveways, and 

parking lots (Schueler, 1994). Contaminants accumulate on 

impervious surfaces. When large amounts of rain fall on these 

surfaces, there are few, if any, porous and natural vegetated 

surfaces available to allow rainfall to soak into the ground, and 

chemicals and debris are therefore rapidly washed into local 

waterbodies. Increased sediment carried into streams during 

storms can smother aquatic organisms and fish spawning areas 

(Waters, 1995); other stream areas can be scoured of fine sediment. Rapid runoff can also lead to flooding and sudden peaks 

in stream discharge (referred to as “flashiness”) with powerful 

erosion effects on habitat in the stream channel and on resident 

aquatic biota (Coles and others, 2012). Even low percentages (10 percent or less) of impervious surface in a watershed 

can have substantial adverse effects on aquatic biota in local 

waterbodies (Schueler, 1994; Arnold and Gibbons, 1996; 

Richards and others, 2010).

Aquatic biota are good indicators of stream water quality 

and overall stream condition even though they may differ in 

their responses to various environmental stressors (Richards 

and others, 2010; Scudder Eikenberry and others, 2010; 

Coles and others, 2012). Benthic organisms—biota attached 

to rocks, woody snags, and other substrates on the bottom or 

sides of the stream—are often regarded as the best sentinels 

for changes in water and sediment quality because of their 

site fidelity and their proximity to any contaminated sediment 

that may be present. Benthic algae reproduce quickly, living 

from days to weeks, and can indicate short-term changes in 

their environment. Diatom algae are especially good indicators 

because they are ubiquitous in aquatic environments, most can 

be identified to species, and their tolerances to a broad range 

of environmental conditions have been well studied. Benthic 

invertebrates, such as clams, snails, and the larvae of many 

insects, are also good indicators of water quality because of 

their relatively longer lifespans of months to years in comparison to algae, their mostly stationary nature that makes them 

indicative of site-specific conditions, and species-specific 

tolerances to environmental conditions. In general, fish have a 

longer lifespan and are more mobile than invertebrates, so fish 

can be potentially indicative of stream condition integrated 

over multiple years within a larger area such as a watershed. 

For these reasons, 3 groups of aquatic biota (algae, invertebrates, and fish) were collected to facilitate a more complete 

and robust assessment of stream condition at 14 sites in southeastern Wisconsin.

Purpose and Scope

The purpose of this report is to summarize 

U.S. Geological Survey (USGS) assessments of the ecological status of aquatic communities in selected wadable streams 
Introduction 3

in the Milwaukee Metropolitan Sewerage District (MMSD) 

planning area in Wisconsin and implications for water quality in the streams. The assessment also included evaluations 

of potential physical and chemical stressors on the aquatic 

communities. The scope of the report includes data collected 

in 2010–13 (referred to as “phase IV”) with comparisons to 

data collected in 2007 (referred to as “phase III”) and 2004 

(referred to as “phase II”) (Schneider and others, 2004; 

Thomas and others, 2007; Scudder Eikenberry and others, 2010).

Aquatic communities were assessed at 14 stream sites 

based on the biological assemblage data and on selected 

biological measures (metrics) computed from these data. 

The potential level of toxicity to aquatic biota from synthetic 

organic compounds is estimated for a subset of six sites where 

passive sampling devices (semipermeable membrane devices 

[SPMDs]) were deployed. In addition, an analysis of selected 

chemical concentrations in SPMDs was completed for a timeintegrated concentration of the bioavailable fraction of polycyclic aromatic hydrocarbon compounds (PAHs). SPMD results 

are compared with biological assemblage data at sampled 

sites. Water-quality data from MMSD, stream discharge and 

water-quality data from USGS streamgages, land-use/landcover data, stream habitat, and measurement of ancillary data 

(pH, specific conductance, light attenuation, and invertebrate 

microhabitat characterization) during ecological sampling 

events were evaluated as potential environmental stressors to 

aquatic biota in the study streams.

Study Areas

All stream sites were within the MMSD planning area 

(fig. 1 and table 1). The mouth of the Milwaukee River 

receives water from the Milwaukee, Menomonee, and 

Kinnickinnic River watersheds in addition to water from Lake 

Michigan (by way of reverse flow). Oak Creek and Root River 

discharge directly into Lake Michigan south of the Milwaukee 

Harbor. Jewel Creek ultimately discharges into the Mississippi 

River by way of the Fox and Illinois Rivers. Aquatic biological communities were sampled at the same 14 sites during 

2004–13.

The site at the Milwaukee River near Cedarburg, 

Wis. (USGS station 04086600; hereafter referred to as the 

“Milwaukee River near Cedarburg site” or MRC), has probably the least visible disturbance of all sampled streams, 

and its biological communities support this observation. The 

lightly stained waters of this stream flow over a substrate of 

cobble and boulder with diverse habitats and, having generally 

good water quality, provide suitable habitat for a large number 

and variety of species of biota. This watershed drains about 

607 square miles (mi2) of mostly agriculture land (56 percent) 

and some urban land (12 percent), including two moderatesized cities; agricultural land decreased by about 1 percent 

since 2004 as development increased. Cedar Creek is a 

major tributary to the Milwaukee River and has a confluence 

1.25 miles (mi) upstream from the sampling site.

At the Lincoln Creek at 47th Street at Milwaukee, Wis., 

site (USGS station 040869415; hereafter referred to as the 

“Lincoln Creek site” or LCM), a major stream-restoration 

project was completed in 2002 and encompassed the sampling reach. Before the 2004 sampling, the USGS completed 

sampling using the same methods used in 1993–5 (Peters and 

others, 1998). The restoration project included restructuring the channel and removing and replacing the streambed; 

all riparian vegetation was removed to allow for the major 

channel restructuring and streambank replacement. Canopy 

cover was minimal, even in 2013 in the sampling reach. These 

substantial modifications to the aquatic habitat contributed to 

ecological changes at this site independent of direct waterquality changes, and biota continue to adapt to the changed 

habitat. This is a small and highly urban stream, of which 

94 percent is total urban, most of which is low- and mediumintensity developed land. Urban land makes up 65 percent of 

the stream buffer (a 100-foot [ft; 30-meter]-wide area on each 

side of the stream), one of the three highest values for urban 

land together with Honey Creek and the Kinnickinnic River. 

This small stream has endured decades of use by industry 

with legacy chemical contamination and downstream effects 

as well (Wisconsin Department of Health Services, 2005; 

Epping Overholt, 2014). Lincoln Creek joins the Milwaukee 

River about 1 mi upstream from the Milwaukee River at 

Milwaukee, Wis., sampling site (USGS station 04087000; 

hereafter referred to as the “Milwaukee River at Milwaukee 

site” or MRM).

The Milwaukee River at Milwaukee site has the largest 

area of all the MMSD study watersheds, draining 696 mi2. The 

sampling site is in Estabrook Park and immediately downstream from Estabrook Dam, removed in 2018, and a large 

forested area on both banks. The watershed integrates a large 

northern area of mixed agriculture (51 percent), forest (14 percent) and low-density urban land with parts of the greater 

Milwaukee metropolitan urban area for a total of 18-percent 

urban land. Despite the urban setting, the river at this site supports quite a diverse aquatic community, including freshwater 

mussels and salmon traveling upstream from Lake Michigan.

Willow Creek at Maple Road, near Germantown, 

Wis., (USGS station 040870195; hereafter referred to as the 

“Willow Creek site” or WCG) is a small watershed of about 

6 mi2 that drains a wooded wetland area in the northwest part 

of the MMSD planning area. Agricultural land, which makes 

up 46 percent of the watershed, is slowly being converted 

to urban land, as urban areas increased by about 1.5 percent 

between 2001 and 2011. Willow Creek is a sand/silt-bottomed 

stream with abundant woody snags but no riffles or rock 

cobbles. For this reason, woody snags and not riffle rocks were 

sampled for algal and invertebrate samples at this site only. 

Although algal and invertebrate assemblages on woody snags 
4 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

Linnie Lac

EXPLANATION

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

Phase II–IV biologysampling site

Honey Wauwat Milwaukee

osa (HCW)

Root River

at Grange Avenue

at Greenfiel

Menomonee River

at Wauwatosa

Milwaukee River

at Milwauk

Milwaukee River

near Cedarburg

ak Creek

at South Milwauk

Oak Creek

at South Milwaukee

Jewel Creek

at Muskego at Muskego

Honey Creek at 

Wauwatosa

Willow Creek at Maple Road

near Germantown

Willow Creek at Maple Road,

near Germantown

Lincoln Creek

at 47th Street

at Milwaukee

Lincoln Creek

at Milwaukee

Underwood Creek

at Wauwatosa

Underwood Creek

at Wauwatosa

Kinnickinnic River

at S. 11th Street at Milwaukee

Kinnickinnic River

at South 11th Street at Milwaukee

Little Menomonee River

at Milwaukee

Root River

near Frankli

Root River

near Franklin

Root River

at Grange Avenue

at Greenfield

Menomonee River

at Wauwatosa

Milwaukee River

at Milwaukee

Milwaukee River

near Cedarburg

Menomonee River

at Menomonee Falls

Menomonee River

at Menomonee Falls

Fox River

Root River

Milwaukee River

Menomonee

River

Rock River

Oak Creek

Kinnickinnic

River

Direct 

Tributary

Direct 

Tributary

Lake 

Michigan

Direct

88°10' 87°50'

42°50'

43°10'

LAKE MICHIGAN

0 42 MILES

0 42 KILOMETERS

Base modified from Southeastern Wisconsin Regional Planning Commission regional base map, 1:2,000, 1995 

U.S. Geological Survey digital line graph hydrography, 1:100,000, 1989

Wisconsin Department of Natural Resources version 2 hydrography, 1:24,000, 2002

Wisconsin Transverse Mercator projection, referenced to North American Datum of 1983, 1991 adjustment

[MMSD, Milwaukee Metropolitan 

Sewerage District]

Milwaukee

ESTABROOK 

DAM

Little

Muskego

Lake

Little

Muskego

Lake

WISCONSIN

MICHIGAN

ILLINOIS

IOWA

MINNESOTA

MMSD

planning area

Figure 1. Sites where biological assessments were completed in 2004–13 in the Milwaukee Metropolitan Sewerage District 

planning area of Wisconsin.
Introduction 5

will often be different from assemblages on rocks, this report 

focused more on identifying any long-term changes at this site 

than comparing this site with other sampled sites.

The Menomonee River at Menomonee Falls, Wis., 

site (USGS station 04087030; hereafter referred to as the 

“Menomonee River at Menomonee Falls site” or MRMF) 

drains about 35 mi2 and is gradually changing from largely 

agricultural to more urban (41 and 36 percent, respectively) 

land use. The Menomonee River at Menomonee Falls is in a 

suburban setting in the middle of the city of Menomonee Falls. 

There is a narrow riparian zone of forest that provides partial 

shade adjacent to a public walkway and immediately upstream 

from a city road and city park. A series of riffles, runs, and 

pools on a natural substrate provides habitat for a variety of 

fish and invertebrates.

The Little Menomonee River at Milwaukee, Wis., site 

(USGS station 04087070; hereafter referred to as the “Little 

Menomonee River site” or LMM) is a mostly turbid and 

shaded reach in greenspace within an urban-industrial area 

and adjacent public access, which has resulted in a large 

amount of urban waste including shopping carts, tires, and 

so on being deposited in the stream channel. The watershed 

is relatively small at 20 mi2 and is about 4 mi downstream 

from a Superfund site (Moss-American Superfund site) where 

remediation of creosote and PAHs was completed in 2010 

(U.S. Environmental Protection Agency, 2010). The ecological sampling site is about 1.5 mi upstream from the confluence 

with the Menomonee River. Just less than half (46 percent) 

of the watershed is urban, and 33 percent is agricultural. Tree 

canopy provides partial to complete shade of the stream reach. 

The only riffle in the reach is at the most upstream end of the 

reach, immediately downstream from a railroad bridge.

The Underwood Creek watershed is also small at about 

18 mi2 and is 90-percent urban, although most of the urban 

land is developed low-intensity land and developed open 

land (parks). The Underwood Creek at Wauwatosa, Wis., 

site (USGS station 04087088; hereafter referred to as the 

“Underwood Creek site” or UCW) is mostly concrete-lined 

channel with natural substrate at the most downstream end of 

the reach, about 0.1 mi upstream from its confluence with the 

Menomonee River and adjacent to the Hansen Golf Course. 

Frequent and powerful high flows created an ever-enlarging 

scour pool immediately downstream from the concrete boundary and off the right bank. Invertebrate and algal samples were 

collected mostly in the concrete part but also in the cobble 

riffle adjacent to the large pool. In 2011, a large stormwater 

detention pond was completed immediately upstream between 

Underwood Creek Parkway and Swan Boulevard to help mitigate water and sediment from large rainfall-runoff events, and 

removal of the concrete in this reach began in November 2016 

(Daniel, 2017) and was completed in August 2018 (Marty 

Melchior, Interfluve, Inc., written commun., February 7, 

2019). For Underwood Creek in 2004 only, the data used 

were those collected about 3 mi upstream on the creek at 

Underwood Creek at Watertown Plank Road at Elm Grove, 

Wis. (USGS station 040870856), as part of the USGS National 

Table 1. U.S. Geological Survey stream sites where biological assessments were completed in 2004–13 in the Milwaukee Metropolitan 

Sewerage District planning area of Wisconsin, showing drainage area.

[Milwaukee Metropolitan Sewerage District water-quality site numbers are listed where water-quality data were obtained for ecological sampling years. USGS, 

U.S. Geological Survey; MMSD, Milwaukee Metropolitan Sewerage District; SPMD, semipermeable membrane device; mi2, square mile; WI, Wisconsin; NC, 

not characterized; S., South]

USGS station 

number Site name Site abbreviation

MMSD water-quality 

site number

SPMDs deployed 

(year)

Drainage 

area 

(mi2)

04086600 Milwaukee River near Cedarburg, WI MRC RI–01 2007, 2010, 2013 607

040869415 Lincoln Creek at 47th Street at Milwaukee, WI LCM LC–04 2007, 2010, 2013 9.56

04087000 Milwaukee River at Milwaukee, WI MRM RI–04 2010, 2013 696

040870195 Willow Creek at Maple Road, near Germantown, WI WCG None NC 6.33

04087030 Menomonee River at Menomonee Falls, WI MRMF RI–16 NC 34.7

04087070 Little Menomonee River at Milwaukee, WI LMM ML–02 NC 19.7

04087088 Underwood Creek at Wauwatosa, WI UCW UC–07 NC 18.2

04087119 Honey Creek at Wauwatosa, WI HCW HC–03 2007, 2010, 2013 10.3

04087120 Menomonee River at Wauwatosa, WI MRW RI–09 NC 123

04087159 Kinnickinnic River at S. 11th Street at Milwaukee, WI KRM RI–13 2007 18.8

04087204 Oak Creek at South Milwaukee, WI OCSM OC–05 2007, 2010, 2013 25.0

04087214 Root River at Grange Avenue at Greenfield, WI RRG RR–04 NC 14.7

04087220 Root River near Franklin, WI RRF RR–05 NC 49.2

05544371 Jewel Creek at Muskego, WI JCM None NC 8.16
6 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

Water-Quality Assessment (NAWQA) Program using the same 

methods as the current study. In 2007, data collection was 

moved to the present site adjacent to the Hansen Golf Course.

The Honey Creek at Wauwatosa, Wis., site (USGS station 04087119; hereafter referred to as the “Honey Creek site” 

or HCW) is near the confluence with the Menomonee River 

and about 0.5 mi upstream from the Menomonee River at 

Wauwatosa site. A small watershed (about 10 mi2), it is nearly 

100-percent urban and mostly low and medium-intensity 

urban land. The reach is in a suburban area along a parkway, 

having only a narrow riparian area (vegetated area along the 

streambank) and a high value of 72-percent urban land in the 

stream buffer. The effects of high-powered storm runoff are 

evident in eroding and collapsing streambanks and associated 

fallen trees with log jams; nevertheless, multiple riffles and 

generally shallow depths over natural substrate provide good 

habitat for invertebrates and fish.

The Menomonee River at Wauwatosa, Wis., site (USGS 

station 04087120; hereafter referred to as the “Menomonee 

River at Wauwatosa site” or MRW) is near the confluence of 

Honey Creek and about 2 mi downstream from its confluence 

with Underwood Creek. The watershed is moderate in size 

at 123 mi2 and is composed of 19-percent agricultural land 

and 65-percent urban land, with a relatively high percentage of urban land in the stream buffer (24 percent). The site 

was moved in 2007 from between 68th and 70th Streets to 

immediately upstream from 70th Street because of problems 

with access and wading after the original reach was restored 

in 2006. Abundant riffles were available for algal and invertebrate sampling at this site. Stream-restoration efforts completed in 2016 removed the final remaining fish barriers in this 

river to allow fish to migrate from Lake Michigan upstream to 

Menomonee Falls.

The Kinnickinnic River, a small watershed with a drainage area of about 19 mi2, is nearly 100-percent urban land 

and more than 50-percent mean impervious surface. Although 

most of the urban land is low and medium intensity, this 

watershed has more high-intensity urban land than any of 

the other watersheds sampled (17 percent in 2013). This site 

has 74-percent urban land in the stream buffer, the highest 

for all sites. The Kinnickinnic River at South 11th Street at 

Milwaukee, Wis., site (USGS station 04087159; hereafter 

referred to as the “Kinnickinnic River site” or KRM) is a generally straight concrete channel with shallow flow most of the 

time. Extreme high flows during some rain events transport 

sediment and debris that scour the concrete channel and likely 

harm or remove aquatic organisms. Algal and invertebrate 

samples were collected at concrete seams and immediately 

upstream from the weir at the streamgage, where small bits of 

concrete and debris accumulate; these small areas were potentially the richest habitat in the reach. MMSD plans call for the 

concrete to be removed and a more natural channel constructed (Milwaukee Metropolitan Sewerage District, 2020).

The Oak Creek at South Milwaukee, Wis., site (USGS 

station 04087204; hereafter referred to as the “Oak Creek 

site” or OCSM) has a small watershed with a drainage area of 

about 25 mi2 and mostly urban land use, which increased from 

62 percent in 2001 to 68 percent in 2011 and was accompanied by a decrease in agricultural land and an increase in mean 

impervious surface from 26 to 29 percent. Oak Creek drains 

directly into Lake Michigan about 3 mi downstream from the 

sampling site. General Mitchell International Airport is in the 

headwaters of the watershed. The streambed is mostly cobble 

and gravel with areas of sand. The main riffle was immediately 

upstream from the bridge on 15th Avenue, and a smaller riffle 

was present, at times, in the upstream part of the reach.

The Root River is mostly urban in the headwaters, with 

93-percent urban land at the Root River at Grange Avenue 

at Greenfield, Wis., site (USGS station 04087214; hereafter 

referred to as the “Root River at Greenfield site” or RRG), 

and then the watershed transitions to more agricultural in the 

lower watershed with only 40-percent urban land overall at the 

Root River near Franklin, Wis., site (USGS station 04087220; 

hereafter referred to as the “Root River near Franklin site” or 

RRF); however, the area by the Root River near Franklin site 

is rapidly urbanizing. The stream is also small at Greenfield 

(14.7 mi2) and medium in size near Franklin (about 49 mi2). 

In most years, the only riffle for sampling at Greenfield was 

immediately downstream from the bridge at Grange Avenue, 

in part because of low water levels during sampling but 

also because of a general lack of cobble in the rest of the 

reach. Large cobble riffles with freshwater mussel beds were 

sampled near the USGS streamgage at the Root River near 

Franklin site.

Jewel Creek, at about 8 mi2, is similar in size to Willow 

Creek and lies between two small lakes. Linnie Lac is a small 

lake about 0.1 mi upstream from the Jewel Creek at Muskego, 

Wis., site (USGS station 05544371; hereafter referred to as the 

“Jewel Creek site” or JCM); Jewel Creek then flows into Little 

Muskego Lake less than 0.5 mi downstream from the sampling site. About 40 percent of the watershed is urban, mostly 

low-intensity urban and developed open space, and 25 percent 

of the watershed is agricultural; nevertheless, mean impervious surface was 13 percent in 2013 and, therefore, above the 

10-percent threshold where adverse effects might be observed 

on aquatic organisms (Richards and others, 2010). Streamrestoration work before the start of sampling in 2004 resulted 

in much of the substrate being composed of large rip rap and 

cobble rock riffles present only at the bottom and top of the 

reach where algae and invertebrates were collected.

Methods

Biological samples were collected once in 2004, 2007, 

2010, and 2013, generally during periods of stable low flow 

when problems with wading were minimized. However, 

beginning July 15, 2010, heavy rains inundated the area and 

peaked on July 22, 2010, when the Milwaukee area received 

about 7 inches of rain in just a few hours (National Weather 

Service, 2010). Widespread flooding of historic proportions 
Methods 7

occurred, and one of the hardest hit areas was along Lincoln 

Creek. All ecological sampling in 2010 was postponed for 

4–5 weeks to allow streams to return to stable flows and to 

provide some time for algal, invertebrate, and fish assemblages 

to recover. To provide a measure of seasonal and temporal 

variability, algal and invertebrate assemblages were sampled 

in spring and fall (late May–June and late August–September) 

in 2011, 2012, and 2013. This information was essential for 

assessing the importance of long-term changes in aquatic communities at individual sites and ultimately for a more complete 

assessment of differences among sites.

Data Collection

Algal, invertebrate, and fish assemblage samples were 

collected in a defined stream reach (492–1,190 ft in length, 

depending on mean stream width) according to standard 

USGS methods documented in Moulton and others (2002)

and Scudder Eikenberry and others (2010). Algal and invertebrate samples were collected concurrently during late August 

or September in each sampling year in the same general area 

of each reach (riffles), and fish were collected July through 

October in each sampling year. Riffles were chosen for algae 

and invertebrates because they are readily identifiable, tend to 

be more uniform than other stream habitats, have generally the 

highest oxygen concentration, and are shallow and wadable 

(Karr and Chu, 1999).

Algal-assemblage samples were collected from a known 

area on cobble in riffle areas, except for Willow Creek 

samples, which were collected from woody snags because 

riffle rocks were not available in this sand and silt substrate 

stream. At each site, 5 discrete collections from riffle rocks 

(or 2 discrete collections for snags) were made at each of 

5 locations and combined into a single composited algal 

sample to represent that site. An aliquot of the algal composite 

sample was removed for analysis of chlorophyll a (Arar and 

Collins, 1997) and ash-free dry mass (Britton and Greeson, 

1987) at the USGS National Water Quality Laboratory in 

Denver, Colorado. Samples for identification were preserved 

to 5 percent (volume per volume) with formalin buffered to 

a pH of 7. The Academy of Natural Sciences in Philadelphia, 

Pennsylvania, identified and counted algae at the lowest practical taxonomic level (generally species or genus) and determined algal biovolume in all samples.

Except for 1 site, the Willow Creek, invertebrate assemblages were collected from 5 discrete cobble riffles in each 

reach using a modified Surber sampler with a 500-micronmesh net. All five subsamples were then combined into a 

single composite sample for each site (Moulton and others, 

2002). At Willow Creek, where cobble riffles were unavailable, 10 discrete invertebrate collections were made from 

woody snags and combined into a single composite sample. 

Samples were preserved with 10-percent formalin buffered 

to a pH of 7; samples were later transferred to 70-percent 

ethanol before analysis by the laboratory. Identification and 

enumeration of invertebrates (generally species or genus) 

for all samples were done by the Aquatic Biomonitoring 

Laboratory at the University of Wisconsin-Stevens Point 

(Stevens Point, Wis.).

Representative fish assemblage sampling was completed at each site using backpack-mounted or towed-barge 

electrofishing units, depending on stream size or width, and 

seines (Moulton and others, 2002). A total of 2 electrofishing 

passes of the sampling reach were supplemented with 3 seine 

hauls per site. Fish were identified to the lowest practical 

taxonomic level (generally species), counted, noted for any 

anomalies, and then released live back to the stream. Rarely, 

when a fish could not be identified with certainty in the field, 

a few representative individuals were preserved for laboratory 

identification.

Stream habitat for the reach was assessed once in each 

sampling year, generally in late summer or early fall, except 

for 2007 when instream reach data were not collected because 

of funding constraints. Each habitat assessment included data 

collection at the reach, transect, and transect point levels. 

Reaches were established at each site using guidance from 

standard protocols used by the USGS NAWQA Program 

(Fitzpatrick and others, 1998) and ranged in length from 492 

to 1,190 ft. Each reach was divided into 11 transects, along 

which more detailed data describing the physical stream channel were collected. Core data were collected across all years 

in accordance with the USGS NAWQA protocol. Beginning in 

2010, additional measurements were added to these core habitat measurements to better quantify the physical conditions of 

each stream (Young and others, 2015).

Mean concentrations for selected water-quality constituents in whole (unfiltered) water samples were provided 

by MMSD for each year of biological sampling (Beth Sauer, 

MMSD, written commun., July 15, 2015); data were collected 

by MMSD at or near the ecological sampling sites except 

for the Lincoln Creek site, which was sampled by USGS in 

2004–10 (no data for 2013), and for the Willow Creek and 

Jewel Creek sites in all years. Water samples collected by 

MMSD were discrete samples from the middle of the stream 

channel or where most of the discharge was occurring and, 

depending on conditions, from one depth (middepth) or two 

depths (1 m below the water surface and 1 m above the stream 

bottom; Milwaukee Metropolitan Sewerage District, 2013).

Discharge data were collected according to standard USGS methods (Rantz and others, 1982) at USGS 

streamgages near each of the ecological sampling sites, except 

for the Willow Creek and Jewel Creek sites where there were 

no nearby USGS streamgages. Water depth and velocity 

were recorded at each invertebrate microhabitat on the day of 

invertebrate sample collections. Light extinction coefficients, 

a measure of light penetration to the stream bottom, were 

obtained on the day of sampling and before other sampling 

components using a LI-COR light meter (Moulton and others, 

2002). Surface-water field measurements, including water 
8 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

temperature, pH, and specific conductance (conductivity), 

were collected concurrently with ecological sampling using a 

multiparameter sonde.

To quantify potential toxicity from hydrophobic organic 

chemicals (PAHs, polychlorinated biphenyls [PCBs], dioxins and furans, chlorinated pesticides, and polybrominated 

diphenyl ether compounds [PBDEs]), passive samplers 

(SPMDs) were deployed in duplicate for about 1 month at a 

subset of the 14 sites as described in Scudder Eikenberry and 

others (2010). The following sites were sampled in 2010 and 

2013: Milwaukee River near Cedarburg, Milwaukee River at 

Milwaukee, Lincoln Creek, Little Menomonee River, Honey 

Creek, and Oak Creek at South Milwaukee, Wis. (USGS station 04087204; hereafter referred to as the “Oak Creek site”). 

In 2007, the Kinnickinnic River site and not the Milwaukee 

River at Milwaukee site was included in the sampling. The 

Milwaukee River at Milwaukee site was added beginning in 

2010, before the planned sediment remediation of an area of 

PCB contamination about 1 mi upstream at Lincoln Park at 

the confluence of Lincoln Creek with the Milwaukee River 

(Lincoln Creek and the west oxbow of the Milwaukee River). 

The SPMDs deployed were 15.2-centimeter mini-SPMDs 

with ultrahigh-pure triolein inside protective metal containers, 

purchased from Environmental Sampling Technologies (EST 

Labs; St. Joseph, Missouri). One additional SPMD per site 

served as a “field blank” or field quality-assurance sample and 

was never deployed into the stream. To measure possible airborne contamination during deployment and retrieval, the cannister for each field blank was opened when the sample SPMD 

cannister was opened for deployment, and it was closed when 

the sample SPMD was placed in the water (total time less 

than 1 minute). For retrieval, the field blank cannister was 

opened when the sample SPMD was brought out of the water 

into air, and it was closed when the sample SPMD cannister 

was closed with the sample SPMD inside. The field blank 

data were used to determine the validity of any observed toxic 

response in the deployed SPMDs. After deployment, chemicals in the SPMDs were extracted for toxicity tests and PAH 

screening. One set of extracts was sent to the USGS Columbia 

Environmental Research Center (Columbia, Mo.) for Microtox 

toxicity tests and fluorescence test PAH screening. The 

Microtox test screens the extracts for acute toxicity from synthetic organic chemicals using strains of bioluminescent bacteria (Strategic Diagnostics, Inc., Newark, Delaware). When 

exposed to a toxicant, the rate of light production is reduced in 

proportion to the sample toxicity. The fluorescence screen for 

PAHs was completed by measuring the fluorescence of chemicals in the sample based on Johnson and others (2004). The 

PAH pyrene was targeted as a surrogate for all PAHs because 

pyrene is a commonly detected PAH in urban settings and is 

a good marker for determining PAH occurrence. A second 

set of extracts was sent to the U.S. Army Corps of Engineers, 

Engineer Research and Development Center—Waterways 

Experiment Station (Vicksburg, Mississippi) for cytochromeP450 reporter gene system (P450RGS) toxicity testing. The 

P450RGS test detects the presence of and potential biological 

response to PAHs, PCBs, dioxins and furans and was completed according to U.S. Environmental Protection Agency 

(EPA) Method 4425 using strains of bioluminescent hepatoma 

cells (Ang and others, 2000).

Data Analysis

Aquatic communities were evaluated by examining the 

number and kinds of organisms (taxa), number of individuals, 

pollution tolerance, and other traits. Many algal metrics have 

been developed by researchers over decades that are useful 

for characterizing water quality and stream condition based 

on environmental tolerances of algal taxa, especially diatoms 

(see summary by Porter [2008]). Algal metrics computed for 

the current study included the number of taxa (“richness”), 

the relative proportion of each algal group (including diatoms) out of all algal taxa, the percentage of eutrophic algae 

(diatoms and nondiatom or “soft” algae), and additional 

metrics specific to diatoms, including tolerances to nitrogen 

and phosphorus, dissolved oxygen (DO), chloride or salinity, and pollution in general (Lange-Bertalot, 1979; Bahls, 

1993; Potapova and Charles, 2007; Porter, 2008). Diversity 

indexes quantify the number of taxa (“richness”) present 

and the evenness in abundances across all species; that is, 

heterogeneity. For algae, Bahls (1993) diversity ratings for 

diatoms in low-gradient streams range from less than 1.5 

(“high stress,” low richness with highly uneven abundance), 

1.50–2.50 (“moderate stress”), and 2.51–3.50 (“minor stress”) 

to greater than 3.50 (“no stress,” high richness with mostly 

even abundance). “High stress” corresponds to few taxa and 

a low number (“abundance”) of individuals except for one 

or two taxa that dominate; “no stress” corresponds to many 

taxa and a relatively even abundance across most or all taxa. 

Computed metrics for invertebrate samples included the number of invertebrate taxa; Shannon index of diversity (Shannon, 

1948); the percentage of invertebrate individuals or genera in 

the orders Ephemeroptera-Plecoptera-Trichoptera (EPT); the 

percentage of invertebrates that are noninsects (leeches, oligochaetes, spiders and mites, nematodes, flatworms, springtails, 

amphipods, crayfish, isopods, and mollusks); scraper (algal 

grazer) invertebrates; the Hilsenhoff Biotic Index (HBI), the 

HBI modified to limit the number of individuals per taxon 

to 10 for index computation (HBI–10 hereafter, also known 

as the 10-Max BI; Hilsenhoff, 1987, 1998); and the macroinvertebrate Index of Biotic Integrity (mIBI) for Wisconsin 

(Weigel, 2003). EPT invertebrates generally are considered 

to be relatively intolerant of degraded water quality (Lenat, 

1988); however, some species of mayflies and caddisflies are 

moderately tolerant. Intolerant (pollution-sensitive) organisms tend to dominate in streams with good water quality and 

habitat, whereas pollution-tolerant organisms dominate in 

streams with degraded water quality and habitat; therefore, 

the percentages of EPT individuals and of EPT genera tend to 

decrease as water quality degrades. Although the percentage 

of noninsects tends to increase with declines in water quality; 
Methods 9

native freshwater mussels, if present, contribute to the noninsect count even though they are considered to be indicative 

of good water quality. The HBI or HBI–10 is a multimetric 

(derived from multiple metrics) that relates water quality to 

the relative abundances of invertebrates that are tolerant or 

sensitive to environmental degradation. A modification of 

the HBI, the HBI–10, was used in the phase II and phase III 

analyses; the HBI–10 is thought to be more accurate than the 

HBI because it is less affected by the dominance of a single 

taxon (Hilsenhoff, 1998). HBI–10 scores can range from less 

than 3.5 (“excellent”) to 10 (“very poor”), and therefore, 

lower HBI–10 scores indicate a better rating and higher scores 

indicate a worse rating. Values for the mIBI, a multimetric 

derived from 11 invertebrate metrics, also can range from 0.00 

to 10.00, but its ratings are opposite of those of the HBI or 

HBI–10 (Weigel, 2003). Assemblage information and metrics for invertebrate samples were provided by the Aquatic 

Biomonitoring Laboratory at the University of WisconsinStevens Point (Stevens Point, Wis.). Metrics computed for fish 

assemblages included the number of species and individuals, 

native fish species, predator fish, number of fish in certain 

groups such as sunfishes and suckers, pollution-sensitive and 

pollution-tolerant fish, and fish Index of Biotic Integrity (IBI) 

for Wisconsin warmwater streams (Lyons, 1992). The fish 

IBI is a multimetric derived from a series of 10 metrics and is 

standardized to 100 such that scores range from 60 or greater 

(“excellent”) to 0 (“very poor”).

A subset of six metrics consisting of some for each group 

of biota were selected to represent the status of each group 

(algae, percentage of most tolerant diatoms and percentage of 

sensitive diatoms; invertebrates, Shannon index of diversity 

scores, percentage of EPT taxa, and HBI–10 scores; fish, IBI 

score). Metrics were selected because of their known sensitivity to water quality and to provide the most complete assessment for each group using multimetrics where possible. These 

metrics were standardized (ranked, lowest rank indicating best 

water quality) and averaged for each biotic assemblage. The 

means of these ranks were then averaged across all assemblages to yield aggregate bioassessment rankings for each 

site. Sites were divided into four groups based on quartiles of 

these aggregate bioassessment rankings: (group 1) less than 

the 25th percentile; (group 2) equal to or greater than the 25th 

but less than the 50th percentiles; (group 3) equal to or greater 

than the 50th but less than the 75th percentiles; and (group 4) 

greater than or equal to the 75th percentile. Group 1 contained 

sites at which aggregate bioassessment rankings indicated 

the least degraded water quality among those sampled, and 

group 4 contained sites at which rankings indicated the most 

degraded water quality.

Physical data were evaluated by calculating representative values for ecological sampling site conditions, by site 

and year. Stream habitat metric calculations were largely 

consistent in content and approach with the metrics outlined 

in Richards and others (2010); the only metric omitted here 

was the streambed substrate index (BedSubIndex) because it 

seemed to be of little use compared with the other metrics. 

In augmentation to Richards and others (2010), all bankfull 

metrics were calculated with and without pool transects (this 

included calculating the metrics with pools [bankfull width 

divided by drainage area and bankfull depth divided by drainage area] and the metrics without pools [bankfull shear stress 

and critical particle size for insipient motion]). Additionally, 

all habitat metrics present for the sites in the USGS BioData database (available at https://aquatic.biodata.usgs.gov/

landing.action) were used. Additional metrics, including mean 

silt depth, velocity multiplied by wetted depth (related to 

discharge), coefficient of variation for bed substrate size, and a 

mixed graphical and arithmetic approach of mean bed substrate size (Trask, 1932; Bunte and Abt, 2001; the sum of the 

25th and 75th quantiles divided by two), were included.

Stream discharge metrics (in cubic feet per second) 

were computed using data from USGS streamgages. Selected 

metrics were calculated for the years of ecological sampling, 

including discharge exceeded 10 percent of the time, discharge exceeded 50 percent of the time, maximum daily mean 

discharge, minimum daily mean discharge, and maximum 

instantaneous discharge, and were standardized by drainage 

area. In addition, mean discharge conditions on the day of 

sample collection were also calculated using data from USGS 

streamgages. Where available, unit values were used to calculate mean flows for the 4 hours after the sample start time, 

otherwise precalculated daily values were used. No discharge 

data were available for the Willow Creek and Jewel Creek 

sites but discharge data for the other sites listed in table 1 are 

available using the USGS station number from the USGS 

National Water Information System database (U.S. Geological 

Survey, 2016).

A geographic information system was used to summarize land cover and percentage of impervious statistics for 

each ecological sampling site using National Land Cover 

Database (NLCD) 2006 and 2011 datasets (U.S. Geological 

Survey, 2014). Data from the NLCD 2001 dataset were used 

to characterize conditions for the 2004 ecological samples, 

data from the NLCD 2006 dataset were used for the 2007 

ecological samples, and data from the 2011 dataset were used 

to characterize conditions for ecological samples collected 

from 2010 to 2013. In summarizing land-cover statistics, total 

urban land was considered the sum of the developed landcover categories (codes 21–24) and total agricultural land was 

considered the sum of the agricultural land-cover categories 

(codes 81–82). The percentage of impervious statistics for 

each site were based on the NLCD Percent Imperviousness 

dataset, generated from the LANDSAT imagery (Xian and 

others, 2011). The NLCD data were converted to a grid file 

before analyzing for the percentage of impervious statistics by 

watershed. Additionally, land-cover statistics were determined 

for the stream buffer at each site by generating a 200-ft-wide 

area (“60-meter stream buffer”), 100-ft (30-meter)-wide area 

on each side of the hydrographic lines, beginning at the most 

upstream point in the watershed and extending downstream 

to the bottom of the sampling reach, and summarizing data 
10 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

from the NLCD 2011 dataset. Total urban land in the stream 

buffer was considered the sum of the low, medium, and highintensity urban land-cover categories (codes 22–24).

SPMD results for Microtox and P450RGS were standardized to 30 days to allow comparison across sites, and 

concentrations of chemicals determined in the PAH screen 

were standardized using the mean number of days deployed 

(37). Microtox results are reported in terms of EPA toxicity 

units (TU50s), which are determined by dividing 100 by the 

effective concentration of the SPMD extract that caused a 

50-percent reduction in light production by the bacteria. For 

the Fluoroscan fluorescence screen, total PAH water concentrations were estimated using pyrene as a representative 

common PAH. Results are presented as the estimated timeweighted average water concentration for all constituents with 

available uptake kinetics (sampling rates) from the literature 

(Alvarez and others, 2008).

Statistical methods used in data analyses included basic 

descriptive statistics, such as means and quartiles, graphing, 

and Spearman’s rank correlation coefficient or “rho” (Data 

Desk version 6.1; Data Description Inc., 1996). Microsoft 

Excel and SigmaPlot 11.0 were used for creating bar plots and 

scatterplots, respectively. Unless otherwise stated, use of the 

term “significant” refers to statistical values of probability (p) 

less than (<) 0.05 in data comparisons. Multivariate statistical 

analyses to examine patterns in the relative abundances of taxa 

were done using routines in the PRIMER 6 software (Clarke 

and Gorley, 2006), including multidimensional scaling (MDS). 

MDS represents objects, such as samples, in plots of two or 

three dimensions where dissimilar objects plot far apart and 

similar objects plot close together. Before multivariate testing, 

taxa relative abundances were determined, and a Bray-Curtis 

similarity matrix was calculated from a fourth-root transformation of relative abundance data. A fourth-root transformation decreases the effects of common taxa and increases 

the effects of intermediate and rare taxa such that more taxa 

have an effect in the final multivariate analyses (Clarke and 

Warwick, 2001). The Bray-Curtis similarity matrices then 

formed the basis of MDS analyses.

Assessment of Aquatic Communities in 

Relation to Stream Condition

Algal, invertebrate, and fish assemblages provided valuable insight into the overall condition of the studied streams 

over the period of study by differences in the abundances of 

various taxa and by sensitivities to disturbance and pollution 

as measured through the computed biological metrics and correlations of metrics to environmental stressors. The following 

sections first provide a comparison across streams for each 

group of biota, followed by SPMD results at a subset of sites, 

relations to environmental stressors across all sites, and finally, 

individual stream summaries. Biological results for 2004 and 

2007 are discussed in detail in Scudder Eikenberry and others 

(2010). All data generated during this study are available as a 

USGS data release (Scudder Eikenberry and others, 2020).

Comparative Bioassessment across Sampled 

Streams

Bioassessments at the 14 study streams revealed the 

importance of sampling multiple groups of aquatic organisms 

and computing multiple biological measures or metrics for 

each group. Some metrics proved more comprehensive for 

evaluating the ecological health of sites, and these included 

metrics composed of several metrics (multimetric indexes). 

The strength and utility of multimetric indexes have been well 

described by numerous researchers in the literature (Karr, 

1981; Hilsenhoff, 1982; Lyons, 1992; Karr and Chu, 1999). 

Differences between years for a single metric could not be 

tested statistically because of the study design of one sample 

per year (or two per year in a few cases); therefore, references 

to one or more metrics being higher or lower at one or more 

sites are numerical and not statistical statements.

Algae

Algal assemblages varied in the abundance and distribution of taxa across years at sites, and the variation was greater 

at some sites than at others. This within-site variation is 

illustrated by an MDS plot where more similar assemblages 

are represented as points grouped closely together and less 

similar assemblages are represented as points more distant to 

each other (fig. 2). Notably, assemblages grouped on the right 

side of the plot for 2004 and 2007 and on the left side of the 

plot for later years. Upon closer examination on a site-by-site 

basis, fall algal assemblages were similar to each other in 2004 

and 2007 but were greatly different in 2010. In 2013, algal 

assemblages returned to a structure more similar to 2007 and 

less so to 2004. For sites with additional sampling in spring 

and fall in 2011 to 2013, the assemblages in fall 2010 and 

spring and fall 2011 were more similar to each other than 

to other years. The assemblages in fall 2012 and 2013 were 

more similar to each other than to 2010 or 2011. Spring and 

fall assemblages for a single year generally grouped together 

at each temporal site; nevertheless, MDS results indicate a 

large part of the variability was because of differences in 

the assemblages in 2010 and 2011, possibly because of the 

extreme flooding during 2010 in many area streams. The general grouping by year evident in the algal MDS plot indicates 

that some of the variability in the algal assemblages can be 

explained by large-scale effects like weather that dominate the 

whole region, as opposed to site-specific factors.

The number of algal taxa collected at each site (richness) 

varied across years and was generally higher in 2013 than in 

2004 (table 2). A total of 199 algal taxa were collected across 

all sites in 2013, compared with 177 taxa that were collected 

in 2004. The median number of taxa was higher in 2013 
MRCLCMMRMWCGMRMFLMMUCWHCWMRWKRMOCSMRRGRRFJCM

Site abbre

[MRC, Milwaukee River near CeCreek at 47th Street at MilwaukRiver at Milwaukee; WCG, Willonear Germantown; MRMF, MenoMenomonee Falls; LMM, Little MMilwaukee; UCW, Underwood CHCW, Honey Creek at WauwatoRiver at Wauwatosa; KRM, Kinn11th Street at Milwaukee; OCSMMilwaukee; RRG, Root River at GGreenfield; RRF, Root River near Creek at Muskego; SP, spring sa

EXPLANAT

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Two-dimensional stress=0.24

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2007 2004

Figure 2. Multidimensional scaling ordination plot for algal assemblages collected at 14 sites in the Milwaukee area, Wisconsin, 2004–13. [The sampas 04, 07, 10, 11, 12, and 13 for 2004, 2007, 2010, 2011, 2012, and 2013] 
Table 2. Algal-assemblage information from surveys completed in 2004, 2007, 2010, and 2013 at 14 stream sites in the Milwaukee Metropolitan SeweWisconsin. [The percentage of nuisance algae is the sum of benthic and sestonic algal producers (Porter, 2008); the percentage of eutrophic diatoms is the sum of mesotrophic-eutrophic, euphic diatoms (van Dam and others, 1994); the percentage of relative abundance of diatoms is based on Bahls (1993). The percentage of difference in metric values between 2013 and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, and blue denotes a potentially beneficial difference; and gray denotes a microliter; cm2, square centimeter; USGS, U.S. Geological Survey; --, no data or not applicable] Sampling year Number of taxa Biovolume (μL/cm2×106) Cell density (cells/cm2×106) Shannon index of diversity Nuisance algae (percent) Percentage of relative abundance of diatom

Eutrophic Pollution tolerant Pollution moderate Pollution sensitive Pollution tolerance unknown Halobion

diatom

Milwaukee River near Cedarburg (USGS station 04086600) 2004 48 5,251 3.1 0.93 0.14 77.5 1.33 16.5 63.2 19.0 22.5 

2007 50 29,944 81 1.75 0.041 93.0 23.3 37.3 32.3 7.01 28.0 

2010 63 8,582 9.4 1.80 0.21 89.8 13.2 43.8 36.3 6.67 25.5 

2013 55 97,276 4.0 2.10 1.1 92.5 11.0 31.8 53.7 3.50 16.0 

Difference 15 1,752 26 130 1.0 15.0 9.67 15.3 −9.50 −15.5 −6.50 

Lincoln Creek at 47th Street at Milwaukee (USGS station 040869415) 2004 37 28,893 16 0.74 0 90.6 8.87 71.1 12.6 7.39 66.7 

2007 40 53,118 16 1.59 1.2 92.3 27.7 46.0 19.5 6.87 42.1 

2010 39 1,503 8.2 1.74 0 89.2 25.5 50.5 14.3 9.67 48.2 

2013 55 13,155 17 2.11 0 94.3 26.8 44.5 25.2 3.50 40.3 

Difference 49 −54.5 6.9 184 0.0 3.69 18.0 −26.6 12.5 −3.89 −26.3 

Milwaukee River at Milwaukee (USGS station 04087000) 2004 70 166,650 5.4 1.47 0 88.7 5.75 38.1 44.7 11.5 17.9 

2007 57 2,608 6.9 2.01 0.65 92.4 11.7 46.1 35.7 6.49 34.7 

2010 72 1,140 5.3 1.93 0 75.0 14.2 38.7 34.3 12.8 25.2 

2013 61 607.2 3.5 1.60 0 89.8 16.0 43.5 35.0 5.50 15.2 

Difference −13 −99.6 −36 8.34 0.0 1.16 10.0 5.40 −9.66 −5.99 −2.73 
Table 2. Algal-assemblage information from surveys completed in 2004, 2007, 2010, and 2013 at 14 stream sites in the Milwaukee Metropolitan SeweWisconsin.—Continued [The percentage of nuisance algae is the sum of benthic and sestonic algal producers (Porter, 2008); the percentage of eutrophic diatoms is the sum of mesotrophic-eutrophic, euphic diatoms (van Dam and others, 1994); the percentage of relative abundance of diatoms is based on Bahls (1993). The percentage of difference in metric values between 2013 and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, and blue denotes a potentially beneficial difference; and gray denotes a microliter; cm2, square centimeter; USGS, U.S. Geological Survey; --, no data or not applicable]

Sampling 

year

Number 

of taxa

Biovolume 

(μL/cm2×106)

Cell density 

(cells/cm2×106)

Shannon 

index of 

diversity

Nuisance 

algae 

(percent)

Percentage of relative abundance of diatom

Eutrophic Pollution tolerant Pollution moderate Pollution sensitive Pollution tolerance unknown Halobion

diatom

Willow Creek at Maple Road, near Germantown (USGS station 040870195)

2004 45 251.9 0.44 2.42 0 73.8 13.2 13.8 65.2 7.83 7.2 

2007 43 4,170 1.5 2.00 0.39 94.2 16.1 35.4 42.5 5.93 22.6 

2010 50 181.6 1.2 2.22 0 85.8 5.67 37.0 36.8 20.5 11.5 

2013 44 56.4 0.37 2.31 0 95.0 14.2 26.2 37.8 21.8 13.8 

Difference −2.2 −77.6 −16 −4.69 0.0 21.2 1.00 12.3 −27.3 14.0 6.67 

Menomonee River at Menomonee Falls (USGS station 04087030)

2004 36 520.0 3.4 1.62 0 92.4 5.43 33.7 53.5 7.40 32.7 

2007 32 506.6 3.0 1.53 0 95.3 2.28 6.03 85.7 6.03 4.07 

2010 59 284.4 1.0 2.20 0 83.9 8.97 25.2 53.2 12.6 13.1 

2013 37 23,300 5.1 1.80 0.20 93.5 7.67 30.2 56.2 6.00 22.5 

Difference 2.8 4,381 51 11.3 0.20 1.07 2.24 −3.55 2.71 −1.40 −10.2 

Little Menomonee River at Milwaukee (USGS station 04087070)

2004 31 409.6 4.7 1.66 0 92.6 5.72 53.3 33.3 7.68 49.0 

2007 30 3,307 16 2.04 0 96.2 26.2 31.4 39.0 3.35 30.2 

2010 45 836.4 12 2.11 0.43 89.2 11.2 65.3 15.0 8.50 55.0 

2013 41 910.8 10 2.25 0 94.7 11.0 27.2 58.5 3.33 20.0 

Difference 32 122.3 120 35.4 0.0 2.02 5.28 −26.1 25.2 −4.35 −29.0 

Underwood Creek at Wauwatosa (USGS station 04087088)

2004 42 769.4 12 0.81 0.66 90.2 9.33 41.5 45.0 4.17 28.0 

2007 35 1,148 13 1.55 0 93.4 10.6 67.0 15.7 6.77 58.1 

2010 48 573.4 4.2 2.36 1.7 89.0 6.33 72.0 12.3 9.33 59.7 

2013 45 37,024 2.2 1.84 0.74 95.8 11.8 62.2 23.7 2.33 55.8 

Difference 7.1 4,712 −81 129 0.09 5.67 2.50 20.7 −21.3 −1.83 27.8 
Table 2. Algal-assemblage information from surveys completed in 2004, 2007, 2010, and 2013 at 14 stream sites in the Milwaukee Metropolitan SeweWisconsin.—Continued [The percentage of nuisance algae is the sum of benthic and sestonic algal producers (Porter, 2008); the percentage of eutrophic diatoms is the sum of mesotrophic-eutrophic, euphic diatoms (van Dam and others, 1994); the percentage of relative abundance of diatoms is based on Bahls (1993). The percentage of difference in metric values between 2013 and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, and blue denotes a potentially beneficial difference; and gray denotes a microliter; cm2, square centimeter; USGS, U.S. Geological Survey; --, no data or not applicable] Sampling year Number of taxa Biovolume (μL/cm2×106) Cell density (cells/cm2×106) Shannon index of diversity Nuisance algae (percent) Percentage of relative abundance of diatom

Eutrophic Pollution tolerant Pollution moderate Pollution sensitive Pollution tolerance unknown Halobion

diatom

Honey Creek at Wauwatosa (USGS station 04087119) 2004 35 57.4 0.12 1.71 0 96.0 8.33 60.0 28.7 3.00 37.3 

2007 29 21,965 8.6 1.55 0.38 98.3 8.41 70.5 19.4 1.68 51.7 

2010 43 16,964 2.4 2.34 1.6 98.8 19.7 72.8 6.50 1.00 61.2 

2013 41 19,813 1.2 2.13 12 98.2 12.3 57.7 29.3 0.67 49.3 

Difference 17 34,400 890 24.8 12 2.17 4.00 −2.33 0.67 −2.33 12.0 

Menomonee River at Wauwatosa (USGS station 04087120) 2004 36 1,241 21 1.15 0 93.1 8.36 58.7 27.9 5.08 51.6 

2007 32 3,752 12 1.67 8.4 96.8 11.1 76.3 9.42 3.19 73.7 

2010 44 694.1 7.4 2.61 5.8 70.0 11.7 49.2 11.5 27.7 43.8 

2013 42 57,086 5.5 1.36 4.2 89.0 11.0 73.7 7.50 7.83 70.2 

Difference 17 4,500 −74 19.0 4.2 −4.11 2.64 15.0 −20.4 2.75 18.5 

Kinnickinnic River at South 11th Street at Milwaukee (USGS station 04087159) 2004 37 277.4 3.2 1.41 0 80.4 28.3 41.3 19.3 11.1 40.8 

2007 26 4,417 2.4 1.42 0.26 98.9 15.9 22.6 60.1 1.44 11.9 

2010 40 12,521 3.0 2.55 2.9 85.5 29.0 35.0 23.0 13.0 16.8 

2013 38 31,309 1.1 1.58 3.5 94.8 17.0 67.2 11.7 4.17 61.3 

Difference 2.7 11,190 −66 12.0 3.5 14.5 −11.3 25.9 −7.63 −6.98 20.6 

Oak Creek at South Milwaukee (USGS station 04087204) 2004 37 445.7 4.3 2.08 0 94.0 8.75 52.2 31.0 8.10 48.6 

2007 48 3,565 2.7 2.76 0 94.9 15.7 45.2 24.8 14.4 27.9 

2010 61 57,285 5.5 2.61 1.5 87.5 4.83 48.0 28.2 19.0 25.3 

2013 63 1,711 2.6 2.50 0 94.5 5.03 40.0 45.5 9.50 22.3 

Difference 70 283.9 −41 20.2 0.0 0.50 −3.75 −12.2 14.5 1.40 −26.3 
Table 2. Algal-assemblage information from surveys completed in 2004, 2007, 2010, and 2013 at 14 stream sites in the Milwaukee Metropolitan SeweWisconsin.—Continued [The percentage of nuisance algae is the sum of benthic and sestonic algal producers (Porter, 2008); the percentage of eutrophic diatoms is the sum of mesotrophic-eutrophic, euphic diatoms (van Dam and others, 1994); the percentage of relative abundance of diatoms is based on Bahls (1993). The percentage of difference in metric values between 2013 and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, and blue denotes a potentially beneficial difference; and gray denotes a microliter; cm2, square centimeter; USGS, U.S. Geological Survey; --, no data or not applicable]

Sampling 

year

Number 

of taxa

Biovolume 

(μL/cm2×106)

Cell density 

(cells/cm2×106)

Shannon 

index of 

diversity

Nuisance 

algae 

(percent)

Percentage of relative abundance of diatom

Eutrophic Pollution tolerant Pollution moderate Pollution sensitive Pollution tolerance unknown Halobion

diatom

Root River at Grange Avenue at Greenfield (USGS station 04087214)

2004 28 1,018 2.3 0.72 0 92.0 5.83 38.7 43.3 12.2 24.0 

2007 30 1,476 3.2 1.95 0 98.9 3.76 24.4 56.0 15.9 16.9 

2010 62 432.9 1.1 2.24 0 90.2 3.83 34.8 49.7 11.7 13.8 2013 70 469.9 2.0 2.23 0 84.8 7.83 25.8 49.2 17.2 19.0 

Difference 150 −53.9 −13 210. 0.0 −7.15 2.00 −12.8 5.83 5.00 −5.00 

Root River near Franklin (USGS station 04087220)

2004 33 946.9 3.2 1.24 0 94.8 17.0 15.8 60.5 6.67 14.0 

2007 49 2,690 6.1 3.01 0 90.8 10.3 29.7 47.4 12.5 14.5 

2010 51 618.3 5.2 2.03 0 86.5 11.2 27.0 50.3 11.5 8.83 2013 63 1,611 2.9 2.16 0.81 88.7 7.83 29.7 52.5 10.0 16.8 

Difference 91 70.2 −7.9 75.0 0.81 −6.17 −9.17 13.8 −8.00 3.33 2.83 

Jewel Creek at Muskego (USGS station 05544371)

2004 40 1,472 2.7 2.17 0 78.8 3.00 11.7 67.2 18.2 12.7 

2007 50 4,075 8.5 2.18 0 85.9 1.82 17.4 65.5 15.3 10.6 

2010 65 44,710 2.7 2.53 2.5 89.7 4.50 27.7 60.0 7.83 7.83 

2013 69 91,031 4.8 2.09 0.76 90.5 6.67 19.8 66.0 7.50 9.00 

Difference 73 6,086 74 −3.83 0.76 11.7 3.67 8.17 −1.17 −10.7 −3.67 
16 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

(median of 50 taxa per site) compared with 2004 (median 

of 37 taxa per site). The most taxa collected from any site 

in 2013 were from the Root River at Greenfield site, and in 

2004, the most taxa were collected from the Milwaukee River 

at Milwaukee site. The fewest taxa collected from any site in 

2013 were from the Menomonee River at Menomonee Falls 

site, and in 2004, the fewest taxa were collected from the Root 

River at Greenfield site. At the three temporal sites where 

spring and fall samples were collected in 2011–13, the highest 

numbers of taxa were measured in fall compared to spring. 

Sample collections were focused on fall because streams were 

generally more wadable at late summer/early fall base flow. 

This finding emphasizes the need to standardize the sampling 

period and the need to sample multiple years when evaluating 

stream algal assemblages.

A total of 4 major algal groups (phyla) were identified among the 14 sites: diatoms and green, blue-green (also 

known as cyanobacteria), and red algae. All 4 groups were 

present at 8 sites in 2013 (table 3). Red algae were missing 

at 5 sites and; red and green algae were missing at 1 site. In 

2004, all 4 algal groups were present at only 2 sites (Honey 

Creek and Menomonee River at Wauwatosa). Six sites were 

missing green algae and six sites were missing red algae. A 

total of 2 additional phyla (Euglenoids and Dinoflagellates) 

were identified at 3 sites in 2013 but relative abundance was 

about 1 percent or less at these sites. The percentage of relative abundance of each algal phylum was calculated by dividing the cell density of each taxon from that algal phylum by 

the total cell density for that site.

Algal biovolume at most sites was higher in 2013 

compared with 2004 (table 2). The total biovolume of algae 

summed for all 14 sites was 80 percent higher in 2013 than 

2004 with 375 billion compared with 208 billion cubic 

microliters per square centimeter, respectively. More than half 

of the total biovolume of algae in 2013 can be attributed to 

Milwaukee River near Cedarburg and Jewel Creek, most of 

which is accounted for by the Cladophora glomerata (green 

algae). This green alga occurred at 7 of the 14 sites in 2013 

(Honey Creek, Jewel Creek, Kinnickinnic River, Milwaukee 

River near Cedarburg, Menomonee River at Menomonee 

Falls, Menomonee River at Wauwatosa, and Underwood 

Creek) and accounted for more than 90 percent of the total 

algal biovolume at the 14 sites.

Diversity in 2013 compared with 2004 was improved at 

seven sites and unchanged at the other seven sites. Diversity 

improved from high stress (diversity index <1.5, low richness 

with highly uneven abundance) in 2004 to moderate stress 

(diversity index =1.5–2.5, medium richness with medium 

evenness of abundance) in 2013 for seven sites based on diversity rankings for diatoms in low-gradient streams according 

to Bahls (1993). Six sites were rated moderate stress for 2004 

and 2013 and the Menomonee River at Wauwatosa site was 

rated high stress in 2004 and 2013.

There was little difference in the percentage of nuisance 

algae between 2004 and 2013 at most sites (table 2). Only one 

site, Honey Creek, was more than 10 percent higher in 2013 

(12) compared with 2004 (0). The percentage of relative abundance of eutrophic diatoms was at least 10 percent higher at 

four sites in 2013 compared with 2004 (Milwaukee River near 

Cedarburg [15.0], Willow Creek [21.2], Kinnickinnic River 

[14.5], and Jewel Creek [11.7]; table 2). Increases in nuisance 

algae and eutrophic diatoms indicate higher overall concentrations of nutrients at these streams.

For some sites, large differences in abundance were 

detected between 2004 and 2013 for pollution-tolerant and 

pollution-sensitive diatoms (table 2, fig. 3A). A greater abundance of pollution-tolerant diatoms indicates degradation of 

water quality at a site. The relative abundance of pollutiontolerant diatoms in 2013 was higher at 11 of the 14 sites and 

changes greater than 10 percent occurred at 2 sites (Lincoln 

Creek and Milwaukee River at Milwaukee). The only stream 

to have a relatively large negative difference in pollutiontolerant diatoms was the Kinnickinnic River, from 28 percent 

in 2004 to 17 percent in 2013, and this may indicate improvement in water quality. Three sites had substantial (greater 

than [>] 10 percent) increases in pollution-sensitive diatoms 

(Lincoln Creek, Little Menomonee River, and Oak Creek) and 

three sites had substantial (>10 percent) decreases in pollutionsensitive diatoms (Willow Creek, Underwood Creek, and 

Menomonee River at Wauwatosa). Five sites in 2013 (Lincoln 

Creek, Underwood Creek, Honey Creek, Menomonee River 

at Wauwatosa, and the Kinnickinnic River) all had less than 

30-percent pollution-sensitive diatoms (fig. 4). All sites except 

Underwood Creek had less than 30-percent pollution-sensitive 

diatoms in 2004 too. Lange-Bertalot (1979) developed a 

pollution-tolerance index based on diatom studies in Europe 

that was later the basis of a multimetric diatom index for water 

quality by Bahls (1993). Lange-Bertalot (1979) determined 

that pollution-sensitive diatoms were dominant where water 

quality was only moderately polluted by nutrients (mean 5-day 

biological oxygen demand [BOD5] less than 4 milligrams 

per liter [mg/L] DO); however, decreases in the dominance 

by pollution-sensitive diatoms in favor of more pollutionmoderate and pollution-tolerant diatoms indicated degradation 

of water quality to eutrophic or highly eutrophic conditions. 

Bahls (1993) determined a mean percentage of relative abundance of 32 percent for plains-ecoregion reference streams in 

Montana. The abundance of sensitive diatoms was determined 

by Porter and others (2008) to decrease with increasing phosphorus concentration. In the current study, the lack of dominance by pollution-sensitive diatoms and less than 30-percent 

relative abundance indicates that water quality at five sites was 

degraded, possibly because of excess nutrients that can lead to 

high oxygen demand and eutrophication. Not surprisingly, the 

more urban sites in the central part of the Milwaukee metropolitan area (Lincoln Creek, Milwaukee River at Milwaukee, 

Little Menomonee River at Milwaukee, Underwood Creek, 

Honey Creek, Menomonee River at Wauwatosa, Kinnickinnic 

River, and Oak Creek at South Milwaukee) had significantly 

(p<0.05) fewer pollution-sensitive diatoms than sites in more 

outlying areas of the metropolitan area (Milwaukee River near 

Cedarburg, Willow Creek, Menomonee River at Menomonee 
Table 3. Comparison of algal-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–[Unknown taxa were not included in the percentage of relative abundance of algae and the percentage of biovolume of algae calculations. The percentage of differences in metrifall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, blue denotes a potentially beneficial diffference of unknown effect. USGS, U.S. Geological Survey; <, less than]

Sampling 

year

Percentage of relative abundance of algae (percent cell density) Percentage of biovolume of alga

Diatoms Green algae Blue-green algae Red algae Euglenoids Dinoflagellates Diatoms Green algae Blue-green algae Red algae Eugl

Milwaukee River near Cedarburg (USGS station 04086600)

2004 16.1 0.405 83.5 0.0 0.0 0.0 11.8 86.5 1.76 0.007 0

2007 11.0 3.03 86.0 0.0 0.0 0.0 14.7 77.6 7.73 0.007 0

2010 9.69 3.90 85.1 1.32 0.0 0.0 7.95 85.8 5.55 0.650 0

2013 5.65 7.20 86.8 0.40 0.0 0.0 0.143 99.7 0.125 0.007 0

Difference −10.5 6.79 3.30 0.40 0.0 0.0 −11.6 13.3 −1.63 0.0 0

Lincoln Creek at 47th Street at Milwaukee (USGS station 040869415)

2004 6.27 3.65 90.1 0.0 0.0 0.0 0.474 0.062 99.5 0.007 0

2007 7.02 14.0 79.0 0.0 0.0 0.0 0.517 99.0 0.528 0.007 0

2010 12.3 12.2 59.9 15.5 0.0 0.0 4.60 55.5 1.89 38.0 0

2013 10.0 10.1 79.9 0.0 0.0 0.0 2.07 11.3 86.7 0.007 0

Difference 3.71 6.43 −10.1 0.0 0.0 0.0 1.60 11.2 −12.8 0.0 0

Milwaukee River at Milwaukee (USGS station 04087000)

2004 26.4 1.14 72.5 0.0 0.0 0.0 1.69 0.037 98.3 0.007 0

2007 20.1 9.54 70.3 0.0 0.0 0.0 15.9 79.9 4.23 0.007 0

2010 7.59 3.82 87.6 0.97 0.0 0.0 58.5 29.0 10.5 2.03 0

2013 5.95 2.46 87.5 4.11 0.0 0.0 32.0 41.8 15.3 10.8 0

Difference −20.4 1.33 15.0 4.11 0.0 0.0 30.3 41.8 −82.9 10.8 0

Willow Creek at Maple Road, near Germantown (USGS station 040870195)

2004 58.7 1.42 39.8 0.0 0.0 0.0 53.5 43.7 2.82 0.007 0

2007 23.9 5.41 64.9 5.80 0.0 0.0 2.55 95.3 1.18 1.01 0

2010 34.6 0.0 63.8 1.56 0.0 0.0 68.5 0.007 27.0 4.50 0

2013 18.2 5.23 68.6 7.92 0.0 0.0 29.3 28.6 18.1 24.1 0

Difference −40.5 3.81 28.8 7.92 0.0 0.0 −24.2 −15.1 15.3 24.1 0
Table 3. Comparison of algal-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–[Unknown taxa were not included in the percentage of relative abundance of algae and the percentage of biovolume of algae calculations. The percentage of differences in metrifall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, blue denotes a potentially beneficial diffference of unknown effect. USGS, U.S. Geological Survey; <, less than] Sampling year Percentage of relative abundance of algae (percent cell density) Percentage of biovolume of alga

Diatoms Green algae Blue-green algae Red algae Euglenoids Dinoflagellates Diatoms Green algae Blue-green algae Red algae Eugl

Menomonee River at Menomonee Falls (USGS station 04087030) 2004 30.2 0.0 53.0 16.8 0.0 0.0 47.9 0.0 2.80 49.3 0

2007 15.1 5.21 75.3 4.33 0.0 0.0 50.6 23.9 13.3 12.2 0

2010 20.8 3.96 41.4 33.7 0.0 0.0 26.3 8.24 10.3 55.1 0

2013 1.35 5.40 74.3 19.0 0.0 0.029 0.057 97.3 0.732 1.90 0

Difference −28.9 5.40 21.3 2.15 0.0 0.0 −47.8 97.3 −2.07 −47.4 0

Little Menomonee River at Milwaukee (USGS station 04087070) 2004 22.3 0.0 70.0 7.64 0.0 0.0 55.1 0.007 5.41 39.5 0

2007 11.3 4.52 79.5 4.69 0.0 0.0 9.69 62.4 16.9 11.0 0

2010 14.4 1.23 84.4 0.0 0.0 0.0 27.0 25.6 47.4 0.007 0

2013 21.6 0.0 78.4 0.0 0.0 0.0 58.2 0.007 41.8 0.007 0

Difference −0.80 0.0 8.44 −7.64 0.0 0.0 3.09 0.0 36.4 −39.5 0

Underwood Creek at Wauwatosa (USGS station 04087088) 2004 8.09 1.88 90.0 0.0 0.0 0.0 47.1 4.93 47.9 0.007 0

2007 14.7 2.80 82.5 0.0 0.0 0.0 23.6 19.0 57.4 0.007 0

2010 31.4 4.76 63.8 0.0 0.0 0.0 94.8 1.31 3.93 0.007 0

2013 11.1 12.7 76.2 0.0 0.0 0.0 0.091 99.8 0.157 0.007 0

Difference 3.02 10.8 −13.9 0.0 0.0 0.0 −47.1 94.8 −47.8 0.0 0

Honey Creek at Wauwatosa (USGS station 04087119) 2004 44.3 0.400 28.4 26.9 0.0 0.0 71.9 0.800 0.800 26.6 0

2007 16.4 2.95 80.6 0.0 0.0 0.0 1.07 98.3 0.628 0.007 0

2010 39.6 12.9 43.5 3.86 0.1 0.0 0.593 99.1 0.061 0.248 0

2013 21.0 17.5 61.5 0.0 0.0 0.0 0.305 99.6 0.082 0.007 0

Difference −23.3 17.1 33.1 −26.9 0.0 0.0 −71.6 98.8 −0.718 −26.6 0
Table 3. Comparison of algal-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–[Unknown taxa were not included in the percentage of relative abundance of algae and the percentage of biovolume of algae calculations. The percentage of differences in metrifall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, blue denotes a potentially beneficial diffference of unknown effect. USGS, U.S. Geological Survey; <, less than]

Sampling 

year

Percentage of relative abundance of algae (percent cell density) Percentage of biovolume of alga

Diatoms Green algae Blue-green algae Red algae Euglenoids Dinoflagellates Diatoms Green algae Blue-green algae Red algae Eugl

Menomonee River at Wauwatosa (USGS station 04087120)

2004 8.26 0.169 91.0 0.59 0.0 0.0 47.5 0.095 47.9 4.59 0

2007 20.2 8.41 69.6 1.74 0.0 0.0 6.38 84.5 6.40 2.75 02010 39.8 6.71 53.5 0.0 0.0 0.0 65.4 30.1 4.49 0.007 02013 7.47 6.11 86.3 0.0 0.2 0.0 0.0 99.8 0.118 0.007 0Difference −0.80 5.94 −4.71 −0.59 0.2 0.0 −47.5 99.7 −47.7 −4.58 0

Kinnickinnic River at South 11th Street at Milwaukee (USGS station 04087159)

2004 12.2 0.617 87.2 0.0 0.0 0.0 68.0 0.649 31.4 0.007 0

2007 21.6 5.90 72.5 0.0 0.0 0.0 4.64 94.5 0.860 0.007 0

2010 22.2 3.03 74.8 0.0 0.0 0.0 1.70 98.0 0.256 0.007 0

2013 14.7 5.42 79.9 0.0 0.0 0.0 0.184 99.8 <0.041 0.007 0

Difference 2.49 4.80 −7.30 0.0 0.0 0.0 −67.8 99.1 −31.3 0.0 0

Oak Creek at South Milwaukee (USGS station 04087204)

2004 33.0 0.0 59.2 7.80 0.0 0.0 59.9 0.0 5.90 34.2 0

2007 43.0 8.56 35.0 13.5 0.0 0.0 46.7 47.6 0.955 4.80 02010 29.6 1.82 48.5 20.0 0.1 0.0 1.44 97.4 0.167 0.862 02013 28.4 5.71 35.9 30.0 0.0 0.0 44.6 32.2 2.66 20.6 0Difference −4.58 5.71 −23.3 22.2 0.0 0.0 −15.3 32.2 −3.24 −13.6 0

Root River at Grange Avenue at Greenfield (USGS station 04087214)

2004 10.2 0.0 2.88 86.9 0.0 0.0 10.8 0.0 0.305 88.9 0

2007 30.4 21.8 6.18 41.6 0.0 0.0 19.9 37.5 0.191 42.5 0

2010 18.0 0.435 47.0 34.6 0.0 0.0 26.1 25.2 7.56 41.1 0

2013 11.4 3.89 60.9 23.7 0.1 0.0 24.4 17.7 11.4 46.0 0

Difference 1.25 3.89 58.0 −63.2 0.1 0.0 13.6 17.7 11.1 −42.9 0
Table 3. Comparison of algal-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–[Unknown taxa were not included in the percentage of relative abundance of algae and the percentage of biovolume of algae calculations. The percentage of differences in metrifall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a potentially adverse difference, blue denotes a potentially beneficial diference of unknown effect. USGS, U.S. Geological Survey; <, less than] Sampling year Percentage of relative abundance of algae (percent cell density) Percentage of biovolume of alga

Diatoms Green algae Blue-green algae Red algae Euglenoids Dinoflagellates Diatoms Green algae Blue-green algae Red algae Eugl

Root River near Franklin (USGS station 04087220) 2004 11.2 0.0 37.1 51.7 0.0 0.0 17.3 0.007 4.38 78.3 

2007 46.7 3.17 33.8 16.4 0.0 0.0 71.1 5.69 5.68 17.5 2010 12.9 1.14 77.1 8.87 0.0 0.0 22.0 8.20 36.1 33.7 2013 17.8 2.43 63.6 15.5 0.6 0.0 9.79 67.7 6.90 12.9 Difference 6.64 2.43 26.5 −36.2 0.6 0.0 −7.50 67.7 2.52 −65.5 

Jewel Creek at Muskego (USGS station 05544371) 2004 38.5 0.0 19.9 41.6 0.0 0.0 63.6 0.0 1.30 35.1 

2007 28.1 12.8 17.5 41.6 0.0 0.0 35.8 21.2 1.76 41.2 2010 38.9 2.76 38.2 19.4 0.3 0.5 1.82 97.5 0.177 0.520 2013 22.3 1.19 46.2 29.1 1.3 0.0 9.31 89.6 0.170 0.700 Difference −16.3 1.19 26.3 −12.5 1.3 0.0 −54.3 89.6 −1.13 −34.4 
Assessment of Aquatic Communities in Relation to Stream Condition 21

2004

2007

2010

2013

Sample year

EXPLANATION

Sensitive

Most 

tolerant

Most 

tolerant

Least 

tolerant

Sensitive

Most 

tolerant

Least 

tolerant

Sensitive

Diatom pollution class, in percentage of relative abundance

A. Diatom pollution class

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

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20

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40

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60

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90

100

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20

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50

60

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80

90

100

0

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20

30

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50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Pollution class (Bahls, 1993)

Figure 3. Selected algal metrics for each of 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, diatom pollution class; 

B, diatom salinity tolerance.
22 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

2004

2007

2010

2013

Sample year

EXPLANATION

Sensitive

Most 

tolerant

Pollution class (Bahls, 1993)

Diatom pollution class, in percentage of relative abundance

Most 

tolerant

Least 

tolerant

Sensitive

Most 

tolerant

Least 

tolerant

Sensitive

A. Diatom pollution class

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

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20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Figure 3. Selected algal metrics for each of 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, diatom pollution class; 

B, diatom salinity tolerance.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 23

2004

2007

2010

2013

Sample year

EXPLANATION

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

Salinity Low chloride

tolerance

High chloride

tolerance

Halobiontic 

diatoms

Fresh-brackish

water

diatoms

Freshwater

diatoms

Halobiontic 

diatoms

Fresh-brackish

water

diatoms

Freshwater

diatoms

Diatom salinity tolerance, in percentage of relative abundance

B. Diatom salinity tolerance

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

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80

90

100

0

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20

30

40

50

60

70

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90

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0

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20

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40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Figure 3. Selected algal metrics for each of 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, diatom pollution class; 

B, diatom salinity tolerance.—Continued
24 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

2004

2007

2010

2013

Sample year

EXPLANATION

Salinity Low chloride

tolerance

High chloride

tolerance

Diatom salinity tolerance, in percentage of relative abundance

B. Diatom salinity tolerance

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

0

10

20

30

40

50

60

70

80

90

100

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90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Halobiontic 

diatoms

Fresh-brackish

water

diatoms

Freshwater

diatoms

Halobiontic 

diatoms

Fresh-brackish

water

diatoms

Freshwater

diatoms

Figure 3. Selected algal metrics for each of 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, diatom pollution class; 

B, diatom salinity tolerance.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 25

88°10' 87°50'

42°50'

43°10'

LAKE MICHIGAN

0 42 MILES

0 42 KILOMETERS

Base modified from Southeastern Wisconsin Regional Planning Commission regional base map, 1:2,000, 1995 

U.S. Geological Survey digital line graph hydrography, 1:100,000, 1989

Wisconsin Department of Natural Resources version 2 hydrography, 1:24,000, 2002

Wisconsin Transverse Mercator projection, referenced to North American Datum of 1983, 1991 adjustment

Milwaukee

MRC

OCSM

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

MRW

EXPLANATION

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

54 to 86

38 to 53

Pollution-sensitive diatoms, 

in percentage of 

relative abundance

25 to 37

6.5 to 24

2004

2010

 2013

2007

[MMSD, Milwaukee Metropolitan 

Sewerage District; MRC, Milwaukee 

River near Cedarburg; LCM, Lincoln 

Creek at 47th Street at Milwaukee; 

MRM, Milwaukee River at Milwaukee; 

WCG, Willow Creek at Maple Road, 

near Germantown; MRMF, 

Menomonee River at Menomonee 

Falls; LMM, Little Menomonee River at 

Milwaukee; UCW, Underwood Creek 

at Wauwatosa; HCW, Honey Creek at 

Wauwatosa; MRW, Menomonee River 

at Wauwatosa; KRM, Kinnickinnic 

River at South 11th Street at 

Milwaukee; OCSM, Oak Creek at 

South Milwaukee; RRG, Root River at 

Grange Avenue at Greenfield; RRF, 

Root River near Franklin; JCM, Jewel 

Creek at Muskego]

LMM

Figure 4. Pollution-sensitive diatom algae scores at 14 stream sites in the Milwaukee area, Wisconsin, 2004–13.
26 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

Falls, Root River at Greenfield, Root River near Franklin, 

and Jewel Creek) (fig. 4). Although there were no differences 

greater than 10 percent in the relative abundance of freshwater diatoms at any site between 2004 and 2013, there were 

decreases of 10 percent or more in the abundance of halobiontic diatoms (having a tolerance or requirements for dissolved 

salts) between 2004 and 2013 at four sites: Lincoln Creek 

(26.3), Menomonee River at Menomonee Falls (10.2), Little 

Menomonee River (29.0), and Oak Creek (26.3). There were 

significant increases at four sites: Underwood Creek (27.8), 

Honey Creek (12.0), Menomonee River at Wauwatosa (18.5), 

Kinnickinnic River (20.6) (table 2, fig. 3B). The abundance 

of salt-tolerant diatoms would be expected to increase with 

increasing chloride and salinity in streams, and the relation 

will be discussed later in this report. This diatom metric could 

serve as a useful indicator of where road salt runoff is affecting 

urban streams.

Invertebrates

Invertebrate assemblages were evaluated using relative 

abundance as represented in MDS plots and metrics for taxa 

richness, percentage of taxa or individuals in certain functional 

groups such as the EPT, the Shannon index of diversity, the 

HBI–10, and the mIBI (table 4). A total of 305 invertebrate 

taxa were collected across all sites in the 4 sampling efforts. 

The number of taxa per site ranged from 13 taxa detected 

at the Little Menomonee River in Milwaukee site in 2010 

to 46 at the Milwaukee River at Milwaukee site in fall 2004 

(table 5). On average, there were about 25 taxa per site in the 

2004–13 samples (excluding additional temporal samples).

In general, the MDS plot for invertebrates indicated that 

the assemblages within most sites remained relatively similar 

across sampling years, as demonstrated by points for each site 

grouping close together (fig. 5). Exceptions were seen for the 

Little Menomonee River site in all years, which seemed to 

have less stable assemblages across time, and for the Honey 

Creek site in 2004. For sites with additional temporal sampling 

in 2011–13, the MDS results indicated a high degree of similarity within each site, demonstrated by most samples grouping tightly and spring and fall samples generally grouping 

together also. However, the fall 2011 sample for the Lincoln 

Creek site was anomalous and grouped away from the rest of 

the site’s samples. At the Milwaukee River near Cedarburg 

site in 2013, the spring sample grouped away from the rest 

of the samples for this site. Otherwise, invertebrate samples 

for this site were stable and similar from 2004 to 2013. The 

assemblages for the two main-stem Milwaukee River sites 

(Milwaukee River near Cedarburg and Milwaukee River 

at Milwaukee) grouped together and away from the other 

12 sites, possibly because of the general nature of large river 

sites that often have higher productivity, more diverse habitat, and higher recolonization potential when compared with 

smaller streams. Samples for the Willow Creek site formed 

a distinct grouping away from all other sites, and this probably reflects the wetland nature of this small tributary and that 

invertebrates from this site only were collected from woody 

snags and not rocks. Overall, there was no larger pattern of 

site differences for 2010 when compared with later years, as 

was observed with the algal MDS results.

From 2004 to 2013, most sites had lower richness as 

demonstrated by fewer species and (or) genera—only three 

sites had more—and almost all sites had lower Shannon index 

of diversity values in 2013. The decreases in richness were 

all substantial (greater than 10 percent). The median number 

of taxa was lower in 2013 (20.5 taxa per site) compared with 

2004 (28 taxa per site). In the four sampling efforts, the highest taxa richness for species was detected in 2004 at the two 

Milwaukee main-stem sites (Milwaukee River near Cedarburg 

and Milwaukee River at Milwaukee) with 45 and 46 species, 

respectively (table 5, fig. 6A). In fall 2013, the most taxa were 

detected at the Milwaukee River at Milwaukee site, and the 

fewest were detected at the Lincoln Creek and Honey Creek 

sites. However, the Menomonee River at Menomonee Falls, 

Underwood Creek, Oak Creek, and Jewel Creek sites ranked 

similarly low for richness in fall 2013. These findings indicate 

that the water quality and overall condition at these latter six 

sites in 2013 are more degraded than at other sampled sites.

The percentage of noninsect metric is a useful but 

complicated metric in that one needs to examine which taxa 

compose the noninsect metric in a sample. Native freshwater 

mussels contribute to the noninsect count but are indicative of 

good water quality. In general, the Milwaukee main-stem sites 

(Milwaukee River near Cedarburg and Milwaukee River at 

Milwaukee) had the lowest values for percentage of noninsects 

across all sampling years, except for a somewhat higher value 

in spring of 2013 at the Milwaukee River near Cedarburg site 

because of the presence of native freshwater mussels in the 

sample (table 5). The percentage of noninsects was also low 

at the Menomonee River at Wauwatosa, Kinnickinnic River, 

Oak Creek, Root River near Franklin, and Jewel Creek sites. 

The highest percentage of noninsects in 2013 was detected 

at the Root River at Greenfield, which also had high percentages in all sampling years relative to other sampled sites. The 

percentages of noninsects were relatively similar at most sites 

in 2004 and 2013; however, the percentages at three sites 

were more than 10 percent higher in 2013; values were more 

than 10 percent higher in 2013 at Willow Creek and the Little 

Menomonee River, indicating degraded water quality at these 

two sites.

Percentages of EPT taxa at most sites seemed relatively 

similar between 2004 and 2013; however, there were four sites 

where EPT taxa were more than 10 percent higher in 2013 

(table 5, fig. 6). Although higher percentages of EPT taxa are 

good generally, some taxa are tolerant (mayfly and caddisfly taxa). For example, higher percentages at Honey Creek 

included taxa known to be relatively pollution tolerant (mayfly 

taxa Baetis flavistriga and Baetis intercalaris with caddisfly 

taxa Hydropsyche betteni and Cheumatopsyche; Barbour and 

others [1999]), and relative abundances of the two tolerant 

caddisfly taxa were higher in 2013 compared with 2004 (more 

than 28 percent and about 5 percent or less, respectively). At 
Assessment of Aquatic Communities in Relation to Stream Condition 27

the Kinnickinnic River site, the tolerant mayfly B. intercalaris

was higher in 2013 compared with 2004 (29 percent and 

5 percent, respectively). Tolerant EPT taxa were also common at other sampled sites. The highest percentages of EPT 

taxa in samples collected in 2013 were from the Milwaukee 

River near Cedarburg, Milwaukee River at Milwaukee, and 

the Menomonee River at Menomonee Falls site. Excluding 

spring temporal samples, the invertebrate assemblages at 

the Root River at Greenfield site had the lowest percentage 

of EPT taxa (13) but the Willow Creek, Little Menomonee 

River, Underwood Creek, Menomonee River at Wauwatosa, 

and Kinnickinnic River sites were similarly low with only 

18–21 percent EPT taxa (table 5). Willow Creek is a sandy 

bottom stream with no riffles, and therefore, the low numbers 

of EPT taxa are not unexpected. Plecoptera (stoneflies), which 

require fast flowing waters with high oxygen content and 

riffles, were not detected at any of the sampling locations.

In many cases, ratings for the invertebrate mIBI indicated 

more degraded water quality than did ratings for the HBI–10 

(table 5, fig. 6B). HBI–10 scores for 2013 invertebrate samples 

ranged from results indicating “fairly poor” water quality at 

four sites (Lincoln Creek, Underwood Creek, Kinnickinnic 

River, and Root River at Greenfield) to “good” water quality at 

the two Milwaukee River main-stem sites, Menomonee River 

at Menomonee Falls, Honey Creek, and Jewel Creek; five 

sites had scores indicating “fair” water quality (Willow Creek, 

Little Menomonee River, Menomonee River at Wauwatosa, 

Oak Creek, and Root River near Franklin). A “fairly poor” 

rating for the HBI–10 would be a “poor” rating in the IBI. 

The mIBI scores for 2013 ranged from values indicating “very 

poor” at one site (Kinnickinnic River) to “fair” at the two 

Milwaukee main-stem sites (Milwaukee River near Cedarburg 

and Milwaukee River at Milwaukee) and three other sites; 

the other seven sites were rated “poor.” HBI–10 scores were 

more than 10 percent higher (indicating a worse rating) at only 

two sites, whereas mIBI scores were more than 10 percent 

lower (also indicating a worse rating) at six sites. The largest 

differences (more than two ranks) between HBI–10 and mIBI 

ratings were for Lincoln Creek in 2010, when HBI–10 ratings 

indicated “fair” and mIBI ratings indicated “very poor,” and 

for Honey Creek in 2004, 2010, and 2013 and Jewel Creek in 

2013 when HBI–10 ratings indicated “good” and mIBI ratings indicated “poor.” The reason for the difference in ratings 

between these two metrics is unclear but it could perhaps be 

due to the fact that the HBI–10 does not weight the percentage of EPT taxa and the mIBI does. For invertebrate metrics 

computed at the three temporal sites, the smallest coefficient of variation was determined for the HBI–10 (less than 

8.3 percent for spring samples and less than 5.3 percent for 

fall samples), indicating the consistency/stability of this metric 

for site assessments and comparisons to other sites (table 5). 

When 2004 and 2013 data are compared for all 14 sites, results 

across invertebrate metrics were not consistent for a given 

site (table 5); however, invertebrate metrics for most sites in 

2013 were lower than in 2004 and indicate that water quality 

for invertebrates at most sampled sites was more degraded 

in 2013. This finding was especially evident for the Lincoln 

Creek, Underwood Creek, and Root River at Greenfield sites 

(fig. 7). Possible reasons for the degradation with respect 

to each sampled site are discussed in more detail later in 

this report.

Fish

Fish assemblages were evaluated using relative abundance, as represented in MDS plots, and metrics for taxa 

richness, percentage of individuals in certain functional 

groups, Shannon index of diversity, and IBI (table 6). A total 

of 45 fish taxa (not including hybrids) were collected across 

all sites in the four sampling efforts, and individual year totals 

ranged from 32 to 37. The number of taxa per site ranged 

from no fish detected at the Kinnickinnic River site in 2013 

to 22 at the Milwaukee River near Cedarburg site in 2010 

(table 7). On average, there were more than 9 species per site 

in the 2004–13 samples, with a mean of 231 individual fish. 

At more than half of the sites, the number of fish collected was 

substantially lower (greater than or equal to [≥] 47 percent) in 

2013 than in 2004; however, the number of fish collected was 

substantially higher (≥86 percent) at three sites and relatively 

unchanged at two sites. The lower numbers of fish collected 

were at times in contrast with positive differences in other 

metrics at many sites.

Similar to the MDS plot for invertebrates, the MDS plot 

for fish indicated that assemblages at most sites were relatively 

similar across years, as demonstrated by values for each site 

grouping fairly closely together (fig. 8). However, the Little 

Menomonee River site fish assemblages demonstrated the 

most variability across years while remaining similar to the 

larger group of small rivers and creeks on the left side of the 

plot, as was also seen for invertebrates. The fish assemblage 

for the Willow Creek site demonstrated relatively high variability across sampling years as well and especially in 2007, 

Table 4. Water-quality ratings for the invertebrate Hilsenhoff 

Biotic Index and macroinvertebrate Index of Biotic Integrity for 

streams.

[HBI, Hilsenhoff Biotic Index (Hilsenhoff, 1987); HBI–10, HBI modified 

to limit the number of individuals per taxon to 10 for index computation 

(Hilsenhoff, 1998); mIBI, macroinvertebrate Index of Biotic Integrity 

(Weigel, 2003); ≤, less than or equal to; >, greater than; NA, not applicable; 

<, less than]

HBI/HBI–10 value Water-quality rating mIBI value

≤3.50 Excellent >8

3.51–4.50 Very good NA

4.51–5.50 Good 6–8

5.51–6.50 Fair 4–6

6.51–7.50 Fairly poor NA

7.51–8.50 Poor 2–4

8.51–10.00 Very poor <2
Table 5. Comparison of invertebrate-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin[The percentage of differences in metric values between fall 2013 and fall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing data for 2011–13 at temporal sampling sites; EPT, EphemeropterHBI–10, HBI modified to limit the number of individuals per taxon to 10 for index computation; mIBI, macroinvertebrate Index of Biotic Integrity; USGS, U.S. Geological Survcharacterized] Collection year Number of species Number of genera Percentage of noninsects Percentage of EPT taxa Shannon index of diversity1 HBI–102 

Score Rating 

Milwaukee River near Cedarburg (USGS station 04086600) 2004 45 39 0.77 51 3.86 5.01 Good 

2007 26 23 0.00 48 3.55 4.79 Good 2010 36 31 0.41 48 3.94 4.71 Good 2011, SP 43 37 0.48 43 3.90 5.44 Good 2011, FL 30 25 1.83 60 3.48 4.83 Good 2012, SP 40 33 0.51 52 4.10 5.16 Good 2012, FL 39 33 0.41 36 3.54 5.15 Good 2013, SP 37 28 11.7 29 2.41 5.60 Fair 2013, FL 25 22 2.06 50 2.41 4.91 Good Difference −44 −44 1.3 −1.0 −37.6 −2.06 No difference −

CV, SP 7.5 14 150 28 26.7 4.15 NC CV, FL 23 21 62 25 20.2 3.36 NC 

Lincoln Creek at 47th Street at Milwaukee (USGS station 040869415) 2004 20 17 34.2 18 3.06 6.30 Fair 

2007 32 24 7.35 21 2.60 6.46 Fair 2010 31 27 20.1 19 2.50 6.41 Fair 2011, SP 14 11 30.7 27 1.06 6.93 Fairly poor 2011, FL 20 20 29.1 14 3.23 6.22 Fair 2012, SP 12 10 48.5 10 2.53 7.09 Fairly poor 2012, FL 29 25 7.00 16 2.93 6.67 Fairly poor 2013, SP 25 18 14.4 11 1.54 7.10 Fairly poor 2013, FL 14 14 29.6 29 1.96 6.89 Fairly poor Difference −30 −18 −4.63 11 −36.0 9.43 Lower −

CV, SP 41 34 54.7 60 44.1 1.37 NC CV, FL 36 28 58.9 41 24.6 5.20 NC 
Table 5. Comparison of invertebrate-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin[The percentage of differences in metric values between fall 2013 and fall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing data for 2011–13 at temporal sampling sites; EPT, EphemeropterHBI–10, HBI modified to limit the number of individuals per taxon to 10 for index computation; mIBI, macroinvertebrate Index of Biotic Integrity; USGS, U.S. Geological Survcharacterized]

Collection year Number of species Number of genera Percentage of noninsects Percentage of EPT taxa Shannon index of diversity1 HBI–102 

Score Rating 

Milwaukee River at Milwaukee (USGS station 04087000)

2004 46 41 0.94 39 3.70 5.20 Good 2007 42 36 8.02 39 4.14 5.52 Fair 2010 35 32 1.23 50 3.43 4.45 Very good 2013 29 26 1.03 38 1.94 5.31 Good Difference −37 −37 0.086 −1.0 −47.6 2.10 No difference −

Willow Creek at Maple Road, near Germantown (USGS station 040870195)

2004 32 29 12.2 17 3.94 5.45 Good 

2007 33 29 19.9 21 3.94 5.61 Fair 2010 26 25 9.09 20 3.84 5.51 Fair 2013 26 25 43.6 20 2.54 5.66 Fair Difference −19 −14 31.4 3.0 −35.5 3.91 Lower 

Menomonee River at Menomonee Falls (USGS station 04087030)

2004 18 16 8.29 44 2.29 5.56 Fair 

2007 24 22 2.93 32 3.27 4.77 Good 2010 18 15 1.56 33 2.69 5.79 Fair 2011, SP 19 16 27.1 25 3.03 5.75 Fair 2011, FL 16 15 2.35 40 2.05 5.54 Fair 2012, SP 18 17 10.7 41 2.79 4.94 Good 2012, FL 23 22 4.37 32 3.21 5.17 Good 2013, SP 23 21 3.14 19 2.03 5.69 Fair 2013, FL 15 14 9.57 50 1.96 5.05 Good Difference −17 −12 1.28 6.0 −14.2 −9.21 Higher CV, SP 13 15 89.6 40 20.0 8.26 NC CV, FL 24 26 68.6 22 28.9 4.92 NC 
Table 5. Comparison of invertebrate-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin[The percentage of differences in metric values between fall 2013 and fall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing data for 2011–13 at temporal sampling sites; EPT, EphemeropterHBI–10, HBI modified to limit the number of individuals per taxon to 10 for index computation; mIBI, macroinvertebrate Index of Biotic Integrity; USGS, U.S. Geological Survcharacterized] Collection year Number of species Number of genera Percentage of noninsects Percentage of EPT taxa Shannon index of diversity1 HBI–102 

Score Rating 

Little Menomonee River at Milwaukee (USGS station 04087070) 2004 23 22 36.5 23 2.28 5.33 Good 

2007 22 18 60.3 17 2.58 6.57 Fairly poor 2010 13 12 7.86 42 1.34 5.96 Fair 2013 28 23 54.0 21 1.98 5.96 Fair Difference 22 4.5 17.5 −2.0 −13.1 11.8 Lower 

Underwood Creek at Wauwatosa (USGS station 04087088) 2004 33 28 3.56 18 2.71 5.96 Fair 

2007 21 17 29.9 12 2.64 6.66 Fairly poor 2010 24 20 5.41 25 3.16 6.74 Fairly poor 2013 17 15 12.3 20 1.61 7.14 Fairly poor Difference −48 −46 8.78 2.0 −40.5 19.8 Lower 

Honey Creek at Wauwatosa (USGS station 04087119) 2004 24 24 49.0 17 2.73 5.28 Good 

2007 17 14 7.28 36 2.96 5.81 Fair 2010 23 19 13.7 26 2.57 5.48 Good 2013 14 13 5.12 31 1.55 5.49 Good Difference −42 −46 −43.9 14 −43.1 4.00 No difference −

Menomonee River at Wauwatosa (USGS station 04087120) 2004 20 16 2.39 31 2.68 5.86 Fair 

2007 22 17 5.56 29 2.21 5.85 Fair 2010 22 19 2.04 26 3.10 6.22 Fair 2013 24 19 3.60 21 1.98 6.26 Fair Difference 20 19 1.21 −10 −26.4 6.76 No difference −

Kinnickinnic River at South 11th Street at Milwaukee (USGS station 04087159) 2004 34 27 22.5 7.0 3.02 6.52 Fairly poor 

2007 21 16 7.25 31 2.04 6.09 Fair 2010 17 13 3.65 23 2.48 6.47 Fair 2013 18 11 1.20 18 1.06 6.55 Fairly poor Difference −47 −59 −21.3 11 −64.8 0.491 No difference −
Table 5. Comparison of invertebrate-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin[The percentage of differences in metric values between fall 2013 and fall 2004 is shown (Difference), and percentages greater than 10 percent are highlighted; yellow denotes a and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing data for 2011–13 at temporal sampling sites; EPT, EphemeropterHBI–10, HBI modified to limit the number of individuals per taxon to 10 for index computation; mIBI, macroinvertebrate Index of Biotic Integrity; USGS, U.S. Geological Survcharacterized]

Collection year Number of species Number of genera Percentage of noninsects Percentage of EPT taxa Shannon index of diversity1 HBI–102 

Score Rating 

Oak Creek at South Milwaukee (USGS station 04087204)

2004 28 23 5.94 22 2.86 5.55 Fair 2007 32 26 21.7 19 3.61 5.77 Fair 2010 24 19 2.30 32 2.62 5.82 Fair 2013 16 14 1.45 36 1.48 5.56 Fair Difference −43 −39 −4.49 14 −48.3 0.162 No difference 

Root River at Grange Avenue at Greenfield (USGS station 04087214)

2004 23 22 54.0 18 2.69 6.15 Fair 2007 25 21 26.6 19 3.38 5.73 Fair 2010 20 16 23.4 25 2.62 6.98 Fairly poor 2013 23 16 59.0 13 1.78 6.63 Fairly poor Difference 0 −27 5.00 −5.0 −33.6 7.85 Lower 

Root River near Franklin (USGS station 04087220)

2004 31 25 4.26 28 3.35 5.92 Fair 

2007 27 24 4.10 25 2.86 5.73 Fair 2010 15 15 1.72 33 2.51 5.99 Fair 2013 33 29 4.17 28 2.75 6.19 Fair Difference 6.4 16 −0.09 0 −17.8 4.53 No difference 

Jewel Creek at Muskego (USGS station 05544371)

2004 28 24 22.7 29 3.07 5.58 Fair 

2007 37 29 6.19 17 3.31 5.79 Fair 2010 30 23 10.6 30 3.03 5.75 Fair 2013 18 15 2.03 27 1.75 5.00 Good Difference −36 −38 −20.7 −2.0 −43.0 −10.4 Higher 

1Shannon diversity, calculated as loge (Shannon, 1948).2Hilsenhoff, 1987, 1998.3Weigel, 2003.
E

[MRC, Milwaukee RivCreek at 47th Street aRiver at Milwaukee; Wnear Germantown; MRMenomonee Falls; LMMilwaukee; UCW, UndHCW, Honey Creek at River at Wauwatosa; 11th Street at MilwauMilwaukee; RRG, RooGreenfield; RRF, Root Creek at Muskego; SP

FL04 FL04 FL04 FL04 FL04 FL04 FL04 FL04 FL04 FL04FL04 FL04 FL04 FL04 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL07 FL10 FL10 FL10 FL10FL10 FL10 FL10 FL10 FL10 FL10 FL10 FL10 FL10 FL10 SP11 FL11 SP11 FL11 SP11FL11 FL11 SP12 FL12 SP12 FL12 SP12 FL12 FL12 SP13 FL13 SP13 FL13 FL13 FL13 SP13 FL13 FL13 FL13 FL13 FL13 FL13 FL13 FL13 FL13 FL13 Two-dimensional stress=0.24 Figure 5. Multidimensional scaling ordination plot for invertebrate assemblages collected at 14 sites in the Milwaukee area, Wisconsin, 2004

shown as 04, 07, 10, and 13 for 2004, 2007, 2010, and 2013, respectively]
Assessment of Aquatic Communities in Relation to Stream Condition 33

2004

2007

2010

2013

Sample year

EXPLANATION

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

GR EPT_GENERA SCR

Taxa richness, in total number of invertebrate genera (GR); number of Ephemeroptera, Plecoptera, and Trichoptera genera (EPT_GENERA); and percentage of scrapers (SCR)

A. Taxa richness

GR EPT_GENERA SCR

0

5

10

15

20

25

30

35

40

45

50

0

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30

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45

50

0

5

10

15

20

25

30

35

40

45

50

Figure 6. Selected invertebrate metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, taxa 

richness; B, ratings for indexes of biotic integrity and diversity.
34 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

2004

2007

2010

2013

Sample year

EXPLANATION

GR EPT_GENERA SCR

GR EPT_GENERA SCR

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

Taxa richness, in total number of invertebrate genera (GR); number of Ephemeroptera, Plecoptera, and Trichoptera genera (EPT_GENERA); and percentage of scrapers (SCR)

A. Taxa richness

0

5

10

15

20

25

30

35

40

45

50

0

5

10

15

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0

5

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15

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25

30

35

40

45

50

Figure 6. Selected invertebrate metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, taxa 

richness; B, ratings for indexes of biotic integrity and diversity.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 35

2004

2007

2010

2013

Sample year

EXPLANATION

For HBI–10

For mIBI

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

Values for Hilsenhoff Biotic Index, modified to limit the number of individuals per taxa to 10 for index computation (HBI–10); 

macroinvertebrate Index of Biotic Integrity (mIBI); and Shannon diversity index (Diversity)

B. Values for indexes of biotic integrity and diversity

HBI–10 mIBI Diversity

HBI–10 mIBI Diversity

Fair

5.51 to 6.50

Very good

3.51 to 4.50

Good

4.51 to 5.00

Excellent

less than or 

equal to 3.50

Very poor

less than

8.51 to 10

Poor

7.51 to 8

Fairly poor

6.51 to 7.50

Fair

4 to 6

Good

6 to 8

Excellent

greater 

than 8

Very poor

less than 2

Poor

2 to 4

0

1

2

3

4

5

6

7

8

9

10

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Figure 6. Selected invertebrate metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, taxa 

richness; B, ratings for indexes of biotic integrity and diversity.—Continued
36 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

For HBI–10

For mIBI

2004

2007

2010

2013

Sample year

EXPLANATION

Fair

5.51 to 6.50

Very good

3.51 to 4.50

Good

4.51 to 5.00

Excellent

less than or 

equal to 3.50

Very poor

less than

8.51 to 10

Poor

7.51 to 8

Fairly poor

6.51 to 7.50

Fair

4 to 6

Good

6 to 8

Excellent

greater 

than 8

Very poor

less than 2

Poor

2 to 4

HBI–10 mIBI Diversity

HBI–10 mIBI Diversity

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

Values for Hilsenhoff Biotic Index, modified to limit the number of individuals per taxa to 10 for index computation (HBI–10); 

macroinvertebrate Index of Biotic Integrity (mIBI); and Shannon diversity index (Diversity)

B. Values for indexes of biotic integrity and diversity

0

1

2

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Figure 6. Selected invertebrate metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, taxa 

richness; B, ratings for indexes of biotic integrity and diversity.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 37

88°10' 87°50'

42°50'

43°10'

LAKE MICHIGAN

Milwaukee

0 42 MILES

0 42 KILOMETERS

Base modified from Southeastern Wisconsin Regional Planning Commission regional base map, 1:2,000, 1995 

U.S. Geological Survey digital line graph hydrography, 1:100,000, 1989

Wisconsin Department of Natural Resources version 2 hydrography, 1:24,000, 2002

Wisconsin Transverse Mercator projection, referenced to North American Datum of 1983, 1991 adjustment

JCM OCSM

HCW

WCG

LCM

UCW

KRM

LMM

RRF

RRG

MRW

MRM

MRMF

EXPLANATION

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

HBI–10 scores (ratings)

2004

2007 2010

2013

5.51 to 6.50 (fair)

4.51 to 5.50 (good)

3.51 to 4.50 (very good)

6.51 to 6.66 (fairly poor)

MRM

MRC

[MMSD, Milwaukee Metropolitan 

Sewerage District; HBI–10, Hilsenhoff 

Biotic Index, modified to limit the 

number of individuals per taxa to 10 for 

index computation; MRC, Milwaukee 

River near Cedarburg; LCM, Lincoln 

Creek at 47th Street at Milwaukee; 

MRM, Milwaukee River at Milwaukee; 

WCG, Willow Creek at Maple Road, 

near Germantown; MRMF, 

Menomonee River at Menomonee 

Falls; LMM, Little Menomonee River at 

Milwaukee; UCW, Underwood Creek 

at Wauwatosa; HCW, Honey Creek at 

Wauwatosa; MRW, Menomonee River 

at Wauwatosa; KRM, Kinnickinnic 

River at South 11th Street at 

Milwaukee; OCSM, Oak Creek at 

South Milwaukee; RRG, Root River at 

Grange Avenue at Greenfield; RRF, 

Root River near Franklin; JCM, Jewel 

Creek at Muskego]

Figure 7. Invertebrate Hilsenhoff Biotic Index scores, modified to limit the number of individuals per taxon to 10 for index computation, 

for fall samples at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–13.
38 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

which differed from the other 3 years. The two main-stem 

Milwaukee River sites (Milwaukee River near Cedarburg 

and Milwaukee River at Milwaukee) grouped tightly together 

but were still distinct and plotted away from the other sites, 

showing close similarity across years within each site. The 

fish assemblage at the Lincoln Creek site was quite similar 

across all years and formed yet another distinct grouping, 

underscoring the different fish assemblage at this site compared to all other sampled sites. MDS results for the Lincoln 

Creek, Milwaukee River near Cedarburg, and Menomonee 

River at Menomonee Falls sites demonstrated little difference 

within each site for assemblages collected during the temporal sampling when compared with the core sampling years of 

2004, 2007, 2010, and 2013, indicating greater differences 

between sites than within these sites. The assemblages for the 

Honey Creek and Underwood Creek sites, close tributaries to 

the Menomonee River at Wauwatosa site, grouped together 

and with their main-stem site. Lastly, the fish assemblages 

for the Kinnickinnic River site are anomalies in the MDS 

plot, emphasizing the small numbers collected of mostly one 

species.

Overall, the two Milwaukee River main-stem sites 

(Milwaukee River near Cedarburg and Milwaukee River at 

Milwaukee) had the highest diversity and the lowest percentages of tolerant fish species compared with other sampled sites 

(table 7). The lowest diversity was at the Kinnickinnic River 

site, where a single species, Pimephales promelas (fathead 

minnow) was collected in 2004 and 2010 (fig. 9A). In 2007, 

a single Luxilus cornutus (common shiner) was collected in 

addition to a fathead minnow, and in 2013 not a single fish of 

any species was detected at the site. At six sites, diversity in 

2013 was more than 10 percent lower than in 2004; diversity 

was more than 10 percent higher in 2013 at only three sites. 

The declines in diversity indicate degraded fish assemblages. 

This is particularly concerning for the Milwaukee River near 

Cedarburg site, which has had the highest fish diversity generally in comparison to all other sampled sites.

Across all metrics computed for the three temporal sites, 

the lowest coefficient of variation was determined for diversity 

at less than 15 percent, indicating that values for this metric 

were fairly consistent or stable for making comparisons among 

sites. Coefficients of variation for two other metrics, number 

of species and number of native fish species, were less than 

or equal to 13 percent at the Milwaukee River near Cedarburg 

and Menomonee River at Menomonee Falls sites; however, 

coefficients for these metrics at the Lincoln Creek site were 

22–23 percent, possibly because of the relatively small numbers of species at this urban site, so even slight changes result 

in large coefficients.

Fish species that are considered tolerant of environmental 

degradation (pollution tolerant and tolerant to low DO) made 

up more than 40 percent of the assemblages at most sites and 

nearly 100 percent at several sites in 2013, notably Honey 

Creek, Menomonee River at Wauwatosa, Kinnickinnic River, 

Oak Creek, and Root River at Greenfield. The most common fish taxa detected were Catostomus commersonii (white 

sucker), Lepomis cyanellus (green sunfish), and Semotilus 

atromaculatus (creek chub). All three taxa are relatively tolerant of disturbance and low DO concentrations (McMahon, 

1982). The Milwaukee River near Cedarburg site had the lowest percentage of pollution-tolerant fish overall, followed by 

the Milwaukee River at Milwaukee site (fig. 9B). Fish that are 

omnivores are considered tolerant because they can subsist on 

a wide variety of food types and are therefore less sensitive to 

environmental degradation (Lyons, 1992). The percentage of 

omnivores was more than 10 percent lower in 2013 than 2004 

at six sites and may indicate an improvement in these assemblages. In addition, percentages of pollution-tolerant fish were 

at least 10 percent lower at four sites, indicating healthier fish 

assemblages at these sites.

Fish IBI scores were computed according to the 

Wisconsin-specific IBI developed by Lyons (1992) and can 

range from 65 or greater (“excellent”) to 0 (“very poor”) 

(table 6). Most sites sampled consistently scored between 

“fair” and “very poor” ratings (table 7, fig. 9A). The only 

sites with “good” or “excellent” IBI scores were the two 

Milwaukee River main-stem sites (Milwaukee River near 

Cedarburg and Milwaukee River at Milwaukee). Lincoln 

Creek rated “very poor” in 2004, “fair” in 2007 and 2010, and 

“very poor” in 2013. The Jewel Creek site was rated “fair” in 

2004 and 2013, and the Willow Creek site was rated “poor” in 

2013 and in 2004. The Menomonee River at Menomonee Falls 

site was rated “fair” in 2013 compared with “poor” in 2004. 

The Underwood Creek site ratings were variable, but the site 

was rated “fair” in 2013. Fish assemblages at the remaining 

sites were generally degraded (“poor” and “very poor”) and 

the condition of the assemblages varied through time (fig. 10). 

The two sites with the poorest fish assemblages across years 

were the Little Menomonee River and the Kinnickinnic 

River sites, where fewer than 50 fish were collected during 

sampling, a number that is too small to compute an IBI with 

confidence and, therefore, resulted in ratings of “very poor.” 

In these cases, macroinvertebrates are better for assessing the 

health of the aquatic communities and better reflect conditions 

at any given site because they are less mobile. Invertebrate 

HBI–10 ratings were “fair” and “fairly poor” for these two 

sites, respectively, and these differences in ratings for sites 

Table 6. Scores and ratings for the fish Index of Biotic Integrity 

for warmwater streams.

[IBI, Index of Biotic Integrity (Lyons, 1992)]

IBI score IBI rating

100–65 Excellent

64–50 Good

49–30 Fair

29–20 Poor

19–0 Very poor

No score Very poor
Table 7. Comparison of fish-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–1[The percentage of difference in metric values between fall 2013 and fall 2004 is shown (“Difference”), and percentages greater than 10 percent are highlighted; yellow denotes and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing 2011–13 at temporal sampling sites; DO, dissolved oxygen; USGnot calculated; *, the score for the Wisconsin warmwater Index of Biotic Integrity (IBI; Lyons, 1992) should be viewed with caution because fewer than 50 individual fish were 

Collection year Number of fish Number of species Number of native species Omnivorous individuals (percent) Pollution- tolerant individuals (percent) Forage fish tolerant to low DO (percent) Shannon index of diversity1 Index of 

IBI Score 

Milwaukee River near Cedarburg (USGS station 04086600)

2004 321 21 20 3.0 7.8 9.0 2.61 67 

2007 173 15 15 3.0 4.0 2.0 2.01 65 

2010 877 22 21 8.0 9.0 1.0 2.30 77 

2011 503 21 20 6.0 6.2 1.0 2.27 82 

2012 782 19 18 11 14 6.0 2.27 65 2013 892 21 20 10 11 2.0 1.91 74 

Difference 178 0 0 7.0 3.0 −7.0 −26.7 10 

CV 23.6 6.1 6.4 25 32 95 8.43 9.6 

Lincoln Creek at 47th Street at Milwaukee (USGS station 040869415)

2004 59 8 7 54 71 84 1.71 5 

2007 170 11 10 16 20 19 1.07 49 

2010 124 12 11 24 48 38 1.94 45 

2011 116 9 7 55 78 59 1.90 12 

2012 269 10 8 31 76 69 1.66 25 

2013 25 7 7 24 80 73 1.50 15 

Difference −58 −13 0 −30 9.0 −11 −12.3 200 

CV 76 22 22.9 44 21 26 11.9 61 

Milwaukee River at Milwaukee (USGS station 04087000)

2004 244 19 17 10 20 35 2.14 57 

2007 295 19 18 7.0 8.0 4.0 2.12 57 

2010 219 18 16 18 20 5.0 2.07 59 

2013 242 19 17 11 14 8.0 2.29 65 Difference −0.8 0 0.0 1.0 −6.0 −28 7.04 14 
Table 7. Comparison of fish-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–1[The percentage of difference in metric values between fall 2013 and fall 2004 is shown (“Difference”), and percentages greater than 10 percent are highlighted; yellow denotes and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing 2011–13 at temporal sampling sites; DO, dissolved oxygen; USGnot calculated; *, the score for the Wisconsin warmwater Index of Biotic Integrity (IBI; Lyons, 1992) should be viewed with caution because fewer than 50 individual fish were 

Collection year Number of fish Number of species Number of native species Omnivorous individuals (percent) Pollution- tolerant individuals (percent) Forage fish tolerant to low DO (percent) Shannon index of diversity1 Index of 

IBI Score 

Willow Creek at Maple Road, near Germantown (USGS station 040870195) 2004 238 6 6 24 60 36 1.36 22 

2007 142 12 12 8.0 80 56 1.96 37 

2010 80 6 6 10 74 48 1.59 14 

2013 116 7 7 10 54 30 1.68 27 

Difference −51 17 17 −14 -6.0 −6.0 23.7 23 

Menomonee River at Menomonee Falls (USGS station 04087030) 2004 296 13 13 5.0 81 46 1.91 25 

2007 212 9 9 5.0 58 16 1.79 15 

2010 121 12 12 2.0 83 65 1.67 20 

2011 425 13 13 6.0 56 17 1.76 25 

2012 433 16 16 7.0 49 26 2.29 35 

2013 117 15 15 8.0 28 24 1.93 45 

Difference −60 15 15 3.0 −53 −22 1.21 80 

CV 65 13 13 45 42 66 14.5 39 

Little Menomonee River at Milwaukee (USGS station 04087070) 2004 14 5 5 21 93 69 1.33 14 

2007 14 4 4 14 86 57 1.15 17 

2010 35 10 9 9.0 49 42 1.83 19 

2013 26 7 7 12 38 64 1.78 19 

Difference 86 40 40 −9.0 −55 −5.0 33.5 36 

Underwood Creek at Wauwatosa (USGS station 04087088)2 2004 256 8.0 7.0 7.0 99 7.0 1.06 10 

2007 1,051 11 11 17 45 0 1.54 30 

2010 59 10 10 22 85 40 1.66 7 

2013 135 11 11 16 20 6.0 1.32 44 

Difference −47 38 57 9.0 −79 −1.0 24.8 340 
Table 7. Comparison of fish-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–1[The percentage of difference in metric values between fall 2013 and fall 2004 is shown (“Difference”), and percentages greater than 10 percent are highlighted; yellow denotes and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing 2011–13 at temporal sampling sites; DO, dissolved oxygen; USGnot calculated; *, the score for the Wisconsin warmwater Index of Biotic Integrity (IBI; Lyons, 1992) should be viewed with caution because fewer than 50 individual fish were 

Collection year Number of fish Number of species Number of native species Omnivorous individuals (percent) Pollution- tolerant individuals (percent) Forage fish tolerant to low DO (percent) Shannon index of diversity1 Index of 

IBI Score 

Honey Creek at Wauwatosa (USGS station 04087119)

2004 135 6 6 24 100 16 1.28 7.0 

2007 520 11 10 32 94 11 1.58 24 

2010 331 10 9 21 98 12 1.34 12 

2013 559 11 11 13 97 4.0 0.85 25 

Difference 314 83 83 −11 −3.0 −12 −33.7 257 

Menomonee River at Wauwatosa (USGS station 04087120)

2004 281 7 7 5.0 100 5.0 0.61 10 

2007 449 8 8 4.0 72 2.0 1.14 20 

2010 266 7 7 5.0 90 1.0 0.86 10 

2013 284 6 6 6.0 95 0 0.51 10 

Difference 1.07 −14 −14 −1.0 −4.9 −5.0 −17 0 

Kinnickinnic River at South 11th Street at Milwaukee (USGS station 04087159)

2004 11 1.0 1.0 100 100 100 0.00 0 

2007 2 2.0 2.0 50 50 50 0.69 4.0 

2010 42 1.0 1.0 100 100 100 0.00 0 

2013 0 0 0 0 0 0 * * 

Difference −100 −100 −100 NC NC NC NC NC 

Oak Creek at South Milwaukee (USGS station 04087204)

2004 218 7 7 22 94 20 1.22 5.0 

2007 35 5 5 46 97 12 1.14 0 

2010 129 7 6 29 95 44 1.37 10 

2013 78 6 5 40 95 53 1.30 7.0 

Difference −64 −14 −29 18 1.4 33 6.51 40 
Table 7. Comparison of fish-assemblage data at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004–1[The percentage of difference in metric values between fall 2013 and fall 2004 is shown (“Difference”), and percentages greater than 10 percent are highlighted; yellow denotes and blue denotes a potentially beneficial difference. The coefficient of variation (CV) is provided for comparing 2011–13 at temporal sampling sites; DO, dissolved oxygen; USGnot calculated; *, the score for the Wisconsin warmwater Index of Biotic Integrity (IBI; Lyons, 1992) should be viewed with caution because fewer than 50 individual fish were 

Collection year Number of fish Number of species Number of native species Omnivorous individuals (percent) Pollution- tolerant individuals (percent) Forage fish tolerant to low DO (percent) Shannon index of diversity1 Index of 

IBI Score 

Root River at Grange Avenue at Greenfield (USGS station 04087214) 2004 179 9 9 12 94 28 1.73 12 

2007 10 4 4 10 100 10 1.17 12 

2010 102 8 8 47 98 6.0 1.32 7.0 

2013 11 3 3 0 100 55 0.99 2.0 

Difference −94 −67 −67 −12 6.0 27 −43 −83 

Root River near Franklin (USGS station 04087220) 2004 184 12 12 55 69 3.0 1.73 27 

2007 7 4 4 0 57 17 1.28 0 

2010 79 7 7 1.0 23 19 1.17 32 

2013 31 9 9 16 84 41 1.75 17 

Difference −83 −25.0 −25 −39 14 38 1.10 −37 

Jewel Creek at Muskego (USGS station 05544371) 2004 511 16 15 36 54 15 1.92 31 

2007 144 10 10 9.0 42 34 1.78 37 

2010 54 6 6 0 17 6.0 1.26 25 

2013 210 7 7 5.0 15 3.0 1.14 35 

Difference −59 −56 −53 −31 −39 −12 −40.5 13 

1Shannon diversity, calculated as loge (Shannon, 1948). 2The 2007 sample included seine hauls at the bottom of the reach; however, we were unable to do this every year because of pool depth.
FL04

FL2007 FL2010

FL2011

FL2012

FL2013

SM04

FL07

FL10

FL11

FL12

FL13

SM04

FL07

FL10

FL13

FL04

FL07

FL10

FL13

SM04 FL07

FL20 FL11

FL12

FL13

SM04 FL07 FL10

FL13

FL04

FL07

FL10

FL13 SM04 FL07

FL10

FL13

FL04

FL07

FL10

FL13

FL04

FL07

FL10

SM04

FL07

FL10 FL13

FL04

FL07

FL10

FL13

FL04

FL07

FL10

FL13

FL04

FL07

FL10

FL13

E

Two-dimensional stress=0.17

[MRC, Milwaukee RivCreek at 47th Street aRiver at Milwaukee; Wnear Germantown; MRMenomonee Falls; LMMilwaukee; UCW, UndHCW, Honey Creek at River at Wauwatosa; 11th Street at MilwauMilwaukee; RRG, RooGreenfield; RRF, Root Creek at Muskego; SPSM, summer samples

S

Figure 8. Multidimensional scaling ordination plot for fish assemblages collected at 14 sites in the Milwaukee area, Wisconsin, 2004–13. [The 04, 07, 10, 11, 12, and 13 for 2004, 2007, 2010, 2011, 2012, and 2013, respectively]
44 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

For Fish IBI

2004

2007

2010

2013

Sample year

EXPLANATION

Fair

30 to 49

Good

50 to 64

Excellent

65 to 100

Very poor

less than 19

Poor

20 to 29

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

Fish IBI Richness pOMNIfish

Fish IBI Richness pOMNIfish

Values for fish Index of Biotic Integrity (Fish IBI) and richness and percentage of omnivores (pOMNIfish)

A. Index of Biotic Integrity, richness, and percentage of omnivores

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

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90

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20

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60

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90

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0

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20

30

40

50

60

70

80

90

100

0

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20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Figure 9. Selected fish metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, Index of Biotic Integrity, 

richness, and percentage of omnivores; B, percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus 

disturbance-tolerant fish.
Assessment of Aquatic Communities in Relation to Stream Condition 45

For Fish IBI

2004

2007

2010

2013

Sample year

EXPLANATION

Values for fish Index of Biotic Integrity (Fish IBI) and richness and percentage of omnivores (pOMNIfish)

Fair

30 to 49

Good

50 to 64

Excellent

65 to 100

Very poor

less than 19

Poor

20 to 29

Fish IBI Richness pOMNIfish

Fish IBI Richness pOMNIfish

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

A. Index of Biotic Integrity, richness, and percentage of omnivores

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

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60

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0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

Figure 9. Selected fish metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, Index of Biotic Integrity, 

richness, and percentage of omnivores; B, percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus 

disturbance-tolerant fish.—Continued
46 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

For percentage of tolerant fish

2004

2007

2010

2013

Sample year

EXPLANATION

Fair

21 to 49

Good

20

Excellent

0 to 19

Very poor

51 to 100

Poor

50

Milwaukee River near Cedarburg Lincoln Creek at 47th Street at Milwaukee

Milwaukee River at Milwaukee Willow Creek at Maple Road, near Germantown

Menomonee River at Menomonee Falls

Underwood Creek at Wauwatosa

Little Menomonee River at Milwaukee

pTOLfish pDISTfish pDODISTspp

Percentages of tolerant fish (pTOLfish), disturbance-tolerant fish (pDISTfish), and low dissolved oxygen plus disturbance-tolerant fish (pDODISTspp)

B. Percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus disturbance-tolerant fish

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

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60

70

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90

100

0

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20

30

40

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60

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90

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0

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20

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0

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20

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60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

pTOLfish pDISTfish pDODISTspp

Figure 9. Selected fish metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, Index of Biotic Integrity, 

richness, and percentage of omnivores; B, percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus 

disturbance-tolerant fish.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 47

For percentage of tolerant fish

2004

2007

2010

2013

Sample year

EXPLANATION

Percentages of tolerant fish (pTOLfish), disturbance-tolerant fish (pDISTfish), and low dissolved oxygen plus disturbance-tolerant fish (pDODISTspp)

Fair

21 to 49

Good

20

Excellent

0 to 19

Very poor

51 to 100

Poor

50

pTOLfish pDISTfish pDODISTspp

pTOLfish pDISTfish pDODISTspp

Honey Creek at Wauwatosa Menomonee River at Wauwatosa

Kinnickinnic River at South 11th Street at Milwaukee Oak Creek at South Milwaukee

Root River at Grange Avenue at Greenfield

Jewel Creek at Muskego

Root River near Franklin

B. Percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus disturbance-tolerant fish

0

10

20

30

40

50

60

70

80

90

100

0

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60

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60

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90

100

0

10

20

30

40

50

60

70

80

90

100

Figure 9. Selected fish metrics for each of the 14 stream sites in the Milwaukee area, Wisconsin, 2004–13. A, Index of Biotic Integrity, 

richness, and percentage of omnivores; B, percentages of tolerant fish, disturbance-tolerant fish, and low dissolved oxygen plus 

disturbance-tolerant fish.—Continued
48 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

88°10' 87°50'

42°50'

43°10'

LAKE MICHIGAN

Milwaukee

0 42 MILES

0 42 KILOMETERS

Base modified from Southeastern Wisconsin Regional Planning Commission regional base map, 1:2,000, 1995 

U.S. Geological Survey digital line graph hydrography, 1:100,000, 1989

Wisconsin Department of Natural Resources version 2 hydrography, 1:24,000, 2002

Wisconsin Transverse Mercator projection, referenced to North American Datum of 1983, 1991 adjustment

[MMSD, Milwaukee Metropolitan 

Sewerage District; IBI, Index of Biotic 

Integrity; MRC, Milwaukee River near 

Cedarburg; LCM, Lincoln Creek at 47th 

Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, 

Willow Creek at Maple Road, near 

Germantown; MRMF, Menomonee 

River at Menomonee Falls; LMM, Little 

Menomonee River at Milwaukee; 

UCW, Underwood Creek at 

Wauwatosa; HCW, Honey Creek at 

Wauwatosa; MRW, Menomonee River 

at Wauwatosa; KRM, Kinnickinnic 

River at South 11th Street at 

Milwaukee; OCSM, Oak Creek at 

South Milwaukee; RRG, Root River at 

Grange Avenue at Greenfield; RRF, 

Root River near Franklin; JCM, Jewel 

Creek at Muskego]

EXPLANATION

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

100 to 65 (excellent)

64 to 50 (good)

Fish IBI scores (ratings)

49 to 30 (fair)

19 to 0 (very poor)

29 to 20 (poor)

2004

2010

2013

2007

LCM

MRC

OCSM

MRW

HCW

UCW

LMM

WCG

LCM

MRM

LCM

MRMF

RRF

RRG

KRM

JCM

Figure 10. Fish Index of Biotic Integrity scores for fall samples at 14 stream sites in the Milwaukee Metropolitan Sewerage District 

planning area, Wisconsin, 2004–13.
Assessment of Aquatic Communities in Relation to Stream Condition 49

based on metrics for fish and invertebrates demonstrate how 

one group of organisms may respond more adversely than 

another to environmental degradation.

Comparative Bioassessment among Algae, 

Invertebrates, and Fish

Results for selected biological metrics were compared 

among algal, invertebrate, and fish assemblages to ensure a 

more complete assessment of water quality and stream condition at the sampled sites. Sites were grouped into four groups 

according to the aggregate bioassessment rankings. The 4 sites 

in group 1 for 2013 had the least degraded water quality 

among the 14 sampled sites: Milwaukee River near Cedarburg, 

Menomonee River at Menomonee Falls, Jewel Creek, and 

Milwaukee River at Milwaukee (table 8). This group of sites 

was also among the least degraded group for 2004 (Thomas 

and others, 2007). These rankings are arithmetic means for the 

three biotic assemblages, and as such, results for each assemblage may vary; although the mean invertebrate and fish rankings for the Milwaukee River at Milwaukee site would have 

placed the site in group 1, the 2013 results for algae placed the 

site in group 4, the most degraded category. In 2013, relative 

abundance of pollution-tolerant diatoms increased by more 

than 10 percent at this site, and this is one of two metrics 

used in the algal ranking. In general, algal assemblages are 

more sensitive to water-quality changes occurring on shorter 

time scales than are invertebrate or fish assemblages. For this 

reason, algae may be the first to demonstrate improvement 

or degradation in the water quality at a site. The aggregate 

assessment rankings for Oak Creek and Honey Creek sites 

indicate that water quality was better in 2013 than in 2004. 

The aggregate assessment rankings for the Menomonee River 

at Wauwatosa and Root River at Greenfield sites indicate that 

water quality was more degraded in 2013 than in 2004. These 

two sites, along with the Lincoln Creek and Kinnickinnic 

River sites composed group 4 in 2013. These aggregate assessments should only be used to compare sites with each other. 

Sites at the top or bottom of the groups do not indicate good or 

bad water quality—only better or worse water quality than the 

other sites evaluated. To fully evaluate the water quality, it is 

necessary to look at the site-specific biota metrics.

Physical and Chemical Stressors at Sampled 

Sites

Physical data were obtained from land use/land cover; 

stream discharge from USGS streamgages (except at the 

Willow Creek and Jewel Creek sites, which were not gaged 

and were not sampled by MMSD for water quality), stream 

habitat, and microhabitat at invertebrate collection locations (depth, velocity, dominant substrate, embeddedness). 

Chemical and other water-quality data were obtained from 

water-quality measurements by MMSD (except at the Willow 

Creek and Jewel Creek sites), field measurements of several 

water-quality constituents (specific conductance and light 

attenuation) at the time of ecological sampling, and measures 

of benthic algal biomass. Additional chemical data for stressor 

evaluations were obtained from toxicity and chemical tests 

on extracts from passive samplers deployed at a subset of 

six sites.

Toxicity and Chemical Assessment with Passive 

Sampling Devices

Deployment of passive samplers (SPMDs) provided 

valuable information on the potential toxicity to stream biota 

from waterborne hydrophobic organic chemicals (PAHs, 

PCBs, dioxins and furans, chlorinated pesticides, and PBDEs). 

SPMDs are designed to mimic potential uptake of bioavailable concentrations of these compounds in water by fish gills 

that could be followed by sequestering of the compounds into 

fatty lipid-containing areas of the fish (Alvarez and others, 

2008; Alvarez, 2010). SPMDs are analyzed by three tests that 

assess the potential toxicity of bioaccumulative compounds in 

waterborne sediments: a Microtox test, a P450RGS test, and a 

fluorescence screen for PAHs.

Microtox tests on SPMDs deployed in 2013 indicated 

moderate to no toxicity at sites (table 9). Results are reported 

in terms of TU50 values, which are determined by dividing 100 

by the effective concentration at which there is a 50-percent 

reduction in light; the larger the calculated TU50 value, the 

more toxic the sample is. SPMDs from the Little Menomonee 

River and Milwaukee River at Milwaukee sites had the 

highest TU50 scores, and thus, mixtures of compounds available for bioaccumulation at these sites could be considered 

to have moderate acute toxicity to aquatic organisms. The 

SPMDs from the Lincoln Creek and Honey Creek sites had 

lower TU50 scores that were higher than the field blanks and, 

therefore, could be considered slightly toxic. Samples from 

the Oak Creek and Milwaukee River near Cedarburg sites had 

responses similar to the field blanks and, therefore, were considered to be nontoxic. Field blanks for three of the six sites in 

2013 had low measurable responses that were similar to that 

of the laboratory blank, which was low and had a TU50 of 8.0, 

and so were considered low/nontoxic (Milwaukee River near 

Cedarburg [7.2], Lincoln Creek [5.9], and Milwaukee River at 

Milwaukee [9.4]). Field blanks for the other three sites in 2013 

did not indicate toxicity (not detected). In 2007 and 2010, all 

the SPMD samples demonstrated little to no Microtox toxicity. 

The lack of toxicity in the 2007 and 2010 Microtox tests was 

somewhat in contrast to results for 2013 and especially for a 

previous study in 2004. In 2004, as part of a separate USGS 

study on the effects of urbanization on stream ecosystems, 

SPMDs were deployed at or near the same sites included in 

the current study, and Microtox and P450RGS tests were run 

(Bryant and Goodbred, 2009; Richards and others, 2010). 

Microtox results for 2004 indicated that the highest potential 

toxicity of all Milwaukee area streams sampled was at the 
50 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

Underwood Creek site. Compounds that were different from 

those tested for by the P450RGS tests were likely causing 

some of the toxicity in those tests because, although results for 

the P450RGS tests were high at the Underwood Creek site, 

those results were still lower than several other sampled sites. 

Based on direct sampling of water and sediment, three possibilities mentioned for toxicity at Underwood Creek in 2004 

were 9,10-anthraquinone; tris(2-butoxyethyl) phosphate; and 

lead (Richards and others, 2010).

In contrast, the P450RGS test results indicated potential 

toxicity from hydrophobic organic chemicals at all six sites 

sampled in 2013 (all TEQ values in blank samples were below 

method detection limits; table 9). High toxic equivalents 

related to an SPMD extract (TEQs) correspond to similarly 

high levels of cytochrome-P450 enzyme activity, which 

are indicators of possible changes in reproduction, growth, 

pathology, and physiology in fish. In 2013, TEQs at all sites 

were lower than in 2010; values at the Lincoln Creek, Little 

Menomonee River, and Honey Creek sites were 2–3 times 

lower than in 2010; nevertheless, TEQs in 2013 were higher 

than in 2007 at the Milwaukee River near Cedarburg, Lincoln 

Creek, and Honey Creek sites. Potential toxicity was indicated at all these sites in 2007 and at the Little Menomonee 

River, Kinnickinnic River, and Oak Creek sites. The Lincoln 

Creek site had the highest potential toxicity in 2007 (set 

A only), 2010, and 2013 for the P450RGS test. Based on 

P450RGS tests completed in 2004, the highest potential toxicity from compounds such as dioxins, PCBs, and PAHs for the 

Milwaukee area was at the Little Menomonee River, Lincoln 

Creek, Honey Creek (at streamgage), Oak Creek, and Root 

River at Greenfield (at streamgage) sites (Thomas and others, 2007; Bryant and Goodbred, 2009; Richards and others, 

2010); PAHs were detected at all seven sites. Concentrations 

of PCBs in a sediment trap were low (0.03 milligram per 

kilogram) at Oak Creek in 2004 (Thomas and others, 2007). 

In a study of wastewater compounds and toxicity at many 

Table 8. Mean trophic-level rankings and aggregate bioassessment rankings for 14 stream sites in the Milwaukee area, Wisconsin, 

2013 and 2004.

[The fill color indicates the group based on percentiles of the ranked data for a group of biota (group 1 or less than the 25th percentile [least degraded], blue; 

group 2 or between the 25th and 49th percentile/median, light blue; group 3 or between the 50th to 74th percentile, light orange; group 4 or greater than the 75th 

percentile [most degraded], orange; each column is considered independently). Lower percentiles indicate better water quality. WI, Wisconsin; S., South]

Site name

Mean trophic-level ranking for 2013 2013 2004

Algae1 Invertebrates2 Fish3

Aggregate 

bioassessment 

ranking

Aggregate 

bioassessment 

ranking

Group 1

Milwaukee River near Cedarburg, WI 5.0 1.7 1.0 2.56 1.44

Menomonee River at Menomonee Falls, WI 3.0 3.3 3.0 3.11 5.44

Jewel Creek at Muskego, WI 1.5 6.7 5.0 4.39 3.50

Milwaukee River at Milwaukee, WI 10.5 5.0 2.0 5.83 3.56

Group 2

Little Menomonee River at Milwaukee, WI 4.0 7.0 8.0 6.33 7.28

Root River near Franklin, WI 4.5 5.7 9.0 6.39 6.39

Willow Creek at Maple Road near Germantown, WI 9.5 6.7 6.0 7.39 6.33

Group 3

Oak Creek at South Milwaukee, WI 4.0 7.7 12.0 7.89 9.61

Honey Creek at Wauwatosa, WI 10.0 7.3 7.0 8.11 9.33

Underwood Creek at Wauwatosa, WI 10.5 12.0 4.0 8.83 9.17

Group 4

Menomonee River at Wauwatosa, WI 10.0 7.7 11.0 9.56 9.11

Root River at Grange Avenue at Greenfield, WI 5.0 11.7 13.0 9.89 8.56

Lincoln Creek at 47th Street at Milwaukee, WI 12.5 8.7 10.0 10.39 11.11

Kinnickinnic River at S. 11th Street at Milwaukee, WI 13.0 12.7 14.0 13.22 13.06

1Averaged bioassessment rankings for algae included the percentage of most tolerant diatoms and the percentage of sensitive diatoms.

2Averaged bioassessment rankings for invertebrates included Shannon index of diversity scores, the percentage of Ephemeroptera-Plecoptera-Trichoptera 

taxa, and Hilsenhoff Biotic Index scores, modified to limit the number of individuals per taxon to 10 for index computation.

3Averaged bioassessment rankings for fish included only Index of Biotic Integrity scores.
Table 9. Results for toxicity tests and selected chemical analyses of passive sampling devices (semipermeable membrane devices) deployed at 10 oarea, Wisconsin, 2004–13.[Each value is a mean of three sample analyses standardized to 30-day exposure times (higher values indicate greater potential toxicity); P450RGS, cytochrome-P450 reporter g

toxicity unit for Microtox toxicity tests with values for moderately to highly toxic results given in bold and bold italics, respectively; TEQ, toxic equivalent for cytochrome-P450 

hydrocarbon compound; mg, milligram; SPMD, semipermeable membrane device; mL, milliliter; pg, picogram; μg, microgram; A, B, replicate sample sets for 2007; MRC, MilNC, not characterized; <, less than; ND, not detected or detection limits not calculated because of a lack of sampling rate information; LCM, Lincoln Creek at 47th Street at Milat Milwaukee; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at River at South 11th Street at Milwaukee; OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield]

Site 

abbreviation

Microtox P450RGS Fluor

TU50 TEQ P

mg SPMD/mL pg TEQ/mL SPMD μg pyrene equiv

12004 2007–A 2007–B 2010 2013 12004 2007–A 2007–B 2010 2013 12004 2007–A 200

MRC NC <1.2 <5.2 ND 6.7 NC 491 547 1,496 871 NC 0.484 0.

LCM 16.3 5.5 12.2 2.3 13.7 2,217 2,430 2,490 9,018 3,024 417.5 2.88 2.

MRM NC NC NC 5.7 42.9 NC NC NC 2,977 1,736 NC NC N

MRMF 41.0 NC NC NC NC 1,776 NC NC NC NC 678.9 NC N

LMM 43.5 <1.2 <5.2 4.3 38.2 2,889 1,980 2,660 7,602 2,209 1,295 3.58 5.

UCW2 270.3 NC NC NC NC 1,028 NC NC NC NC 148.6 NC N

HCW2 13.1 <1.2 <5.2 4.9 11.5 2,162 2,280 1,900 7,004 2,762 580.4 3.85 0.

KRM NC <1.2 <5.2 NC NC NC 970 3,360 NC NC NC 8.07 8.

OCSM 29.7 <1.2 <5.2 5.8 7.3 2,392 457 2,000 2,154 1,397 362.3 2.02 1.

RRG2 31.3 NC NC NC NC 2,459 NC NC NC NC 587.2 NC N

1Results from a separate U.S. Geological Survey study as reported in Thomas and others (2007).2Underwood Creek at Watertown Plank Road at Elm Grove (about 3 miles upstream from Underwood Creek at Wauwatosa), Honey Creek near Portland Avenue at Wauwatos

Honey Creek at Wauwatosa), and Root River at Layton Avenue at Greenfield (about 2 miles upstream from the Root River at Grange Avenue at Greenfield).
52 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

of the same streams, Baldwin and others (2013) reported 

that the lowest weights for toxicity tests with Ceriodaphnia 

dubia were measured at the two Milwaukee main-stem sites 

(Milwaukee River near Cedarburg and Milwaukee River at 

Milwaukee) and also the Willow Creek site.

Results from the Fluoroscan fluorescence screen for 

PAHs in SPMDs indicated that the concentrations of the PAH 

indicator pyrene were low in 2013, generally at only a factor 

of two greater than the field blanks, and concentrations were 

highest at the Lincoln Creek and Honey Creek sites (table 9). 

PAH concentrations in 2010, however, were several times 

higher at all six sites and the highest pyrene concentrations 

were at the Lincoln Creek and Little Menomonee River sites; 

concentrations in all blanks were less than method detection limits. These results were similar to the 2010 results for 

P450RGS tests, where TEQs were much higher than in other 

years. SPMDs in 2010 were deployed 5–12 days after historic 

floods in July 2010, and samplers may have been exposed 

to additional PAH-laden runoff in floodwaters. In general, 

concentrations in 2007 were more similar to concentrations 

in 2013, except for the Lincoln Creek site where the highest pyrene and total PAHs among all six sample sites were 

measured in 2007 (Scudder Eikenberry and others, 2010). 

In 2004, the highest PAH concentrations were at the Little 

Menomonee River and Menomonee River at Menomonee 

Falls sites, and the highest pyrene concentrations were at the 

Little Menomonee River site, followed by the Menomonee 

River at Menomonee Falls and the Root River at Greenfield 

sites. Concentrations of PAHs were also high at the Lincoln 

Creek, Honey Creek, and Oak Creek sites in 2004 (Thomas 

and others, 2007); relative comparisons only are made for the 

2004 values because they are orders of magnitude higher than 

values for other years (table 9).

Baldwin and others (2013) determined that concentrations of PAHs in Milwaukee area stormflows were related to 

the percentage of urban land in the watershed and that urban 

storm runoff was an important source of PAHs and other 

organic waste compounds to area streams. In a later study, 

Baldwin and others (2017) identified coal-tar sealcoat from 

parking lots and roads as the primary source of PAHs to area 

streams; the City of Milwaukee banned coal-tar sealcoats in 

2017 (Milwaukee Journal Sentinel, 2017). PAHs are the largest class of suspected human carcinogens and are common 

urban contaminants, formed mainly during incomplete burning 

of fuel, primarily petroleum, oil, coal, and wood (Bjørseth and 

Ramdahl, 1985; Van Metre and others, 2000, 2009). Urban 

sources include not only emissions and wastes from these 

processes but also commonly used coal-tar pavement sealants 

(Mahler and others, 2005; Van Metre and others, 2009). PCBs 

are highly toxic at low concentrations and break down slowly 

in the environment; thus, despite a ban on PCBs in 1979, they 

are still a concern (Mahler and others, 2005). The Milwaukee 

Estuary was named a Great Lakes Area of Concern in the late 

1980s because of severe sediment contamination, primarily from PCBs but also from PAHs (Wisconsin Department 

of Natural Resources, 2013). PBDEs are a component of 

flame retardants in many consumer products and are persistent, bioaccumulative, and toxic (Siddiqi and others, 2003; 

U.S. Environmental Protection Agency, 2017). Dioxins and 

furans are also highly toxic and persistent chemicals that are 

produced as byproducts of certain industrial processes; they 

are still present in the environment despite control of industrial sources beginning in the late 1980s (National Institute of 

Environmental Health Sciences, 2017).

In summary, tests with SPMDs indicate potential toxicity from synthetic organic chemicals at all six sites sampled in 

2013 (table 9), with the highest potential toxicity at the Little 

Menomonee River, Milwaukee River at Milwaukee, Lincoln 

Creek, and Honey Creek sites. In 2013, the Milwaukee River 

at Milwaukee and Little Menomonee River sites had moderate acute toxicity based on Microtox tests. The Lincoln Creek, 

Honey Creek, and Little Menomonee River sites ranked the 

highest for toxicity from compounds such as dioxins, PCBs, 

and PAHs based on the P450RGS test, and the Lincoln Creek 

and Honey Creek sites were highest for PAHs in 2013, based 

on Fluoroscan tests with pyrene as an indicator.

Relations between Biological Metrics and 

Environmental Stressors

Relations between biological metrics and measured environmental stressors, including chemical and physical stressors 

and stream habitat, were examined across sampling years from 

2004 to 2013. The relations to environmental stressors were 

examined separately for each group of aquatic biota. Many of 

the correlations detected were not simple linear relations but 

instead had an “L” or inverted “L” shape that may indicate 

a threshold effect—at low values of the explanatory variable, there are decreases in the biological metric and then at 

some point, the biological metric drops markedly to zero or a 

minimal value. There were also wedge-shaped distributions 

commonly seen in ecological studies that represent factor 

ceilings, the highest biological metric value attained given the 

environmental stressors present (Carter and Fend, 2005; Carter 

and others, 2009). Factor ceilings can be useful management 

tools. Environmental metrics correlated to algae, invertebrates, 

and fish are shown in figures 11–13 and are summarized in 

table 10.

Algae

Several algal metrics correlated significantly with 

environmental stressors: high total phosphorus-indicator 

diatoms (optima greater than or equal to 0.100 mg/L), 

α-mesosaprobous diatoms (moderately tolerant taxa associated 

with DO saturations of 25–70 percent and BOD5 values of 

4–13 mg/L), diatoms sensitive to nutrient and organic enrichment, facultative nitrogen-heterotrophic diatoms (taxa requiring periods of high organically bound nitrogen), nitrogenautotrophic diatoms (indicating low organic nitrogen), fairly 

high oxygen tolerance or requirements (more than 75-percent 

saturation) diatoms, high calcium optima (more than 40 mg/L) 
Assessment of Aquatic Communities in Relation to Stream Condition 53

diatoms, and diatoms with tolerance or requirements for dissolved salts (halobiontic) (fig. 11). Nondiatom metrics that 

correlated significantly with environmental stressors were soft 

algae with low chloride optima (less than 15 mg/L), soft algae 

with low suspended-sediment optima (less than 15 mg/L), 

and sestonic (planktonic) algae. Several other algal metrics 

also correlated with environmental metrics but with poorer 

relations and redundancy with the algal metrics mentioned 

previously.

With respect to water quality, algal metrics indicated high 

concentrations of nitrogen and DO. Higher mean concentrations of ammonia nitrogen correlated positively to higher 

abundances of diatoms with fairly high oxygen tolerance 

or requirements and to lower abundances of sestonic algae 

(p<0.001; fig. 11A and B). Sestonic algae are more common 

in settings with higher nutrient concentrations (Heiskary and 

Bouchard, 2015). The highest mean concentrations of ammonia nitrogen were measured at the Little Menomonee River 

site in 2007–13 but, with mean pH considered (mean pH was 

7.7 during the same period), mean ammonia nitrogen concentrations at this site did not seem to exceed chronic toxicity levels. Ammonia nitrogen is a potential toxin to aquatic 

organisms. Ammonia nitrogen has anthropogenic sources 

(for example, sewage effluent and runoff from industry, urban 

areas, and agriculture), and it has natural sources (for example, 

fixation of atmospheric nitrogen and hydrogen by microorganisms such as blue-green algae [U.S. Environmental Protection 

Agency, 2013]). In a study of the effects of urbanization on 

aquatic communities, Coles and others (2009) determined that 

differences in algal assemblages correlated with higher total 

nitrogen, alkalinity, and specific conductance for streams in 

the Milwaukee and Green Bay areas (with some site overlap 

with the current study). Other indicators of high nutrients were 

also reflected by algal metrics. Higher concentrations of total 

nonpurgeable inorganic carbon, the form of which (carbon 

dioxide, bicarbonate, and carbonate) is pH dependent and 

important in photosynthesis, correlated to lower abundances 

of diatom taxa that are indicative of organic enrichment: 

α-mesosaprobous diatoms and facultative nitrogen-heterotrophic diatoms (p<0.001; fig. 11C and D). Streams affected by 

excess nutrients can also experience large diurnal swings in 

DO concentrations, with high DO from algal photosynthesis 

during sunlight hours followed by low DO from algal respiration at night. Higher mean DO concentrations correlated negatively with lower abundances of three moderate to sensitive 

algal groups: diatoms with fairly high oxygen tolerance, algae 

with low chloride optima, and soft algae with low suspendedsediment optima (p<0.001; fig. 11E, F, and G). Also, higher 

values for BOD5 (an indicator of the amount of biodegradable 

organic material in the water; that is, the degree of organic 

pollution) and fecal coliform bacteria (an indicator of human 

or other animal waste in the water) correlated significantly to 

higher abundances of high total phosphorus-indicator diatoms 

(p<0.001; fig. 11H and I). BOD5 and animal waste serve as 

nutrient sources to algae in streams.

Runoff into streams was reflected in the algal metrics. 

Higher concentrations of total zinc also correlated to higher 

abundances of high total phosphorus-indicator diatoms 

(p<0.001; fig. 11J). Zinc is a common pollutant in urban storm 

runoff from outdoor galvanized surfaces (siding and roofs) and 

parking lot and road surfaces (tire wear debris) (University 

of Wisconsin-Extension and Wisconsin Department of 

Natural Resources, 1997; Davis and others, 2001; California 

Stormwater Quality Association, 2015). The maximum instantaneous discharge per drainage area correlated significantly to 

higher abundances of high total phosphorus-indicator diatoms 

(p<0.001; fig. 11K). The metric for maximum instantaneous 

discharge per drainage area is an indicator of flood and scour 

effects, and values greater than about 80 cubic feet per second 

per square mile correlated to a large decrease in the percentage 

of diatoms with high calcium optima associated with higher 

conductivity water (p<0.001; fig. 11L). This finding may 

simply reflect dilution of major ion concentrations at higher 

stream discharge but concentrations can also be higher on 

initial flush during a runoff event.

With respect to land-use/land-cover relations to algae, 

correlations again reflected an urban signature. Higher percentages of medium and high-intensity developed land, and 

urban land in the stream buffer, and higher percentages of 

impervious surface in the watershed were all highly correlated with each other (Spearman’s rank correlation coefficient 

[rho] ≥0.93), and these metrics correlated to higher abundances of high total phosphorus-indicator diatoms (p<0.001; 

fig. 11M–O, T). Higher percentages of deciduous forest in 

the watershed were significantly related to decreases in high 

total phosphorus-indicator diatoms and facultative nitrogenheterotrophic diatoms (p<0.001; fig. 11Q and R). At about 

14-percent deciduous forest, a large decrease was seen in 

these diatom metrics that indicated a possible benefit for having higher percentages of deciduous forest in the watershed. 

In contrast, higher percentages of impervious surface in the 

watershed were correlated to lower abundances of diatoms 

sensitive to nutrient and organic enrichment. Similar to the 

effect of deciduous forest on high nutrient-indicator diatoms, 

higher percentages of mixed forest correlated significantly to 

decreases in diatoms with a tolerance or requirement for dissolved salts, indicating that as little as 1-percent mixed forest 

in the watershed might be beneficial with regard to reducing 

salt runoff into these streams (p<0.001; fig. 11S).

Lastly, stream habitat metrics related to nutrients and 

oxygen also correlated significantly with algal metrics. The 

abundance of total phosphorus-indicator diatoms increased 

with urban land in the stream buffer (p<0.001; fig. 11T). 

Higher coefficients of variation in the stream depth correlated 

significantly with higher abundances of facultative nitrogenheterotrophic diatoms (p<0.001; fig. 11U). This group of 

diatoms requires periodic high concentrations of organically 

bound nitrogen in the water that are associated with organic 

enrichment. Related to this, higher mean embeddedness 

correlated significantly with higher abundances of nitrogenautotrophic diatoms, taxa that are usually intolerant of high 
54 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Ammonia nitrogen, in milligrams per liter 

Diatoms with fairly high oxygen tolerance 

(more than 75-percent saturation), 

in percentage of relative abundance

0 0.05 0.10 0.15 0.20 0.25 0.30

0

20

40

60

80

100

A rho=0.56

p<0.001

RRG2007

LMM2013

LMM2007

HCW2007

LMM2010

Ammonia nitrogen, in milligrams per liter

Sestonic algae, in percentage of relative abundance 

0

2

4

6

8

10

12

14

16

18

20

0 0.05 0.10 0.15 0.20 0.25 0.30

B

LMM2013

UCW2010 p<0.001

rho=−0.59

Total nonpurgeable inorganic carbon, in milligrams per liter

α-mesosaprobous diatoms, 

in percentage of relative abundanve

0 20 40 60 80 100

0

20

40

60

80

100

LMM2007

RRG2010

p<0.001

C rho=−0.65

Total nonpurgeable inorganic carbon, in milligrams per liter

Facultative nitrogen-heterotrophic diatoms, 

in percentage of relative abundance

0 20 40 60 80 100

0

20

40

60

80

100

p<0.001

UCW2010

LMM2007

D rho=−0.61

Dissolved oxygen, in milligrams per liter

Diatoms with fairly high oxygen tolerance 

(more than 75-percent saturation), 

in percentage of relative abundance

0 42 86 1210 1614 18

0

20

40

60

80

100

KRM2007

p<0.001

E rho=−0.63

Algae with low (less than 15 milligrams per liter) 

chloride optima, in perentage of relative abundance

Dissolved oxygen, in milligrams per liter

0 42 86 1210 1614 18

0

20

40

60

80

100

RRG2004

RRG2010

RRG2007

RRG2013

p<0.001

F rho=−0.58

Figure 11. Relations between algal metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.
Assessment of Aquatic Communities in Relation to Stream Condition 55

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Dissolved oxygen, in milligrams per liter

Soft algae with low suspended-sediment optima 

(less than 15 milligrams per liter), 

in percentage of relative abundance

0

20

40

60

80

100

G rho=−0.63

p<0.001

RRG2004

RRG2007

RRG2010

RRG2013

MRMF2010

0 42 86 1210 1614 18

Biological oxygen demand, 5 day, in milligrams per liter

High total phosphorus-indicator diatoms, 

in percentage of relative abundance

0

20

40

60

80

100

H

rho=0.57

p<0.001

KRM2007

HCW2004

HCW2007

UCW2013

UCW2004

0 1 2 3 4 5 6

High total phosphorus-indicator diatoms, 

in percentage of relative abundance

0

20

40

60

80

100

I

rho=0.65

p<0.001

HCW2013

HCW2007 KRM2010

Fecal coliform bacteria, in colony forming units per 100 milliliters

0 5,000 10,000 15,000 20,000 25,000 30,000 35,000

High total phosphorus-indicator diatoms, 

in percentage of relative abundance

0

20

40

60

80

100

rho=0.59

p<0.001

J

HCW2013

HCW2004

Total zinc, in micrograms per liter

0 20 40 60 80 100

High total phosphorus-indicator diatoms, 

in percentage of relative abundance

0

20

40

60

80

100

K

rho=0.56

p<0.001

LCM2010

Maximum instantaneous discharge/drainage area,

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

Diatoms with high (greater than 40 milligrams per liter)

calcium optima, in percentage of relative abundance

0

20

40

60

80

100

L rho=−0.63

p<0.001

LCM2010

Maximum instantaneous discharge/drainage area,

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

Figure 11. Relations between algal metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.—Continued
56 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Medium-intensity developed land in the watershed, in percent

High total phosphorus-indicator diatoms,

in percentage of relative abundance

0

20

40

60

80

100

0 10 20 30 40 50

M rho=0.61

HCW2004

p<0.001

High total phosphorus-indicator diatoms,

in percentage of relative abundance

0

20

40

60

80

100

High-intensity developed land in the watershed, in percent

0 42 6 8 10 12 1614 18

KRM2007

KRM2013

KRM2004 KRM

2010

N

rho=0.67

p<0.001

High total phosphorus-indicator diatoms,

in percentage of relative abundance

0

20

40

60

80

100

Mean impervious surface in the watershed, in percent

0 10 20 30 40 50 60

O

rho=0.60

p<0.001

Diatoms sensitive to nutrient and organic enrichment, 

in percentage of relative abundance

0

20

40

60

80

100

Mean impervious surface in the watershed, in percent

0 10 20 30 40 50 60

MRMF2007

KRM2007

P rho=−0.49

p<0.001

High total phosphorus-indicator diatoms,

in percentage of relative abundance

0

20

40

60

80

100

Deciduous forest in the watershed, in percent

0 5 10 15 20 25

Q rho=−0.70

p<0.001

Facultative nitrogen-heterotrophic diatoms, 

in percentage of relative abundance

0

20

40

60

80

100

Deciduous forest in the watershed, in percent

0 5 10 15 20 25

R rho=−0.57

p<0.001

Figure 11. Relations between algal metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 57

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Diatoms with tolerance or requirements for 

dissolved salts, in percentage of relative abundance

0

20

40

60

80

100

Mixed forest in the watershed, in percent

0 1 2 3 4 5

S rho=−0.58

p<0.001

High total phosphorus-indicator diatoms,

in percentage of relative abundance

0

20

40

60

80

100

Urban land in the stream buffer, in percent

0 20 40 60 80 100

T rho=0.58

p<0.001

Facultative nitrogen-heterotrophic diatoms,

in percentage of relative abundance

0

20

40

60

80

100

Coefficient of variation of stream depth

0 50 100 150 200

U rho=0.57

UCW2013

UCW2010

p<0.001

Mean embeddedness, in percent

Nitrogen-autotrophic diatoms (indicating low organic 

nitrogen), in percentage of relative abundance

0

5

10

15

20

25

0 20 40 60 80 100

V rho=0.62

WCG2013

WCG2010

WCG2004

RRG2010

p<0.001

Soft algae with low suspended-sediment optima, 

in percentage of relative abundance

0

20

40

60

80

100

Mean open canopy angle, in degrees

0 20 40 60 80 100 120 140

MRMF2010

MRC2010

W rho=−0.64

p<0.001

Figure 11. Relations between algal metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.—Continued
58 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego; EPA, U.S. Environmental 

Protection Agency; mg/L, milligram per liter]

EXPLANATION

Hilsenhoff Biotic Index, modified to limit the number 

of individuals per taxa to 10 for index computation

4

5

6

7

8

Chloride, in milligrams per liter

0 100 200 300 400 500

A rho=0.57

EPA chronic water-quality 

criterion = 230 mg/L

HCW2013

LCM2007

p<0.001

Macroinvertebrate Index of Biotic Integrity 

0

2

4

6

8

10

Chloride, in milligrams per liter

0 100 200 300 400 500

B rho=−0.55

p<0.001

EPA chronic water-quality 

criterion = 230 mg/L

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

Chloride, in milligrams per liter

0 100 200 300 400 500

C rho=−0.73

p<0.001

EPA chronic water-quality 

criterion = 230 mg/L

Hilsenhoff Biotic Index, modified to limit the number 

of individuals per taxa to 10 for index computation

4

5

6

7

8

Specific conductance, in microsiemens per centimeter at 25 degrees Celsius

0 500 1,000 1,500 2,000 2,500

UCW2013

RRG2007

D rho=0.57

p<0.001

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

Total solids, in milligrams per liter

400 500 600 700 800 900 1,000 1,100 1,200

E rho=−0.71

p<0.001

Mean nutrient value of invertebrate taxa

5

6

7

8

9

10

Total solids, in milligrams per liter

0 200 400 600 800 1,000 1,200 1,400

UCW2013

HCW2013

F rho=0.76

p<0.001

Figure 12. Relations between invertebrate metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 

2004–13. Environmental metrics for water quality are means for the year of ecological sampling.
Assessment of Aquatic Communities in Relation to Stream Condition 59

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Scraper invertebrates, in percent

0

10

5

15

20

25

30

35

Fecal coliform bacteria, in colony forming units per 100 milliliters

0 500 10,000 15,000 20,000 25,000 30,000 35,000

G rho=−0.73

MRM2010

KRM2010 HCW2007 HCW2013

p<0.001

Scraper invertebrates, in percent

0

10

5

15

20

25

30

35

Biological oxygen demand, 5 day

0 1 2 3 4 5 6

H rho=−0.72

MRM2007

KRM2007

p<0.001

Scraper invertebrates, in percent

0

10

5

15

20

25

30

35

Zinc, in micrograms per liter

0 20 40 60 80 100

HCW2004 HCW2013

I rho=−0.56

p<0.001

UCW2010 LCM2010

J rho=−0.68

p<0.001

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

Maximum instantaneous discharge/drainage area, 

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

K rho=−0.75

p<0.001

UCW2010

LCM2010

Maximum instantaneous discharge/drainage area, 

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

Macroinvertebrate Index of Biotic Integrity 

0

2

4

6

8

10

Developed open space, in percent

0 20 40 60 80 100

L rho=0.66

p<0.001

Hilsenhoff Biotic Index, modified to limit the number 

of individuals per taxa to 10 for index computation

4

5

6

7

8

Figure 12. Relations between invertebrate metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 

2004–13. Environmental metrics for water quality are means for the year of ecological sampling.—Continued
60 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

M rho=0.65

p<0.001

Hilsenhoff Biotic Index, modified to limit the number 

of individuals per taxa to 10 for index computation

4

5

6

7

8

Urban land in the stream buffer, in percent

0 20 40 60 80 100

N rho=−0.74

p<0.001

Urban land in the stream buffer, in percent

0 20 40 60 80 100

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

O rho=0.66

p<0.001

Hilsenhoff Biotic Index, modified to limit the number 

of individuals per taxa to 10 for index computation

4.0

4.5

5.0

5.5

6.0

6.5

7.0

7.5

Mean impervious surface in the watershed, in percent

0 20 40 60 80 100

P rho=−0.74

p<0.001

Mean impervious surface in the watershed, in percent

0 20 40 60 80 100

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

Q rho=−0.71

p<0.001

Medium-intensity developed land in the watershed, in percent

0 20 40 60 80 100

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

LCM2013

MRC2004

MRM2010

MRC2010

R rho=−0.58

p<0.001

Stream channel stability as a ratio of mean bankfull area 

to wetted cross-sectional area

0 2 4 6 8 10 12 14

Number of Ephemeroptera-Plecoptera-Trichoptera 

genera

0

4

6

8

2

10

12

14

16

18

20

22

Figure 12. Relations between invertebrate metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 

2004–13. Environmental metrics for water quality are means for the year of ecological sampling.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 61

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego; EPA, U.S. Environmental 

Protection Agency; mg/L, milligram per liter]

EXPLANATION

Fish Index of Biotic Integrity

0

20

40

60

80

Chloride, in milligrams per liter

0 100 200 300 400 500

100

A rho=−0.53

p<0.001

EPA chronic water-quality 

criteria = 230 mg/L

LCM2007

UCW2013

HCW2013

B rho=−0.53

p<0.001

Specific conductance, in microsiemens per centimeter at 25 degrees Celsius

600 800 1,000 1,200 1,400 1,600 1,800 2,000

Fish Index of Biotic Integrity

0

20

40

60

80

100

LCM2007

UCW2013

UCW2007

HCW2013

C rho=−0.54

p<0.001

Nitrite, in milligrams per liter

0 0.02 0.04 0.06 0.08 0.10

Total fish species

0

5

10

15

20

25

HCW2013

LMM2007

D rho=−0.54

p<0.001

Total fish species

0

5

10

15

20

25

Total solids, in milligrams per liter

0 200 400 600 800 1,000 1,200

E rho=−0.56

p<0.001

Number of native fish species

0

5

10

15

20

25

UCW2013

Total nonpurgeable dissolved organic carbon, in milligrams per liter

0 2 4 6 8 10 12 14

F rho=−0.49

MRMF2004

p<0.001

Fecal coliform bacteria, in colony forming units per 100 milliliters, (log10)

0 1 2 3 4 5

Number of native fish species

0

5

10

15

20

25

Figure 13. Relations between fish metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.
62 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Fish Index of Biotic Integrity

0

20

40

60

80

100

G rho=−0.51

p<0.001

LCM2010

Maximum instantaneous discharge divided by drainage area,

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

Tolerant fish individuals, in percent

0

20

40

60

80

100

H rho=0.49

p<0.001

LCM2010

Maximum instantaneous discharge divided by drainage area,

in cubic feet per second per square mile

0 200 400 600 800 1,000 1,200

Fish Index of Biotic Integrity

0

20

40

60

80

100

I rho=−0.66

p<0.001

LCM2007

LCM2010

Urban land in the stream buffer, in percent

0 20 40 60 80 100

J rho=−0.57

p<0.001

Urban land in the stream buffer, in percent

0 20 40 60 80 100

Number of native fish species

0

5

10

15

20

25

Fish Index of Biotic Integrity

0

20

40

60

80

100

K rho=−0.69

p<0.001

LCM2010

LCM2007

Medium-intensity developed land in the watershed, in percent

0 20 40 60 80 100

Fish Index of Biotic Integrity

0

20

40

60

80

100

L rho=−0.64

p<0.001

High-intensity developed land in the watershed, in percent

0 5 10 15 20 25

Figure 13. Relations between fish metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.—Continued
Assessment of Aquatic Communities in Relation to Stream Condition 63

MRC

LCM

MRM

WCG

MRMF

LMM

UCW

HCW

MRW

KRM

OCSM

RRG

RRF

JCM

[rho, Spearman's rank correlation coefficient; p, probability value; <, less than; MRC, Milwaukee River near Cedarburg; LCM, Lincoln Creek at 47th Street at Milwaukee; MRM, 

Milwaukee River at Milwaukee; WCG, Willow Creek at Maple Road, near Germantown; MRMF, Menomonee River at Menomonee Falls; LMM, Little Menomonee River at Milwaukee; 

UCW, Underwood Creek at Wauwatosa; HCW, Honey Creek at Wauwatosa; MRW, Menomonee River at Wauwatosa; KRM, Kinnickinnic River at South 11th Street at Milwaukee; 

OCSM, Oak Creek at South Milwaukee; RRG, Root River at Grange Avenue at Greenfield; RRF, Root River near Franklin; JCM, Jewel Creek at Muskego]

EXPLANATION

Mean impervious surface in the watershed, in percent

0 20 40 60 80 100

Fish Index of Biotic Integrity

0

20

40

60

80

100

M rho=−0.66

p<0.001

LCM2007

LCM2010

Developed open space in the watershed, in percent

0 10 20 30 40 50

Fish Index of Biotic Integrity

0

20

40

60

80

100

N rho=−0.52

p<0.001

Standard deviation of bankful width-to-depth ratio

0 10 20 30 40 50

Fish abundance

0

200

400

600

800

1,000

O rho=0.58

p<0.001

MRC2013

MRC2010

MRC2004

MRM2013

MRM2010

Standard deviation of the velocity-to-depth ratio

0 0.1 0.2 0.3 0.4 0.5

Forage fish tolerant to low dissolved oxygen, 

in percent

0

20

40

60

80

100

P rho=−0.54

p<0.001

KRM2004 KRM2010

Ratio of run to riffle area in stream reach

0 10 20 30 40 50

Fish abundance

0

200

400

600

800

1,000

Q rho=−0.55

MRC2010 p<0.001

MRC2013

Figure 13. Relations between fish metrics and environmental metrics for 14 streams in the Milwaukee area, Wisconsin, 2004–13. 

Environmental metrics for water quality are means for the year of ecological sampling.—Continued
64 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

concentrations of organically bound nitrogen (p<0.001; 

fig. 11V); however, Willow Creek ranked as the most embedded because it is all sand and is a small stream with low productivity. Lastly, as the mean canopy angle of vegetation over 

the stream increased, the abundance of soft algae with low 

suspended-sediment optima decreased significantly, especially 

for canopy angles greater than about 36 degrees (p<0.001; 

fig. 11W). In 2010, the Milwaukee River near Cedarburg site 

was an anomaly for having high mean open canopy angles 

without also having a low abundance of this soft algal group.

Invertebrates

The invertebrate metrics that correlated most with 

environmental stressors included the number of EPT genera, 

HBI–10, mIBI, percentage of scraper invertebrates, and mean 

nutrient tolerance of invertebrate taxa. Scraper invertebrates 

graze on algae and associated material attached to submerged 

surfaces such as rocks, and this feeding group includes some 

mayflies, caddisflies, and other insects (Merritt and Cummins, 

1996). Although all scrapers are not necessarily indicators of 

good water quality, many are and some (mayflies and caddisflies) are also included in EPT metrics.

For water quality, higher mean chloride concentrations in water at stream sites were significantly correlated to 

higher HBI–10 ratings, lower mIBI scores, and lower EPT 

genera values (p<0.001; fig. 12A–C). These results indicate 

degrading invertebrate assemblages with increasing chloride 

concentrations. The invertebrate salinity index (Williams and 

others, 2000) did not correlate significantly with chloride in 

water (rho=−0.33, graph was inconclusive because of many 

values at 10, the maximum value), nor did it correlate significantly with other environmental variables. The narrow range 

Table 10. Summary of environmental metrics correlated to metrics for algae, invertebrates, and (or) fish in streams of the Milwaukee 

Metropolitan Sewerage District planning area of Wisconsin, 2004–13.

[X, metric was present; --, metric was not present]

Environmental metric Algae Invertebrates Fish

Fecal coliform bacteria X X X

Biological oxygen demand, 5 day X X --

Dissolved oxygen X -- --

Ammonia nitrogen X -- --

Total nonpurgeable inorganic carbon X -- --

Total nonpurgeable dissolved organic carbon -- -- X

Chloride -- X X

Specific conductance -- X X

Nitrite -- -- X

Zinc X X --

Total solids -- X X

Maximum instantaneous discharge/drainage area X X X

Developed open space -- X X

Low-intensity developed land -- -- X

Medium-intensity developed land X X X

High-intensity developed land X X X

Urban land in the stream buffer X X X

Impervious surface in the watershed X X X

Deciduous forest X -- --

Mixed forest X -- --

Stream open canopy angle X -- --

Coefficient of variation of stream depth X -- --

Standard deviation of the bankfull width-to-depth ratio -- -- X

Standard deviation of the velocity-to-depth ratio -- -- X

Stream channel stability -- X --

Stream run-to-riffle ratio -- -- X

Stream substrate embeddedness X -- --
Assessment of Aquatic Communities in Relation to Stream Condition 65

of Chloride Contamination Index scores at sites in our study 

(scores ranged from 8 to 10), reflecting generally salt-tolerant 

taxa at all sites, may have made it difficult to detect a significant relation. Mean chloride concentrations were greater than 

230 mg/L, the EPA chronic water-quality criterion for protection of aquatic life (U.S. Environmental Protection Agency, 

1988), in one or more sampling years at several sites (Lincoln 

Creek [2007], Underwood Creek and Honey Creek [2004–13], 

Menomonee River at Wauwatosa [2007, 2013], Kinnickinnic 

River [2007–13], Oak Creek [2004, 2013], and Root River at 

Greenfield [2004–13]). Trends in increasing chloride concentrations of streams in all seasons as a result of road salt were 

reported in the literature for urban areas of the northern United 

States where salt is used to deice roads and parking lots (Judd, 

1970; Corsi and others, 2010, 2015). Corsi and others (2015)

determined that stream chloride concentrations increased in 

13 Milwaukee area streams from 1980 to 2010, including 11 

of the 14 streams sampled in the current study. At only about 

10-percent impervious surface (about 25-percent urban land), 

chloride concentrations began to exceed the criterion. Specific 

conductance, in microsiemens per centimeter at 25 degrees 

Celsius, measured on the day of biological sampling, a useful surrogate measure for chloride and other major ions, 

also correlated positively with chloride (rho=0.68) and the 

HBI–10 (rho=0.57) (p<0.001; fig. 12D). The advantage of 

using specific conductance is that it can be more simply measured than chloride using a multiparameter sonde to provide 

instantaneous values during sampling. Chloride concentrations increased strongly with the percentage of urban land 

in the stream buffer (rho=0.82) and with the percentages of 

low, medium, and high-intensity urban land in the watershed 

(rho>0.77). Other chemical metrics that demonstrated significant negative correlations with invertebrate metrics were total 

solids (which were positively correlated with impervious surface [rho=0.98; not shown]), fecal coliform bacteria, BOD5, 

and zinc, an indicator of urban runoff (p<0.001; fig. 12E–I). 

Lastly, higher values of the maximum instantaneous discharge 

during the year of biological sampling, normalized by drainage area, were significantly related to lower numbers of EPT 

genera and mIBI scores (p<0.001; fig. 12J–K), especially for 

normalized discharge values greater than 40 cubic feet per 

second per square mile.

Percentages of developed open space, urban land in the 

stream buffer, mean impervious surface in the watershed, and 

medium-intensity developed (urban) land in the watershed all 

demonstrated significant adverse relations with the HBI–10 

or number of EPT genera (p<0.001; fig. 12L–Q). Richards 

and others (2010) determined significant positive correlations 

between chloride and several urban-related land-use/landcover metrics, especially the percentage of impervious surface 

in the watershed, urban land, and road coverage. Urban land 

in the stream buffer reduces the ability of natural vegetation 

and uncompacted soil surfaces to absorb rainfall in significant 

amounts and thereby increases the amount of runoff (Roy and 

others, 2006).

Channel stability (the ratio of mean bankfull area to wetted cross-sectional area) correlated negatively with the number 

of EPT genera, and this was the only instream habitat variable that correlated significantly with computed invertebrate 

metrics (p<0.001; fig. 12R). This metric potentially represents 

the possible intensity of flood discharge relative to base flow 

(perennial discharge), and high values represent channels 

prone to erosion. So, in essence, less stable channels were 

related to fewer EPT taxa, which is an adverse effect. Perhaps 

the controlling factor for the invertebrate assemblages is not 

velocity during low flow but instead flashiness and the relation 

of floods to channel substrates. For microhabitat data—data 

for the algal and invertebrate sampling subsites such as depth, 

velocity, and dominant substrate—only depth correlated significantly to metrics computed for invertebrates in the current 

study. Although the relation demonstrated poor predictability, 

HBI–10 values indicated a wedge-shaped distribution with 

microhabitat depth, such that better HBI–10 ratings were more 

likely to be associated with greater riffle depth (p<0.01). The 

reason for the weak or missing relations to microhabitat is 

not clear but it may be due to a general lack of variability in 

microhabitat because shallow cobble riffles were targeted for 

invertebrate sampling at all sites except Willow Creek, where 

they were not available. Still, mean velocity of the reach correlated positively with microhabitat velocity (p<0.001).

Fish

The IBI was the fish metric most commonly correlated 

with the environmental metrics, likely because it is composed 

of 10 fish metrics that were selected by Lyons (1992) because 

they are useful in distinguishing differences in the environmental quality of streams. The IBI developed by Lyons (1992)

is the fish IBI used for warmwater streams in the State of 

Wisconsin. Related fish metrics that also correlated to environmental metrics were the number of fish (abundance), number 

of species (richness), number of native taxa, and fish tolerant 

to low DO. Correlations with fish metrics were determined for 

metrics related to water quality, discharge, land use/land cover, 

and stream habitat (fig. 13).

Fish assemblage metrics related to water quality and 

discharge in a variety of ways. Higher mean chloride concentration and specific conductance correlated significantly 

to lower fish IBI values (p<0.001; fig. 13A–B), similar to the 

adverse response of invertebrates to chloride and specific 

conductance. Declines in fish IBI scores in relation to increasing chloride and specific conductance could be the result of 

direct effects upon the fish by physiological changes, such as 

osmoregulation, and indirect effects, such as from a decline in 

invertebrate food sources. Nutrient effects on fish were also 

seen. As mean nitrite concentrations increased in water, the 

number of fish species decreased significantly as a wedgeshaped or factor-ceiling distribution (p<0.001; fig. 13C). 

Nitrite and ammonia are known to be toxic to fish; however, 

nitrite concentrations are generally low in natural waters 

unless the process of microorganisms converting ammonia to 
66 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

nitrite and then to nitrate is disrupted (Russo and Thurston, 

1977). Significant correlations to fish metrics were not determined for phosphorus. The number of fish species decreased 

as total solids increased, a correlation similar to that seen with 

invertebrates (p<0.001; fig. 13D). Although higher concentrations of total nonpurgeable dissolved organic carbon correlated significantly to higher abundances of native fish species 

(p<0.001; fig. 13E), this relation is probably an artifact of 

the two main-stem Milwaukee River sites (Milwaukee River 

near Cedarburg and Milwaukee River at Milwaukee), which 

have more species. The highest and second highest dissolved 

organic carbon values were for these sites. These two large 

river sites would be expected to have more native species than 

streams that are much smaller in drainage area. In addition, the 

number of native fish species decreased with increasing fecal 

coliform bacteria across sampled sites (p<0.001; fig. 13F). 

Higher values of maximum instantaneous discharge during 

the year of biological sampling, normalized by drainage area, 

were significantly correlated to lower IBI scores and more 

tolerant fish (p<0.001; fig. 13G–H), and fewer native fish species (p<0.001). The correlation with maximum instantaneous 

discharge indicates that more frequent flood and scour effects 

from high flows at some sampled streams, a common problem 

with streams subject to urban runoff, can adversely affect fish 

assemblages.

More urban land in the stream buffer and higher percentages of the watershed as medium and high-intensity developed 

land, developed open space, and impervious surface correlated 

significantly to lower fish IBI values and fewer native fish species (p<0.001; fig. 13I–N). Similar to land-cover correlations 

determined with algae and invertebrates, these results underscore the adverse effects of increased urban land on the aquatic 

communities of nearby waterways.

Instream habitat metrics that correlated to fish metrics 

were related to stream depth and the amount of riffle habitat. 

As expected, higher fish abundance corresponded to more 

available habitat as measured by the standard deviation of 

the bankfull width-to-depth ratio, with the exception of the 

Milwaukee River at Milwaukee site in 2010 and 2013 where 

fish abundance was lower than expected and lower than in 

2004 and 2007 (p<0.001; fig. 13O). The reason for the lower 

fish abundance is not known but, in 2010, the flow was higher 

than in prior sampling events with turbid conditions, the 

current was swift in some areas, and no fish were captured 

in seine hauls. This was also the first year that the invasive 

Neogobius melanostomus (round goby) was detected at this 

site. Higher percentages of forage fish tolerant to low DO 

were more likely at sites with a lower standard deviation in 

the velocity-to-depth ratio (Lincoln Creek, Willow Creek, 

Menomonee River at Menomonee Falls, Little Menomonee 

River, and Kinnickinnic River) when compared to sites with 

a higher standard deviation in the velocity-to-depth ratio 

(Milwaukee River near Cedarburg, Milwaukee River at 

Milwaukee, Menomonee River at Wauwatosa, Honey Creek, 

and Jewel Creek; p<0.001; fig. 13P). A lower standard deviation relates to less variability and may therefore reflect less 

“complexity” in velocity-to-depth combinations and fewer 

types of habitat for fish. In general, fish abundance was higher 

at sites where the ratio of run to riffle area was lower, meaning that the riffle area was greater than the run area (p<0.001; 

fig. 13Q). Channelization of a stream generally is done by 

increasing the depth and straightening the channel uniformly 

(Hohensinner and others, 2018). Riffles are usually an indication that habitat overall has not been degraded by channelization or sedimentation, whereas more runs are an indication that 

a stream is channelized and lacks habitat complexity. Riffles 

play an important role in the production of food, and DO in 

stream sections is key to healthy fish assemblages (Simonson 

and others, 1993).

Summary Bioassessments of Individual Streams

In this section, we consider each stream individually, 

summarize how each group of biota has fared in the years 

from 2004 to 2013, and attempt to relate measured environmental stressors to any changes over time. Where possible, 

assessment results in one group of organisms are compared 

with results for another group to confirm or contradict the 

overall ecological assessment of the stream. This summary is 

not meant to provide a comprehensive, general background on 

each stream or river because such information is readily available in other publications. Instead, the focus is on the aquatic 

communities and possible changes in their status.

Milwaukee River near Cedarburg

This site has remained at the top of the aggregate bioassessment rankings in 2004 and 2013, reflecting its overall 

good condition and diverse aquatic habitat (table 8). For 

algae, three phyla (diatoms and green and blue-green algae) 

were collected in 2004; these three phyla were collected in 

2013 also, with the addition of red algae in 2010 (table 3). 

Biovolume was several orders of magnitude higher in 2013 

than 2004. This site had more than 1.7 times the biovolume 

in 2013 compared with other sites, and this held true for all 

years with the exception of Jewel Creek in 2013, where total 

biovolume was similar to Milwaukee River near Cedarburg 

(table 2). Algal diversity improved from high stress (diversity 

index <1.5) in 2004 to moderate stress in 2013 (table 2). The 

percentage of relative abundance of eutrophic diatoms in 2013 

was greater than 10 percent higher than in 2004, and relative 

abundance of diatoms in 2013 was about 10 percent lower 

than in 2004 (table 3). The higher overall algal biovolume, the 

lower relative abundance of diatoms, and the greater relative 

abundance of eutrophic diatoms indicate adverse changes in 

the algal assemblage, in contrast with higher diversity metrics 

noted in 2013 compared with 2004. Higher diversity with 

adverse indicators may occur if additional taxa and abundance 

stem from nuisance algae. Environmental explanations related 

to these results are unclear; however, water chemistry data 
Assessment of Aquatic Communities in Relation to Stream Condition 67

demonstrated that mean Escherichia coli and fecal coliform 

bacteria counts were unusually high for this site in 2010 but 

not in 2013 though nutrients were consistent across years.

The invertebrate assemblage at this main-stem site 

includes diverse and abundant aquatic insect larvae and 

freshwater mussels. Although the percentage of noninsects 

increased slightly from 0.77 percent in 2004 to 2.06 percent in 

2013, this was because freshwater mussels were collected in 

2013 but not in 2004 (table 5). Freshwater mussels are indicators of good water quality that are not adequately sampled by 

our collection methods because of the highly patchy nature 

of these organisms. Although the percentage of EPT taxa and 

the HBI–10 were relatively constant over the sampling years, 

diversity and the mIBI were lower in 2013 (5.94, “fair”) compared with 2004 (7.59, “good”). Genera richness and EPT genera were highest in 2004 and lowest in 2013 (fig. 6A). These 

results, although somewhat conflicting, may indicate adverse 

changes in the invertebrate assemblage at this site.

There were no discernable changes in the fish assemblage during 2004–13 at the site. The site is a scenic, meandering stream that supports a diverse variety of fish species, 

including desirable game fish such as Micropterus dolomieu

(smallmouth bass), Esox lucius (northern pike), and pan fish. 

Of the 48 fish species collected in the greater MMSD area 

during the study, 29 were detected at the Milwaukee River 

near Cedarburg site, the highest richness at any site. The IBI 

scores have consistently been the highest of all sampling sites 

in the study area (table 7, fig. 9A). For richness, 21 species 

were collected in 2013, compared with 22 in 2010 and 21 in 

2004. In 2007, severe weather restricted electrofishing and the 

crew was unable to complete more than a single pass of the 

reach. The number of species (15) and individual fish collected 

reflect that not all habitats were thoroughly sampled that year. 

Oddly, diversity was about 27 percent lower in 2013 (1.91) 

than in 2004 (2.61). On July 20, 2016, the sampling crew 

detected 60 invasive round gobies, which we believe is a first 

for this site. It is not clear how this new invader will affect the 

assemblage going forward in future assessments of ecosystem 

condition.

Environmental stressors at the Milwaukee River near 

Cedarburg site are currently few but runoff from urban and 

agricultural land is a concern in addition to invasive species. 

As mentioned earlier, toxicity tests from SPMDs indicated 

some potential toxicity from hydrophobic organic compounds 

such as PCBs, PAHs, and so on, but PAH screening indicated 

low concentrations of pyrene in 2007 and 2013 and moderate concentrations in 2010 (table 9). However, Thomas and 

others (2007) noted moderately high PCBs in 2004–5 that 

may have originated from a PCB-contaminated site on Cedar 

Creek, which joins the Milwaukee River upstream from the 

sample site (for information about the Cedar Creek site, see 

U.S. Environmental Protection Agency, 2014). Although 

Baldwin and others (2013) determined that the Milwaukee 

River near Cedarburg during 2006–9 was one of two sites with 

the lowest detection frequencies and concentrations of organic 

waste compounds, at least 80 percent of stormflow samples 

had detections of PAHs, plasticizers, solvents, herbicides, 

insecticides, flavors/fragrances, and steroids. In the same study 

for a larger suite of organic waste compounds, detection frequencies in porewater samples were also 80 percent or greater. 

In the current study, mean specific conductance was similar 

for all ecological sampling years but was lowest in 2004 at 

721 microsiemens per centimeter at 25 degrees Celsius (μS/

cm at 25 °C). Although the mean chloride concentration of 

79.6 mg/L in 2013 was low relative to other sites, chloride 

was 29 percent higher than in 2004 (61.7 mg/L). Values for 

maximum instantaneous discharge were similar between 2013 

and 2004, indicating no difference between the two years 

with regard to scour from flooding; even in 2010 when other 

streams in the Milwaukee area experienced significant flooding, this metric was relatively low compared with the downstream site at Estabrook Park in Milwaukee. In general, water 

quality at this site seems good, but there are some potential 

environmental stressors on the aquatic community and cause 

for concern.

Lincoln Creek

Mean bioassessment rankings for Lincoln Creek were relatively consistent across algae, invertebrates, and fish assemblages in 2013, placing this site with the lowest water-quality 

sites in group 4, although the aggregate ranking in 2013 was 

slightly better than in 2004 (table 8). Algal assemblages at 

Lincoln Creek included three phyla (diatoms and green and 

blue-green algae) in 2004 and 2013, and the percentage of relative abundance of blue-green algae was more than 10 percent 

lower in 2013 compared with 2004 (table 3). Algal biovolume 

was also lower in 2013 than in 2004 (table 2). Pollutiontolerant diatom abundance in 2013 was about 18 percent 

higher compared with 2004. Pollution-sensitive diatom 

abundance also increased by about 13 percent from 2004 to 

2013; however, there were less than 30-percent pollutionsensitive diatoms in 2013 at this site. Diversity improved from 

high stress (diversity index <1.5) in 2004 to moderate stress 

(diversity index 1.50–2.50) in 2013. The percentage of relative 

abundance of halobiontic diatoms (tolerance or requirements 

for dissolved salts) was more than 26 percent lower in 2013 

compared with 2004. These results are mixed but indicate 

slightly positive changes in the algal assemblage at this highly 

urban site.

Fewer invertebrate taxa and lower diversity detected in 

2013 compared with previous sampling years were in contrast 

to the percentage of EPT taxa, which was 11 percent higher 

in 2013 than 2004 (table 5 and fig. 6A). However, some EPT 

taxa are known to be relatively tolerant (Barbour and others, 

1999), including some mayfly (Baetis intercalaris) and caddisfly (Cheumatopsyche) taxa that dominated in 2013 at this 

site for orders Ephemeroptera and Trichoptera, respectively. 

The percentage of noninsects was greater than 20 percent in 

most sampling years except 2007, and the percentage was only 

slightly changed in 2013 compared with 2004. This likely contributed to “fairly poor” and “poor” ratings by the HBI–10 and 
68 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

mIBI, respectively, for invertebrate assemblages at this site in 

2013. Overall, the invertebrate assemblage at this site has not 

yet shown the improvements hoped for after the 2002 restoration. The invertebrate assemblage in 1993 was rated “fair” 

based on HBI scores (Peters and others, 1998).

Changes in habitat as a result of the 2002 restoration were 

initially reflected in generally positive differences in the fish 

assemblage but sampling results for 2013 were not positive. 

Sampling at the site before the restoration detected six species 

of disturbance-tolerant fish (fathead minnow, green sunfish, 

Lepomis gibbosus [pumpkinseed], green sunfish × pumpkinseed hybrid, and Ameiurus melas [black bullhead]) in 1993 but 

only one to two species (fathead minnow and green sunfish) 

in 1994 and 1995 (Sullivan, 1997). Sample collection resulted 

in the collection of 8 species in 2004; 11 and 12 species in 

2007 and 2010, respectively; and 7 species in 2013 (table 7). 

Fish abundances in USGS sample collections during the 1990s 

at this site were fewer than 50 individuals, and IBI scores 

rated “poor” in 1993–5 (Sullivan, 1997; Peters and others, 

1998). In 2007, abundance peaked at 170 individuals and, in 

2013, abundance was only 25, too few to compute a standard 

IBI (value of 15). Of 25 individuals, 13 were green sunfish; 

therefore, the IBI was rated “very poor.” Because of the low 

numbers of fish captured, invertebrates are probably a better 

indicator of the water quality here. Diversity was 12 percent 

lower in 2013 than in 2004 with values of 1.50 and 1.71, 

respectively.

Several environmental stressors are present at the Lincoln 

Creek site. In 2004, 2010, and 2013 (no data collected in 

2007), maximum instantaneous discharge normalized by 

drainage area was high at Lincoln Creek relative to the other 

sampled sites, and this metric is an indicator of flood and 

scour effects on stream channels with higher values indicating 

greater effects (fig. 11L). Fecal coliform counts were many 

times higher than at less urban sites such as the Milwaukee 

River near Cedarburg; chronic human fecal contamination 

of Lincoln Creek from sanitary sewage sources has been a 

well-known issue (Sauer and others, 2011). Thomas and others (2007), who studied the same ecological monitoring sites, 

determined that fecal coliform counts increased with increasing total urban land. The Milwaukee River near Cedarburg 

site had the lowest fecal coliform counts and urban land 

percentage, followed by the Milwaukee River at Milwaukee 

site. Sites with the highest urban land percentages also had 

the highest fecal coliform counts: Lincoln Creek, Underwood 

Creek, Root River at Greenfield, and Kinnickinnic River. 

The highest mean total phosphorus of all sites was at Lincoln 

Creek in 2007 at 0.260 mg/L, which is greater than the State 

of Wisconsin’s criterion of 0.075 mg/L, averaged May through 

October, to minimize nuisance algal/plant growth in wadable 

streams (Wisconsin Department of Natural Resources, 2019). 

Although most phosphorus in Milwaukee area watersheds is 

thought to come from urban and agricultural nonpoint sources, 

some municipal water supplies in Milwaukee began adding a 

soluble phosphate additive as an anticorrosive agent for copper 

and lead pipe abatement in the 1990s; through industrial and 

wastewater treatment sources, this can contribute additional 

phosphate to streams including Lincoln Creek (Wisconsin 

Department of Natural Resources, 2013; William Wawrzyn, 

Wisconsin Department of Natural Resources, written commun., December 5, 2014). Chloride concentrations at Lincoln 

Creek were high relative to other sites, and mean chloride 

concentrations in 2007 greatly exceeded the EPA chronic 

water-quality criterion of 230 mg/L and Wisconsin’s chronic 

criterion of 395 mg/L (Wisconsin Department of Natural 

Resources, 2019), reflecting this site’s highly urban setting and 

contributions from road salt runoff. PAH analyses of SPMD 

extracts in 2007 indicated estimated water concentrations of 

130 nanograms per liter (ng/L) pyrene and 520–560 ng/L total 

PAHs, the highest concentrations among six sites sampled that 

year. Baldwin and others (2013) detected a variety of organic 

waste compounds at the Lincoln Creek site in 2006–9; in at 

least 80 percent of sediment samples, PAHs, antimicrobial 

disinfectants, and detergent metabolites were detected in 

moderately high concentrations (>1,000 micrograms per liter 

[μg/L]) and steroids were detected in high concentrations 

(≥10,000 μg/L). In the same study for a larger suite of organic 

waste compounds, detection frequencies in porewater samples 

were also 80 percent or greater. With regard to stream habitat, 

the channel stability at Lincoln Creek was the highest of any 

sampled streams. This finding reflected the construction design 

of having a low flow channel for fish passage within a much 

larger channel for passage of frequent flood flows. Regardless, 

higher values for channel stability across all sites and dates 

were significantly correlated with lower numbers of invertebrate EPT genera (p<0.001). High stream discharges that carry 

urban runoff with sewage, nutrients, chloride, and organic 

waste compounds are important environmental stressors in this 

and many other small urban streams.

Milwaukee River at Milwaukee

Although the aggregate bioassessment ranking for this 

site in 2013 was in the top tier of sites in group 1, the actual 

value was worse than in 2004 (table 8). The mean bioassessment ranking for algae in 2013 fell to the bottom tier of sites 

in group 4, which was in contrast to relatively high rankings 

for invertebrates and fish and a high aggregate bioassessment 

ranking in 2013 and 2004. The algal assemblage at this site 

reflects the diverse and complex nature of a large river. The 

most algal taxa (70) collected from any site in 2004 were 

detected here (table 2), including three phyla (diatoms and 

green and blue-green algae) in 2004 and the addition of red 

algae in 2010 and 2013 (tables 2 and 3). Samples collected 

in 2013 had lower algal biovolume than in 2004. The relative 

abundance of diatoms was more than 20 percent lower in 2013 

compared with 2004 and the relative abundance of blue-green 

algae was also more than 15 percent higher in 2013 compared 

with 2004. The abundance of pollution-tolerant diatoms in 

2013 was about 10 percent higher compared with 2004, and 

this metric is one of the two metrics used in the aggregate 

bioassessment ranking. Diversity improved from high stress 
Assessment of Aquatic Communities in Relation to Stream Condition 69

(diversity index <1.5) in 2004 to moderate stress in 2013. 

Overall, the algal assemblage remains diverse but the shift 

to more pollution-tolerant diatoms, including fewer diatoms 

overall and a greater abundance of blue-green algae, indicates 

a decline in water quality at this site from 2004 to 2013.

The numbers of invertebrate taxa (species and genera) 

collected were lower each year after 2004 (table 5), which 

also supports the water-quality assessment based on algal 

assemblages. The total number of invertebrate species and 

genera, and diversity, were more than 36 percent lower in 

2013 compared with 2004. In 2013, the diversity of 1.94 

was much lower than in all previous sampling years and was 

similar to Lincoln Creek. The invertebrate mIBI score rated 

“fair” in 2013, in contrast with “good” ratings in all previous 

sampling years and scored 15 percent lower than in 2004. In 

2007, the percentage of noninsects was higher than in other 

sample years because of the presence of worms, oligochaetes, 

and flatworms. Increasing percentages of noninsects at this 

site, together with the decrease in total taxa, lower diversity, 

and mIBI ratings, all point toward declines in water quality and stream condition at this site, especially in comparison to upstream near Cedarburg. This pattern indicates that 

water-quality degradation is fairly localized, because the 

upstream Cedarburg site does not indicate a similar waterquality decline.

Similar to the upstream site near Cedarburg, the 

Milwaukee River at Milwaukee’s fish assemblage benefits 

from its size and diversity of habitat but fish abundance has 

scored lower than Cedarburg with the exception of 2007, 

when sampling at Cedarburg was limited to one upstream pass 

because of severe weather (table 7). The fish IBI was rated 

“good” in 2004–10 to “excellent” in 2013. Fish metrics for 

this site were similar across years except that no darter species 

were collected in 2013. Specifically, Percina caprodes (common logperch), which made up 17 percent of fish abundance 

in 2004, were less than 2 percent in 2007 and 0 in 2013. In 

2010, the sample from this site included round gobies for the 

first time, and the 2013 survey detected abundant individuals of this invasive fish again at the site. The round goby was 

16 percent of the overall fish abundance in 2010 and about 

5.8 percent in 2013.

With respect to potential environmental stressors at this 

Milwaukee River site, mean fecal coliform bacteria counts 

were much higher in 2010 and 2013 at 7,209 and 1,078 colony 

forming units per 100 milliliters (CFU/100 mL), respectively, 

when compared with <700 CFU/100 mL in 2004 and 2007. 

The mean E. coli bacteria counts for 2010 were more than 

twice that of other sampling years and may have been related 

in part to the historic flooding on July 22, 2010 (also high in 

2010 at the Cedarburg site). These results indicate possible 

sanitary waste contamination at this site. Across all sites and 

years, increasing fecal coliform bacteria concentrations were 

significantly correlated to higher abundances of high total 

phosphorus-indicator diatoms (fig. 11I) and lower abundances 

of scraper invertebrates (fig. 12G). Results from SPMD tests 

indicated potential toxicity at this site in 2010 and 2013 from 

hydrophobic organic chemicals such as PCBs and (or) PAHs, 

and so on, although PCBs are more likely than PAHs, based 

on PAH screening that detected low pyrene concentrations in 

2013 (table 9). PCB deposits less than 1 mile upstream from 

the Estabrook Park site represent the largest known deposit in 

the Milwaukee Estuary Area of Concern (Epping Overholt, 

2014). Sediment remediation is in progress by the State 

and Federal government (Wisconsin Department of Natural 

Resources, 2016). Chloride concentrations that may be a problem in smaller streams are more diluted out. Embeddedness 

at the invertebrate microhabitat sites in 2013 was more than 

double that seen in 2004 (30 and 82, respectively) and this can 

adversely affect streambed-dwelling organisms, especially the 

freshwater mussel assemblage at this site. The percentage of 

urban land and percentage of impervious surface increased by 

about 1 percent from 2004 to 2013 (that is, between NLCD 

datasets for 2006 and 2011). The stressors listed above are 

commonly associated with urban runoff (Coles and others, 2012).

Willow Creek

The aggregate bioassessment ranking for Willow Creek 

in 2013 was at the low end of the group 2 tier of sites, yet the 

ranking still indicated fairly good water quality relative to 

other sampled sites (table 8). However, algae ranked much 

lower than invertebrates and fish in 2013. Three algal phyla 

(diatoms and green and blue-green algae) were collected in 

2004, with the addition of red algae in 2007 (table 3). Lower 

algal biovolume was measured in 2013 than 2004 (table 2). 

The percentage of relative abundance of diatoms was more 

than 40 percent lower in 2013 compared with 2004, and the 

percentage of relative abundance of blue-green algae was 

more than 28 percent higher in 2013 compared with 2004. 

Pollution-sensitive diatoms were about 27 percent lower in 

2013 compared with 2004, whereas the percentage of relative abundance of eutrophic diatoms was 20 percent higher in 

2013 than 2004. The decrease in diatom abundance, especially 

pollution-sensitive diatoms, together with an increase in bluegreen algae and eutrophic diatoms indicate a more degraded 

algal assemblage in 2013.

Most metrics for the invertebrate assemblage in Willow 

Creek were more than 10 percent lower in 2013 than in 2004 

(table 5). The mIBI and percentage of EPT taxa did not demonstrate much variation between sampling years. The largest 

negative difference in metric values was seen for diversity, and 

the percentage of noninsects more than tripled from 12.2 to 

43.6 percent among years. Noninsect taxa, which are generally considered to be more tolerant of degraded environmental 

conditions (amphipods, isopods, and snails), were more common in 2013. Both differences in metric values indicate a more 

degraded invertebrate assemblage in 2013 than 2004.

The fish assemblages at this site are affected by its lowgradient and sand-bottomed habitat with cover provided by 

overhanging grasses in the lower part of the reach and relatively dense tree cover in the upper part of the reach. Most of 
70 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

the fish were collected in the lower part of the reach. In 2013, 

the fish assemblage was dominated by Etheostoma nigrum

(johnny darter), followed by creek chub, Culaea inconstans

(brook stickleback), and Umbra limi (central mudminnow). 

Although the number of fish collected was more than 51 percent lower in 2013 than 2004, the number of taxa (genera and 

species) was 17 percent higher in 2013 (table 7). Although the 

IBI score was more than 23 percent higher in 2013 than 2004, 

this still indicated a rating of “poor” for the fish assemblage in 

2013 and 2004.

Environmental data for this site are incomplete because 

of missing data for flow and water chemistry, and it is therefore difficult to evaluate potential stressors on the biota. 

In 2013, the percentage of relative abundance of nitrogenautotrophic diatoms (indicating low organic nitrogen concentrations) was 19.5 percent and was higher than in other 

sampling years, especially 2004, and higher than for all other 

sites and dates. This finding indicates algal assemblages at 

Willow Creek may be nitrogen limited. Chlorophyll a in benthic algal samples was an order of magnitude higher in 2013 

(188 milligrams per square meter [mg/m2]) compared with 

2007 and 2010 (20.8 mg/m2 and 11.3 mg/m2, respectively); 

chlorophyll a was not characterized in 2004. The percentage 

of urban area increased slightly (about 1 percent) from 2004 

to 2013 to 25 percent and may have contributed additional 

urban runoff.

Menomonee River at Menomonee Falls

Aggregate bioassessment scores for algae, invertebrates, and fish at this site ranked the Menomonee River at 

Menomonee Falls second in group 1 for 2013, improving from 

fourth in 2004 and indicating better water quality than most 

other sites in the study (table 8). Four algal phyla (diatoms and 

green, blue-green, and red algae) were collected in 2013 and 

2004 (table 3); however, the fewest algal taxa (37) from any 

site in 2013 were collected here when compared with all other 

sampled sites (table 2). The relative abundance of diatoms was 

more than 25 percent lower in 2013 compared with 2004; relative abundance of blue-green algae was more than 20 percent 

higher in 2013 compared with 2004 (table 3). Higher algal 

biovolume was collected in 2013 than 2004. These metric 

changes all indicate the algal assemblage was degraded in 

2013 compared with 2004. However, the relative abundance of 

halobiontic diatoms was more than 10 percent lower in 2013 

compared with 2004 despite a steady increase in waterborne 

chloride concentrations from 2004 to 2013; the mean chloride 

concentration in 2013 was less than the EPA chronic waterquality criterion of 230 mg/L.

The total number of invertebrate taxa was more than 

10 percent lower in 2013 compared with 2004 (table 5). 

Although the HBI was lower, resulting in a “good” rating in 

2013, diversity and the mIBI were more than 10 percent lower 

in 2013 than in 2004, and the ratings for the mIBI were “fair” 

in both years. The percentage of EPT was similar between 

2013 and 2004, as was the percentage of noninsects. The use 

of the HBI and EPT metrics in the bioassessment rankings 

gave a more positive ranking for the 2013 sample than was 

indicated by other invertebrate metrics. Dominant taxa were 

a tolerant mayfly, followed by a riffle beetle (Stenelmis), and 

several species of sensitive and tolerant caddisflies.

The fish IBI was higher in 2013, resulting in a “fair” rating despite a 60 percent lower total number of fish collected 

when compared with 2004 (table 7). Sampling crews did not 

indicate any major issues that would have caused such variability in the total number of fish collected. The number of 

species, IBI, and number of native species were all more than 

10 percent higher in 2013, and the percentages of pollutiontolerant fish and forage fish tolerant to low DO decreased. 

These results indicate the fish assemblage, water quality, and 

stream condition remain relatively good overall.

Environmental stressors at this upstream Menomonee 

River site may be related to urban runoff that delivers nutrients, chloride, and other contaminants to the stream. In 2013, 

the maximum instantaneous discharge, normalized by drainage area, was about 50 percent of that recorded for 2004 (16.3 

compared with 31.4) but, as with several other area streams 

in 2010, this metric was high compared with other sample 

years. Historical water-quality data for this site from the 

MMSD indicated that this site met water-quality criteria for 

total phosphorus and fecal coliform less than 50 percent of 

the time (Milwaukee Metropolitan Sewerage District, 2004). 

Mean concentrations for total phosphorus in all sampling 

years ranged from 0.066 to 0.090 mg/L, greater than the State 

of Wisconsin’s criterion of 0.075 mg/L, averaged May through 

October, to minimize nuisance algal/plant growth in wadable 

streams (Robertson and others, 2006; Wisconsin Department 

of Natural Resources, 2019). Occasional excess nutrients from 

phosphorus and fecal contamination from runoff and wastewater contamination could be contributing to the declines 

in the algal assemblage, marked by fewer diatoms and more 

blue-green algae, which would have cascading effects on 

the invertebrate assemblage. Mean specific conductance has 

gradually increased since 2004 and was slightly higher in 2013 

compared with 2004 (984 and 903 μS/cm at 25 °C, respectively), indicating an increase of dissolved solids such as chloride in runoff. Similarly, mean chloride concentrations steadily 

increased from 92 to 142 mg/L in 2004 to 2013 but were still 

less than the EPA water-quality criterion of 230 mg/L chloride. 

Although SPMDs were not deployed at this site in later years, 

fluorescence screening of SPMD extracts deployed in 2004 

demonstrated high concentrations of PAHs.

Little Menomonee River

In 2013, the mean bioassessment rankings for this site 

were variable across all three groups of biota, and the aggregate bioassessment ranking was similar to 2004 (table 8). 

Three algal phyla (diatoms and blue-green and red algae) 

were detected in 2004; however, only diatoms and blue-green 

algae were detected in 2013 (table 3). Change in the relative 

abundance of any of the algal groups was less than 10 percent 
Assessment of Aquatic Communities in Relation to Stream Condition 71

between 2013 and 2004, and red algal abundance was only 

7.6 percent in 2004. Algal biovolume was more than two 

times higher in 2013 than 2004 (table 2). Pollution-sensitive 

diatoms were 25 percent higher in 2013 than 2004, and this 

metric is one of two metrics used in the aggregate bioassessment ranking. The relative abundance of halobiontic diatoms 

was 29 percent lower in 2013 than 2004. Overall, these metric 

results indicate less degraded algal assemblages at this site in 

2013 than 2004.

The invertebrate assemblage at this site demonstrated 

mixed results for metrics. The number of species was 22 percent higher in 2013 than 2004, and the mIBI scored about 

30 percent higher in 2013, resulting in a “fair” rating compared with a “poor” rating in 2004 (table 5). These metric 

outcomes were in contrast, however, with a diversity value 

that was more than 13 percent lower in 2013. The percentage 

of noninsects increased by more than 17 percent in 2013, and 

this may be the reason behind the increase in species number. 

The assemblage in 2013 was dominated by isopods, followed 

by midges. The HBI–10 score was about 12 percent higher in 

2013 and, although the rating was worse than the “good” rating for this site in 2004, it corresponded to the same rating of 

“fair” as the mIBI in 2013.

In general, fish abundance at this site is low (less than 

50), yet abundance was 86 percent higher in 2013 than in 2004 

with 26 fish captured compared with 14 in 2004 (table 7). A 

55-percent decrease in the percentage of pollution-tolerant fish 

was seen in 2013 and the fish IBI score was 36 percent higher 

in 2013; however, because fewer than 50 fish were captured 

in any sampling event, the IBI was still rated “very poor” in 

2013 as it was in 2004. The IBI values for this site should be 

taken with caution because fewer than 50 fish were captured in 

any year and, therefore, invertebrates provide a more accurate 

assessment than fish for this site.

The Little Menomonee River seems to have several 

stressors based on anomalous values for this site in significant 

correlations to the biota. This site was an anomaly for high 

ammonia nitrogen compared with all other sites, with mean 

concentrations greater than 0.17 mg/L in 2007, 2010, and 

2013. Water-quality data were not collected by the MMSD at 

this site in 2004. The highest mean ammonia concentration 

among all sites was here in 2013 at 0.24 mg/L, but this value 

is less than the EPA chronic water-quality criterion. Higher 

nitrogen ammonia concentrations were significantly correlated 

to higher relative abundances of diatoms with fairly high oxygen tolerance (more than 75-percent saturation) and sestonic 

algae. The highest average nitrite concentration among sites 

was at the Little Menomonee River in 2007 and, as noted 

earlier, nitrite is toxic and higher nitrite was significantly 

related to lower total fish species. Mean soluble phosphorus 

was more than twice as high in 2013 when compared with 

2007 and 2010 at this site, and this higher amount of nutrients 

was reflected in algal biomass in 2013, when the chlorophyll a

concentration in benthic algal samples was 232 mg/L, more 

than five times higher than in 2004. Mean calcium, magnesium, nickel, and zinc concentrations, and hardness and fecal 

counts, were successively lower each year from 2007 to 2013 

and may indicate improvements in other aspects of water 

quality that could help explain the higher aggregate bioassessment ranking in 2013 compared with 2004. Although fluorescence screening from SPMDs in 2013 indicated relatively low 

pyrene concentrations, Microtox and P450RGS tests indicated 

moderate acute toxicity from synthetic organic chemicals, 

indicating that chemicals other than PAHs are causing toxicity 

at this site.

Underwood Creek

Mean bioassessment rankings in 2013 differed greatly 

among biota, and the highest ranking was for fish, followed by 

algae and then invertebrates (table 8). The aggregate bioassessment ranking for 2013 was at the bottom of the group 3 

sites and similar to 2004. Three algal phyla (diatoms and green 

and blue-green algae) were collected at this site in 2004 and 

2013 (table 3). The relative abundances of blue-green algae 

were more than 13 percent lower in 2013 compared with 2004, 

and the relative abundance of green algae was about 10 percent higher in 2013. About 99.8 percent of all algal biovolume 

was green algae. Pollution-sensitive diatoms were 21 percent 

lower in 2013 compared with 2004, and the algal assemblage 

was less than 30-percent pollution-sensitive diatoms in 2013 

(table 2). Diversity improved from high stress (diversity index 

<1.5) in 2004 to moderate stress in 2013; however, algal biovolume in 2013 was more than an order of magnitude higher 

than in 2004, and the percentage of relative abundance of 

halobiontic diatoms was about 28 percent higher in 2013 compared with 2004. Overall, these results are mixed for the algal 

assemblage but indicate that runoff may be contributing excess 

nutrients and salt to this reach, which in turn, were related to a 

nearly complete dominance in biomass by green algae.

The invertebrate assemblage was more degraded in 2013 

compared with 2004, as evidenced by more than 40-percent 

decreases in the number of taxa (species and genera) and 

also diversity (table 5). The HBI–10 rating was “fairly poor” 

in 2013 compared with “fair” in 2004 because of an about 

20-percent change in the HBI–10 value. Although the mIBI 

value was 22 percent higher in 2013 compared with 2004, the 

mIBI rating was “poor” in all years. The lower diversity and 

HBI–10 metrics resulted in the low average bioassessment for 

the invertebrate sample from this site in 2013, second only to 

the Kinnickinnic River sample.

Most fish in this reach of Underwood Creek were captured in the downstream end below the concrete. The large 

scour pool at the bottom of the reach was not wadable for 

electrofishing except in 2007. Fish abundance was several 

times higher in 2007 when lower depths permitted seining in 

the lower part of the reach and electrofishing seemed ineffective, perhaps because of high conductance (1,490 μS/cm at 

25 °C). Two salmon were seen in the pool in 2004 but not captured and likely came upstream from the nearby Menomonee 

River. The number of fish captured in 2013 was about half 

the number captured in 2004; however, the numbers of total 
72 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

species and native species were more than 37 percent higher 

in 2013 compared with 2004 (table 7). Also, the percentage of 

pollution-tolerant fish was 79 percent lower in 2013 compared 

with 2004. The higher number of total and native species and 

lower abundance of pollution-tolerant fish together indicate 

the fish assemblage was less degraded in 2013 than 2004 and 

was reflected in an IBI rating of “fair” in 2013, compared with 

“very poor” in 2004.

The environmental stressors at this Underwood Creek 

site are related to urban runoff from frequent high storm flows, 

as evidenced by ongoing efforts by MMSD in the past decade 

to mitigate these effects. The most egregious effects of runoff 

are the mean chloride concentrations that were greater than 

267 mg/L and greater than the EPA chronic water-quality 

criterion in all sampling years. Similarly, mean specific conductance values at this site in 2007 and 2013 were among the 

highest across all sampled sites. This site was also an anomaly 

for high total solids in 2013, and higher total solids concentrations were significantly related to higher mean nutrient 

tolerance values of invertebrate taxa (p<0.001; fig. 12F). The 

mean total nonpurgeable dissolved organic carbon was the 

highest across all sites in 2013 (fig. 13). High mean fecal coliform counts (2,500–8,500 CFU/100 mL) during all sampling 

years indicate chronic problems with untreated sewage at this 

site (Sauer and others, 2011). These water-quality metrics 

underscore multiple stressors at this site that are related to 

urban runoff.

Honey Creek

In 2013, the mean bioassessment rankings for Honey 

Creek were relatively consistent among algae, invertebrates, 

and fish, and this resulted in an aggregate bioassessment 

placing the site in group 3 (table 8). This was higher than the 

group 4 ranking computed for 2004. The relative proportions 

of algal groups were similar among 2007, 2010, and 2013. 

Four algal phyla (diatoms and green, blue-green, and red 

algae) were collected in 2004 but only three were detected 

in 2013; red algae were absent in 2013 (table 3). The relative 

abundances of green and blue-green algae were more than 

17 and 33 percent higher, respectively, in 2013 compared 

with 2004. Green algae dominated in all years, making up 

98–100 percent of the algal biovolume. In addition, higher 

algal biovolume was collected in 2013 than 2004 (table 2). 

The algal assemblage was made up of less than 30-percent 

pollution-sensitive diatoms in 2013. The percentage of relative 

abundance of nuisance algae was more than 12 percent higher 

in 2013 compared with 2004 (0). The percentage of relative 

abundance of halobiontic diatoms was more than 10 percent 

higher in 2013 compared with 2004.

Although similar differences were seen for the invertebrate assemblage as for the algal assemblage in a comparison 

between 2013 and 2004, diversity between 2013 and 2007 

decreased by 47 percent (table 5). Although the HBI–10 scores 

rated “good” in 2013, “fair” in 2007, and “good” in 2004, 

the invertebrate mIBI rating was “poor” in 2013, lower than 

the “fair” rating in 2007. These two metrics are apparently 

reflecting different aspects of the invertebrate assemblage. 

The numbers of invertebrate taxa, percentages of noninsects, 

and percentages of EPT taxa were similar between 2013 and 

2007. Overall, the mixed results for the metrics do not indicate 

improvements in the invertebrate assemblage over time.

In 2013, a total of 559 fish as 11 species were collected 

at Honey Creek; dominant taxa (more than 78 percent) were 

Rhinichthys atratulus (blacknose dace), followed by white 

sucker and creek chub (table 7). Although richness and number of native fish species in 2013 were greater than upstream 

in 2004, the values for these metrics were similar for 2013 and 

2007 at the downstream site. The percentages of omnivorous 

fish and forage fish tolerant to low dissolved oxygen were 

more than 10 percent lower in 2013 when compared with 

2004, indicating a less degraded assemblage. The IBI score in 

2013 was similar to 2007, which corresponded to “poor” ratings compared with a “very poor” rating in 2004. These metric 

values indicate the fish assemblage at the current site was less 

degraded in 2013 compared with 2007 but still poor (fig. 4).

Multiple environmental stressors may be having adverse 

effects on the aquatic community at this highly urbanized 

Honey Creek site. Although the mean chloride concentration in 2007 was just less than the EPA chronic water-quality 

criterion at 229 mg/L (fig. 12), values in all other ecological 

sampling years exceeded the EPA chronic water-quality criterion of 230 mg/L. Although the HBI–10 value in 2013 was 

higher than predicted, the mIBI scores rated “poor” when the 

highest mean chloride concentration for this site was recorded 

at 403 mg/L. The high chloride value in 2013 was reflected 

in the second highest chloride concentrations among all sites 

and dates (fig. 13C). Although the mean ammonia nitrogen 

concentration in 2007, at 0.15 mg/L, was among the four highest values for all sites and years (fig. 11A–B), concentrations 

in other sample years were relatively low (from the minimum reporting limit as nitrogen of 0.01 mg/L to 0.05 mg/L). 

However, the mean nitrite concentration in 2013 was the 

second highest value among all sites and years. The BOD5 

values at the upstream site in 2004, 2007, and 2013 were 

among the top five highest values among all sites and were 

more than 3.0 mg/L; fecal coliform bacteria counts in 2007 

and 2013 were the highest values among all sites at 22,269 and 

28,780 CFU/100 mL, respectively (figs. 11 and 12). The mean 

zinc concentration of 94 μg/L in 2013 was the highest value 

across all sites and years, and the concentration of 46 μg/L in 

2004 was the second highest. The highest mean concentrations 

of copper and total solids in 2013 were the highest across all 

sites and years at 24.5 and 1,149 mg/L, respectively. In 2013, 

the mean chromium concentration was 16.5 μg/L, which was 

greater than mean values in other years and other sampled 

sites. These results indicate that urban runoff containing high 

chloride, fecal contamination, and other urban-associated 

chemicals are primary stressors at this site. This finding is supported by comparisons with other sites and relations of these 

stressors to biological metrics. In 2013, the second highest 

potential toxicity for P450RGS tests of SPMDs was measured 
Assessment of Aquatic Communities in Relation to Stream Condition 73

at this site relative to other sampled sites, including a value 

higher than in 2007 and nearly three times higher than was 

measured at the Milwaukee River near Cedarburg (table 9). 

This finding indicates that the potential toxicity at this site was 

from synthetic organic compounds other than pyrene, which 

was relatively low in spite of findings for 2004 that PAH concentrations were high relative to other sampled sites (Thomas 

and others, 2007). With nearly 100-percent urban land in the 

watershed and more than 72-percent urban land in the stream 

buffer, there is little vegetation to slow or absorb runoff from a 

mean of 47-percent impervious surface in the watershed. This 

stream has relatively high runoff from storms. In 2010 and 

2013, values for maximum instantaneous discharge per drainage area were high compared with most other sites, especially 

those with less urban land in the stream buffer, and values 

were similar to the Kinnickinnic River site with its concretelined streambed. High flows and scour are evident in many 

areas of severely eroded streambanks and loss of large canopy 

trees into the stream channel.

Menomonee River at Wauwatosa

Mean bioassessment rankings for the Menomonee River 

at Wauwatosa site in 2013 were similar between algae and 

invertebrates (table 8). In contrast, the ranking for fish in 2013 

was much worse and the resulting aggregate bioassessment 

ranking placed the site into group 4, the lowest group with 

regard to water quality. Mean bioassessment rankings for fish 

assemblages in 2004 also ranked poorly but the aggregate 

ranking for the site was in group 3. The algal assemblage at 

this site included four phyla (diatoms and green, blue-green, 

and red algae) in 2004 but only three phyla in 2013 with the 

loss of red algae (table 3). The change in the percentage of 

relative abundance of any of the algal groups was less than 

10 percent between 2004 and 2013. Higher algal biovolume 

was measured in 2013 than 2004 (table 2). The percentage of 

relative abundance of pollution-sensitive diatoms was more 

than 20 percent lower in 2013 compared with 2004, and the 

assemblage had only 7.5-percent pollution-sensitive diatoms 

in 2013. The percentage of relative abundance of halobiontic 

diatoms was more than 18 percent higher in 2013 compared 

with 2004, indicating higher salt concentrations in this stream.

The numbers of invertebrate taxa (species and genera) 

were more than 18 percent higher in 2013 compared with 

2004 when the downstream reach was sampled and were also 

higher when compared with 2007 (table 5); however, diversity 

was 1.98 in 2013, more than 26 percent lower than in 2004. 

The percentage of EPT taxa in 2013 was 10 percent lower than 

in 2004 and steadily decreased from 2004 to 2013. HBI–10 

scores rated “fair” and remained unchanged from 2004 to 

2013, as did the “poor” mIBI rating, but mIBI scores were 

about 22 percent lower than in 2004 and more than 40 percent 

lower than in 2007. These latter metric results indicate that the 

invertebrate assemblage at this site has degraded since 2004 

and 2007.

Similar numbers of fish taxa were measured in 2013 compared with 2004, including six in 2013 and seven in 2004. The 

sampling reach in 2004 had a nonwadable pool at the apex of 

the only bend; a few fish may have retreated into this deep and 

clear pool during electrofishing and a large trout or salmon 

was observed to escape seine sampling. The early 2006 restoration of the reach around 68th Street and 70th Street made a 

larger area of the bend area nonwadable and necessitated moving the sample reach upstream to just above 70th Street. There 

were no barriers to fish movement between the 2004 reach and 

the new adjacent reach that was sampled in 2007–13. The restoration removed all trees on the left bank from downstream 

from 68th Street through most of the current reach. The fish 

IBI rated “very poor” in 2004 and 2013. In 2016, the last of all 

fish barriers were removed downstream from the sample site, 

and if migration for most fish species is unimpeded from Lake 

Michigan to Menomonee Falls, this could result in positive 

changes to the fish assemblage.

A comparison between this site and the upstream site 

at Menomonee Falls is useful in evaluating important environmental stressors at the Wauwatosa site. For example, the 

maximum instantaneous discharge, normalized by drainage area, was higher in each ecological sampling year at the 

downstream Wauwatosa site and more than double in 2010 (42 

and 87 cubic feet per second per square mile at Menomonee 

Falls and Wauwatosa, respectively). The mean DO concentration in ecological sampling years was between 7 and 9 mg/L 

at Menomonee Falls but 11 mg/L in all years at Wauwatosa. 

Perhaps most importantly, the mean chloride concentrations 

in 2007–13 at Wauwatosa were greater than the EPA chronic 

water-quality criterion of 230 mg/L. Mean chloride concentrations at Menomonee Falls, although steadily increasing from 

2004 to 2013, were lower than the mean value for Wauwatosa 

in all years including 2004. Higher specific conductance 

values at Wauwatosa reflected this difference in chloride. Fecal 

coliform concentrations were an order of magnitude higher 

at Wauwatosa in all years compared with concentrations at 

Menomonee Falls. At Wauwatosa, Baldwin and others (2013)

detected a large suite of organic waste compounds in more 

than 80 percent of stormwater samples, including antioxidants, 

dyes/pigments, fire retardants, PAHs, plasticizers, solvents, 

herbicides, insecticides, detergent metabolites, flavors and 

fragrances, human drugs (nonprescription), and steroids. 

Many of these same compounds were detected in sediment, 

especially PAHs at ≥10,000 μg/L. For one PAH compound, 

they also measured the highest fluoranthene concentration (14,900 micrograms per kilogram) among all sites in a 

sediment sample collected from the Wauwatosa site during 

2006–9. Similar to its tributary, Honey Creek, these results 

indicate that urban runoff containing high chloride, fecal 

contamination, and other urban-associated chemicals are all 

important stressors at the Menomonee River at Wauwatosa.
74 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

Kinnickinnic River

The concrete-lined channel of the Kinnickinnic River site 

was the lowest ranked of the group 4 sites in aggregate bioassessment rankings for 2013 and 2004, with consistently low 

mean bioassessment rankings for algae, invertebrates, and fish 

(table 8). The algal assemblage at this site included three phyla 

(diatoms and green and blue-green algae) in 2004 and 2013 

(table 3). The change in the percentage of relative abundance 

of any of the algal groups was less than 10 percent. Higher 

algal biovolume was collected in 2013 than 2004 (table 2). 

The percentage of pollution-tolerant diatoms dropped from 

about 28 percent in 2004 to 17 percent in 2013. Diversity was 

rated as high stress (diversity index <1.5) in 2004 and moderate stress in 2013. The percentage of relative abundance of 

eutrophic diatoms was more than 14 percent higher in 2013 

compared with 2004. The percentage of relative abundance of 

halobiontic diatoms was more than 20 percent higher in 2013 

compared with 2004. The algal assemblage at this site had less 

than 30-percent pollution-sensitive diatoms in all years except 

2007. Although diversity was higher in 2013 than 2004, the 

higher percentages of eutrophic and halobiontic diatoms and 

lower percentage of pollution-sensitive diatoms in 2013 indicate that the assemblage is more degraded than in 2004.

The number of invertebrate species and genera was at 

least 47 percent lower in 2013 than 2004 and, as a result, 

diversity was about 65 percent lower in 2013 than 2004 

(table 5). Good indicators were that the percentage of noninsects was more than 21 percent lower and the percentage of 

EPT taxa was 11 percent higher in 2013. The site rated “fairly 

poor” by the HBI–10 in 2013 and 2004 but it rated “very 

poor” by the mIBI in 2013 compared with “poor” in 2004; 

the mIBI score was 50 percent lower in 2013. These mostly 

adverse results indicate that the already poor invertebrate 

assemblage has further degraded since 2004.

Most fish collected during sampling were fathead minnows, a species that is tolerant of poor water quality. Only 

one common shiner and one fathead minnow were collected 

in 2007, and no fish were seen or captured in 2013. As such, 

there were too few fish captured during all years at this site 

to confidently calculate an IBI, resulting in a “very poor” IBI 

rating (table 7). With the highly urban setting (99-percent 

urban land), shallow water with meager habitat, and little 

or no refuge from effects of high storm flows, “very poor” 

ratings for fish were not unexpected in this reach of the 

Kinnickinnic River.

Several environmental stressors at the Kinnickinnic 

River site were significantly correlated to poor rankings of the 

aquatic community. During ecological sampling years, mean 

values for maximum instantaneous discharge, normalized 

by drainage area, were high relative to most other sites and 

emphasize the high storm flows that are commonly recorded 

at this site. Four of the five highest mean DO concentrations 

(greater than 14 mg/L) across all sites and years were at this 

site (fig. 11E). Such high mean DO concentrations often result 

from excessive nutrients and algae that can cause contrasting 

low mean DO concentrations at other times of the day when 

algal respiration dominates. All fish captured in 2004 and 

2010 (fathead minnow, common shiner) are forage fish known 

to be tolerant to low DO concentrations. In 2007, the mean 

BOD5 value of 4.9 mg/L was one of the four highest values 

across all sites and dates, and higher BOD5 was correlated 

to fewer scraper invertebrates (fig. 12H). Concentrations of 

fecal coliform bacteria at the Kinnickinnic River site were 

many times higher than at sample sites in less urbanized areas 

(fig. 12G) and likely contributed to high BOD5 values. This 

agrees with findings by Templar and others (2016) that indicated chronic human fecal contamination in the Kinnickinnic 

River. Related to nutrients and algae, high total phosphorusindicator diatoms (optima greater than or equal to 0.10 mg/L 

total phosphorus) were abundant at more than 73 percent of 

the algal cells in all years (fig. 11N); mean total phosphorus 

concentrations were 0.11 or higher in all ecological sampling 

years and greater than the State of Wisconsin’s criterion of 

0.075 mg/L, averaged May through October, to minimize 

nuisance algal/plant growth in wadable streams (Wisconsin Department of Natural Resources, 2019). The high total 

phosphorus concentrations correlated to the higher percentage 

of total phosphorus-indicator diatoms and likely had indirect 

effects on the invertebrates and fish in this urban stream. Mean 

chloride concentrations were already high at 220 mg/L in 2004 

but were greater than the EPA chronic water-quality criterion 

of 230 mg/L for all recent years, including 302 mg/L in 2013. 

Mean chloride concentrations this high were correlated with 

invertebrate HBI–10 and mIBI values, and fish IBI values that 

indicated more degraded assemblages (fig. 12A–C, fig. 13A). 

Baldwin and others (2013), in a study in 2006–9 at many of 

the same sites as the current study, determined some of the 

highest detection frequencies and concentrations of organic 

waste compounds were from the Kinnickinnic River site. They 

also determined that the highest stormflow concentrations of 

three PAHs (fluoranthene, phenanthrene, and pyrene) were in 

one sample from this highly urban site. In the current study, 

moderately high PAHs compared with the Milwaukee River 

near Cedarburg site were detected in SPMDs deployed at the 

Kinnickinnic River site in 2007 during base flow (table 9). In 

summary, high storm flows, DO, BOD5, fecal coliform, total 

phosphorus, chloride, and PAHs are important stressors on 

aquatic communities at the Kinnickinnic River site.

Oak Creek

The aggregate bioassessment ranking for Oak Creek 

was better in 2013 than in 2004, placing the site in group 3 

(table 8); however, the 2013 mean bioassessment rankings 

differed greatly among algae, invertebrates, and fish and 

this underscores the importance of assessment with multiple 

groups of aquatic organisms. Algal assemblages at this site 

were made up of three phyla (diatoms and blue-green and red 

algae) in 2004 and four phyla in 2013 with the addition of 

green algae (table 3). The percentage of relative abundance 

of blue-green algae was more than 23 percent lower in 2013 
Assessment of Aquatic Communities in Relation to Stream Condition 75

compared with 2004; the percentage of relative abundance of 

red algae was more than 22 percent higher in 2013 compared 

with 2004. Higher algal biovolume was collected in 2013 

than 2004 (table 2). The percentage of relative abundance of 

halobiontic diatoms was more than 26 percent lower in 2013 

compared with 2004, an indicator of improved water quality. 

Another indicator is that pollution-sensitive diatom abundance 

increased by more than 14 percent from 2004 to 2013, which 

partly accounts for the higher ranking in mean bioassessment 

for algae for this site in 2013.

Invertebrate metrics indicated more degraded water 

quality at Oak Creek compared with algal metrics, with more 

than 39 percent fewer species and genera in 2013 compared 

with 2004 (table 5). As a result, diversity at this site was about 

48 percent lower in 2013. The 14 percent higher value for 

the percentage of EPT taxa was apparently due to the loss of 

several midge taxa and riffle beetles, such that the remaining caddisfly taxa contributed more to the total invertebrate 

abundance and a higher percentage of EPT taxa. There was no 

difference in the HBI–10 or invertebrate mIBI when compared 

with 2004, indicated by ratings of “fair” or “poor” for the 

HBI–10 and mIBI, respectively; however, differences in the 

other metrics between 2004 and 2013 seem to indicate degradation of the invertebrate assemblage.

A total of 78 fish were collected at this site in 2013, 

compared with 218 in 2004, and several fish metrics indicated 

degradation in the 2013 assemblage when compared with 

2004 (table 7). The total number of species was 14 percent 

lower, and the number of native species was 29 percent lower 

than in 2004. In addition, there were 33 percent more forage 

fish tolerant to low DO. Green sunfish and white suckers made 

up 81 percent of the fish individuals in 2013; green sunfish 

especially are known to be tolerant of environmental extremes 

including low DO. The creek chub, a species that is tolerant 

to short-term low DO, made up more than half the individuals 

in 2004 but declined in abundance with each passing year and 

made up only 7.7 percent of fish in 2013. Based on the fish 

IBI, the assemblage was rated as “very poor” in each sampling 

year, including a score of 7 in 2013 compared with a score of 

5 in 2004. The IBI was the only fish metric used in the aggregate bioassessment.

The environmental stressors on the aquatic community at 

the Oak Creek site include chemicals from runoff and extreme 

high flows from impervious surfaces. Mean chloride concentrations were at and greater than the EPA chronic water-quality 

criterion of 230 mg/L in 2004 and 2013, respectively. Higher 

chloride was correlated with worse rankings for the invertebrate HBI–10 and mIBI and the fish IBI (fig. 12A, B; fig. 13A). 

The maximum instantaneous discharge, normalized by drainage area, was higher overall than at other less urban sites and 

was 34 percent higher in 2013 compared with 2004, indicating 

more high flows from storms that scour the streambed and can 

damage or kill aquatic organisms. This indication of increased 

urban runoff was in addition to more than 80 percent higher 

fecal concentrations in water in 2013 compared with 2004, 

an indication of higher wastewater input as well. Synthetic 

organic chemicals, likely from runoff, are also a concern at 

this site as evidenced by TEQs from P450RGS toxicity tests 

that were more than three times as high in 2013 than in 2007 

(table 9).

Root River at Greenfield

The aggregate bioassessment ranking for Root River 

at Greenfield placed it with the lowest water-quality sites, 

placing it in group 4 in 2013 compared with group 3 in 2004, 

indicating a lower rank compared with the other sampled 

sites (table 8). This low ranking in 2013 was because of low 

mean rankings for invertebrates and fish, in spite of a higher 

mean ranking for algae. The mean bioassessment ranking for 

algae in 2004 was also a higher ranking than for invertebrates 

or fish (Scudder Eikenberry and others, 2010); however, this 

difference for algae alone from 2004 to 2013 indicates more 

degraded algal assemblages in 2013. Algal assemblages at 

the Root River at Greenfield site were quite different between 

2013 and 2004 (table 3). This site had the fewest (28) algal 

taxa of all sites in 2004 but the most (70) taxa of all sites 

in 2013 (table 2). Three phyla (diatoms and blue-green and 

red algae) were collected in 2004, and five phyla (diatoms; 

green, blue-green, and red algae; and euglenoids) were collected in 2013. Lower algal biovolume was collected in 2013 

than 2004. Although the percentage of biovolume of diatoms 

was about 14 percent higher, the percentages of biovolume 

of green and blue-green algae were about 18 and 11 percent higher, respectively, in 2013 compared with 2004. The 

percentage of biovolume of red algae was only 46 percent in 

2013 compared with about 89 percent in 2004. Diversity for 

algae improved from high stress (diversity index <1.5) in 2004 

to moderate stress in 2013, but the higher biovolume of green 

and blue-green algae in 2013 and lower mean bioassessment 

ranking for algae in 2013 indicate that the algal assemblage is 

more degraded than in 2004.

Invertebrate assemblages were more degraded in 2013 at 

this site as evidenced by a “fairly poor” HBI–10 rating, compared with a “fair” rating in 2004 (table 5). Also, the number 

of genera was 27 percent lower even though there was no 

difference in the overall number of species. This decrease in 

genera was reflected in the diversity, which was about 34 percent lower in 2013 than in 2004. The invertebrate mIBI rating 

was “poor” in all sampling years. The dominant taxon in 2013 

was an isopod (Caecidotea intermedia, 53 percent) that is 

known to be a relatively pollution-tolerant noninsect (Barbour 

and others, 1999), followed by two pollution-tolerant taxa, a 

caddisfly (H. betteni, 8.2 percent) and a black fly (Simulium 

vittatum group, 6.0 percent).

Although 179 fish were collected from this site in 2004, 

only 11 fish were collected at this site in 2013, a decrease of 

94 percent (table 7). Seining was not possible at this site in 

2013 because of abundant woody debris, but it is doubtful 

that this was the reason for the substantially lower abundance. From field notes, rain the night before and morning 

of sampling in 2013 resulted in runoff and turbid water that 
76 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

probably contributed to sampling inefficiency by the fish crew. 

The total of 11 fish captured was too few to have confidence in 

the 2013 IBI score of 2 (“very poor”); however, the Wisconsin 

Department of Natural Resources also sampled the Root River 

at Greenfield site in 2013 and computed an IBI score of 10, 

again “very poor” (Craig Helker, Wisconsin Department of 

Natural Resources, oral commun., January 16, 2015).

The Root River at Greenfield has multiple environmental stressors including nutrients, such as high mean ammonia 

nitrogen and total nonpurgeable inorganic carbon, indicated by 

the anomalous values for these constituents (figs. 11A and D). 

The lowest values for mean DO among all sites in all ecological sampling years occurred at this site (fig. 11F) and low DO 

is a known problem for the Root River because of low water 

levels (Milwaukee Metropolitan Sewerage District, 2005). 

Fecal coliform and BOD5 were at least two times higher 

than downstream at the Root River near Franklin site in all 

sampling years. The mean chloride concentration was greater 

than the EPA chronic water-quality criterion of 230 mg/L in 

each sampling year, and this was also reflected in high mean 

specific conductance. Specific conductance at the time of ecological sampling in 2007 was the highest among all sites. Zinc, 

as an indicator of urban runoff at this site, was again much 

higher than at the Root River near Franklin site. Maximum 

instantaneous discharge, as normalized by drainage area, was 

high relative to several other sites including downstream at the 

Root River near Franklin except in 2010, indicating that scour 

from high discharge affects habitat at this site.

Root River near Franklin

Mean bioassessment rankings in 2013 for the Root River 

near Franklin site differed among algae, invertebrates, and 

fish; the lowest ranking was for fish, followed by invertebrates 

and then algae (table 8). The mean of these rankings placed 

the site in group 2 for the aggregate bioassessment ranking 

and within the same group and with the same ranking as 2004. 

The algal assemblage at this site included three phyla (diatoms 

and blue-green and red algae) in 2004 and five phyla (diatoms; 

green, blue-green, and red algae; and euglenoids) in 2013 

(table 3). The percentage of relative abundance of blue-green 

algae was more than 26 percent higher in 2013 compared 

with 2004, whereas the percentage of relative abundance of 

red algae was more than 36 percent lower in 2013 compared 

with 2004. Higher algal biovolume was collected in 2013 

than 2004, and green algal biovolume dominated in 2013 at 

about 68 percent (tables 2 and 3). Diversity improved from 

high stress (diversity index <1.5) in 2004 to moderate stress 

in 2013. The percentages of pollution-tolerant diatoms and 

pollution-sensitive diatoms were lower in 2013, and the percentage of pollution-moderate diatoms was higher. The higher 

abundance of blue-green and green algae in 2013 than 2004, 

together with the presence of euglenoids, indicate poorer water 

quality. In summary, the 2013 results for algal assemblages 

were mixed.

The number of invertebrate genera was 16 percent higher 

in 2013 than 2004; however, diversity decreased by about 

18 percent (table 5). The lower diversity in 2013 is probably 

because of a change in dominance of taxa (evenness), which is 

a component of diversity in addition to taxa richness. Several 

midge taxa were present in much higher abundance in 2013 

than 2004. Even though there was no change in the invertebrate mIBI, which rated “fair” from 2004 and 2013, the mIBI 

rated “poor” in 2007 and 2010. Plentiful live native freshwater 

mussels were observed at this site in 2004, though none were 

collected in the invertebrate sample. The 2013 sample contained one Potamilus alatus (pink heelsplitter mussel); however, our methods are not designed to quantify mussel populations because of their highly patchy nature of their distribution 

in streams.

Similar to the decrease seen upstream in the Root 

River at Greenfield, total abundance of fish in the river near 

Franklin was about 83 percent lower in 2013 compared with 

2004 (table 7). In 2013, only 31 fish were captured, too few 

to have high confidence in the computed IBI (17 or “very 

poor”) and this rating was lower than the “poor” IBI rating 

in 2004. Seining was not possible at this site in 2013 because 

of abundant woody debris that snagged the net. In addition, 

recent rains had caused runoff and high turbidity that may 

have decreased sampling efficiency. Richness has remained 

relatively low at this site throughout the sampling years and 

was 25 percent lower in 2013 compared with 2004. Dominant 

fish in 2013 were tolerant taxa: green sunfish (35 percent) 

and creek chub (29 percent). Although white suckers made up 

nearly one-third of all fish in 2004, no suckers were detected 

in 2007 and their abundance was low in subsequent years.

Environmental stressors at the Root River near Franklin 

site were fewer than upstream at the Root River at Greenfield 

site after traveling miles through less developed land. Values 

for maximum instantaneous discharge as normalized by 

drainage area were 40 percent higher in 2013 than 2004 and 

indicate higher flood effects and scour, yet mean zinc concentrations were nearly one-third lower in 2013 than 2004 and 

higher concentrations of zinc are generally considered to be 

indicators of urban runoff as mentioned earlier. Mean chloride 

concentration was also 40 percent higher in 2013 at 204 mg/L 

but still less than the EPA chronic water-quality criterion. 

Means for total and dissolved solids in water were 10–12 percent higher in 2013 than 2004. Fortunately, mean fecal 

coliform counts in 2013 were an order of magnitude lower 

than in 2004 and were lower in 2010 also. Mean silt depth for 

the reach was three times higher in 2013 than 2004, at 2.9 and 

0.75, respectively. These increases could have adverse effects 

on the freshwater mussel populations at this site and may be 

related to increased construction in the watershed as agricultural land is transformed into urban land.
Summary and Conclusions 77

Jewel Creek

This small stream ranked in group 1 for 2013 and 2004, 

with relatively similar mean bioassessment rankings among 

invertebrates and fish for 2013. The algal assemblage at Jewel 

Creek included three phyla (diatoms and blue-green and red 

algae) in 2004 and five phyla (diatoms; green, blue-green, and 

red algae; and euglenoids) in 2013 (table 3). The percentages 

of relative abundance of diatoms and red algae were more than 

16 and 12 percent lower, respectively, in 2013 compared with 

2004, and the percentage of relative abundance of blue-green 

algae was more than 26 percent higher in 2013 compared with 

2004. Higher algal biovolume was collected in 2013 than 

2004 (table 2), and green algal biovolume dominated at about 

90 percent (table 3). The percentage of relative abundance of 

eutrophic diatoms was more than 10 percent higher in 2013 

compared with 2004. The higher algal abundance, the change 

from no green algae to a dominance of green algal biovolume, the presence of euglenoids, and a higher abundance 

of eutrophic diatoms indicate excess nutrients and a more 

degraded algal assemblage in 2013 than 2004, which disagrees 

with the metrics used for the mean bioassessment ranking for 

algae in 2013.

The numbers of invertebrate species and genera at Jewel 

Creek were more than 35 percent lower in 2013 than 2004, 

and diversity was 43 percent lower; however, this was related 

to about 21 percent lower noninsects. In 2004, the assemblage was about 20-percent isopods (C. intermedia), which 

tend to be relatively tolerant to pollution, but also 22-percent 

pollution-moderate riffle beetles (Stenelmis), and 20-percent 

pollution-tolerant mayflies (B. flavistriga and 

B. intercalaris). In 2013, isopods made up about 1 percent of 

the invertebrate assemblage. Riffle beetles were still important 

in dominance; instead, pollution-tolerant caddisflies (H. betteni and Cheumatopsyche) made up 60 percent of the invertebrate abundance. The HBI–10 rating was “good” in 2013 and 

“fair” in 2004 and was in contrast to an unchanged invertebrate mIBI across all sampling years.

Jewel Creek is little more than a connector between 

two lakes, Linnie Lac and Little Muskego Lake, and it has 

a small drainage area (table 1). The fish assemblage reflects 

this position on the landscape; species that are more common 

in lakes than in small streams are common in Jewel Creek, 

including Lepomis macrochirus (bluegill), pumpkinseed, and 

Micropterus salmoides (largemouth bass). Nocomis biguttatus

(hornyhead chub) were dominant in all sampling years, with a 

34-percent relative abundance in 2004, and higher each year, 

with a 67-percent relative abundance in 2013. The numbers 

of fish, species, and native species were more than 53 percent lower in 2013 than in 2004, and diversity was more than 

40 percent lower in 2013 than in 2004. In contrast, there were 

differences in some metrics that indicate a positive response; 

however, these changes may simply reflect the large loss in 

fish abundance: the percentage of forage fish tolerant to low 

DO decreased by 12 percent, and the percentages of omnivorous fish and pollution-tolerant fish were more than 30 percent 

lower in 2013 compared with 2004.

Some stressors at Jewel Creek were not characterized 

because of the lack of water-quality and discharge data. Mean 

impervious surface increased slightly in this watershed, from 

11.5 percent in 2004 to 13 percent in 2013. For stream habitat 

metrics in 2013, measured silt depth was one-fifth of what it 

was in 2004 and mean erosion length was more than double 

what it was in 2004, both indicating possible high flows at 

some point between the two sampling years, such as the 

July 2010 flooding in southeastern Wisconsin.

At most of the sampled streams, there are indications 

of adverse changes in the aquatic communities and many 

stressors linked to urban runoff. Increases in urban runoff as 

more land is developed, resulting in larger discharges, were 

also noted by Thomas and others (2007). For the period from 

October 1, 2003, to September 30, 2004, Thomas and others 

determined that annual mean discharges were greater than 

long-term annual mean discharges at many of these sites with 

long-term discharge records. The greatest differences were 

detected at the Milwaukee River at Milwaukee (84 percent), 

Milwaukee River near Cedarburg (56 percent), Menomonee 

River at Menomonee Falls (47 percent), and Menomonee 

River at Wauwatosa (44 percent) sites.

Summary and Conclusions

Aquatic communities including algal, invertebrate, and 

fish (biota) assemblages were sampled at 14 stream sites in the 

Milwaukee metropolitan area by the U.S. Geological Survey 

(USGS) in cooperation with the Milwaukee Metropolitan 

Sewerage District in 2004–13. Physical characteristics 

(stream habitat, flow at gaged sites) and chemical characteristics (water quality) were also assessed. In addition, passive 

samplers (semipermeable membrane devices) were deployed 

at a subset of six sites to assess potential toxicity to biota 

from synthetic organic chemicals. The objectives of aquatic 

community sampling were to assess the ecological status of 

aquatic communities and potential environmental stressors to 

gain a better understanding of overall stream conditions in the 

Milwaukee area.

The taxonomic richness (total number of different kinds) 

of each assemblage in the aquatic communities provided some 

insight into the ecological health of each site; however, additional measures or metrics, such as indexes of biotic integrity 

for each group of biota, yielded more complete assessments. 

For a subset of three sites where additional temporal sampling 

was done in spring and early fall in 2011–13, higher numbers of algal taxa were detected in fall compared with spring, 

indicating fall as an important time for sampling after algal 

assemblages have had adequate time to develop. Taxonomic 

signatures indicated that, in general, spring samples from sites 

aligned more with other samples from the same site than with 
78 Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13

other sites and indicated that variation was greater between 

sites than within sites for these two times of year. In addition, 

fall samples collected during temporal sampling aligned most 

with the sampled sites than with other sites and affirmed the 

ability to distinguish sites.

In aggregate bioassessments, algal, invertebrate, and 

fish rankings sometimes assigned different quality to a site 

based on metric outcomes. Rankings at three sites were 

worse for invertebrates than for fish, and rankings at four 

sites were worse for fish than for invertebrates. There were 

two sites that ranked worse for algae than for invertebrates 

or fish. This finding underscores differences in environmental tolerances between groups of biota and the importance 

of carefully selecting biological measures or metrics computed for each group in assessments. For 2013 and for 2004, 

aggregate bioassessment rankings across all groups of biota 

indicated the least degraded water quality at Milwaukee 

River near Cedarburg, Wisconsin (USGS station 04086600); 

Menomonee River at Menomonee Falls, Wis. (USGS station 04087030); Jewel Creek at Muskego, Wis. (USGS 

station 05544371); and Milwaukee River at Milwaukee, 

Wis. (USGS station 04087000). The aggregate bioassessment rankings for Honey Creek at Wauwatosa, Wis. (USGS 

station 04087119); and Oak Creek at South Milwaukee, Wis. 

(USGS station 04087204), were better in 2013 than in 2004. 

The aggregate assessment rankings for Menomonee River at 

Wauwatosa, Wis. (USGS station 04087120), and Root River at 

Grange Avenue at Greenfield, Wis. (USGS station 04087214), 

were worse in 2013 than in 2004; together with Lincoln Creek 

at 47th Street at Milwaukee, Wis. (USGS station 040869415), 

and the Kinnickinnic River at South 11th Street at Milwaukee, 

Wis. (USGS station 04087159), these four sites ranked the 

lowest for water quality in 2013. In total, from 2004 to 2013, 

rankings were better at 2 sites, worse at 2 sites, and did not 

change at 10 sites.

Summary metrics for physical and chemical stressors 

correlated significantly to biological metrics for algae, invertebrates, and fish, indicating these stressors may be related 

to adverse effects at some sites. Algal metrics that correlated 

most to environmental stressors were those related to nutrients, oxygen, salt, and suspended sediment. For invertebrate 

metrics, the number of Ephemeroptera-Plecoptera-Trichoptera 

genera; the Hilsenhoff Biotic Index, modified to limit the number of individuals per taxon to 10 for index computation; the 

macroinvertebrate Index of Biotic Integrity; the percentage of 

scraper invertebrates; and the mean nutrient tolerance of invertebrate taxa correlated most with environmental stressors. The 

Index of Biotic Integrity was the fish metric most commonly 

correlated with the environmental metrics. Stressors reflected 

an urban signature related to medium and high-intensity 

developed land, urban land in the 200-foot (60-meter) stream 

buffer, and higher percentages of impervious surface in the 

watershed. Rapid runoff from impervious surfaces can damage 

stream habitat and wash road salt, nutrients, fecal matter, and 

other chemical contaminants into local streams. Higher percentages of medium and high-intensity developed land, urban 

land in the stream buffer, and higher percentages of impervious surface in the watershed were all significantly correlated 

with each other. Potential toxicity from synthetic organic 

chemicals was detected at all six sites where passive samplers were deployed. Mean chloride concentrations in water 

were greater than the U.S. Environmental Protection Agency 

chronic water-quality criterion for the protection of aquatic 

life in one or more ecological sampling years at several sites. 

Algal metrics at the 14 sites correlated to fecal coliform, dissolved oxygen, 5-day biological oxygen demand, ammonia 

nitrogen, zinc, maximum instantaneous discharge per drainage area as an indicator of flood and scour effects, developed 

land in the watershed (medium and high intensity) and in the 

stream buffer, impervious surface in the watershed, deciduous 

and mixed forest, stream open canopy angle, variability of 

stream depth and bankfull width-to-depth ratio, and substrate 

embeddedness. The stressors correlated with invertebrate 

metrics were fecal coliform, 5-day biological oxygen demand, 

chloride, specific conductance, zinc, total solids, maximum 

instantaneous discharge (tentatively greater than 

40 cubic feet per second per square mile), developed open 

space, developed land in the watershed (medium and high 

intensity) and in the stream buffer, impervious surface in the 

watershed, and stream channel stability. Similar physical and 

chemical stressors correlated significantly with fish metrics, including fecal coliform; total nonpurgeable dissolved 

organic carbon; chloride; specific conductance; nitrite; total 

solids; maximum instantaneous discharge per drainage area; 

developed open space; developed land in the watershed (low, 

medium, and high intensity) and in the stream buffer; impervious surface in the watershed; low variability in stream channel 

morphology (bankfull width-to-depth and velocity-to-depth 

ratios); and limited riffle habitat that can help mitigate low 

dissolved oxygen conditions. In summary, these results underscore the effects of urban developed land through runoff from 

impervious surfaces with subsequent harm to aquatic communities of nearby waterways; however, algal results indicated 

that as little as 1-percent mixed forest in a watershed might be 

beneficial with regard to salt runoff in streams.

Long-term monitoring of aquatic communities coupled 

with physical and chemical data collected with sufficient 

frequency proved highly useful in evaluating the ecological 

status of aquatic communities and overall stream condition at 

the 14 sites. Because of variability that can occur in any single 

year, long-term monitoring is needed to fully understand the 

dynamics of any trends that may be occurring at these sites. 

This combination of biological, physical, and chemical data 

also provided insight into the environmental stressors that 

may be contributing to the ecological status and that may be 

removed or lessened with stream rehabilitation and changes in 

watershed management. Looking forward, a better understanding of the relative importance of different stressors at sites in 

a watershed or region can be key to finding ways to minimize 

degradation at area streams during earlier stages of transition 

to developed urban land.
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For more information about this publication, contact:

Director, USGS Upper Midwest Water Science Center

8505 Research Way

Middleton, WI 53562

608–828–9901

For additional information, visit: https://www.usgs.gov/centers/umid-water

Publishing support provided by the Rolla Publishing Service Center

Scudder Eikenberry and others—Ecological Status of Aquatic Communities in Selected Streams in the MMSD Planning Area of Wisconsin, 2004–13—SIR 2020–5035

ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20205035