Biological Water-Quality Assessment of Selected 

Streams in the Milwaukee Metropolitan Sewerage 

District Planning Area of Wisconsin, 2007

Scientific Investigations Report 2010–5166

Prepared in cooperation with the Milwaukee Metropolitan Sewerage District 

U.S. Department of the Interior

U.S. Geological Survey
Cover artwork by Benjamin J. Siebers, U.S. Geological Survey, Wisconsin Water Science Center, 

Middleton, Wisconsin
Biological Water-Quality Assessment 

of Selected Streams in the Milwaukee 

Metropolitan Sewerage District Planning 

Area of Wisconsin, 2007

By Barbara C. Scudder Eikenberry, Amanda H. Bell, Daniel J. Sullivan, Michelle A. Lutz, 

and David A. Alvarez

Prepared in cooperation with the Milwaukee Metropolitan Sewerage District

Scientific Investigations Report 2010–5166

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2010

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reproduce any copyrighted materials contained within this report.

Suggested citation:

Scudder Eikenberry, B.C., Bell, A.H., Sullivan, D.J., Lutz, M.A., and Alvarez, D.A., 2010, Biological water-quality 

assessment of selected streams in the Milwaukee Metropolitan Sewerage District Planning Area of Wisconsin, 2007: 

U.S. Geological Survey Scientific-Investigations Report 2010–5166, 28 p.
iii

Contents

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

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

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

Methods...........................................................................................................................................................3

Study Area..............................................................................................................................................3

Data Collection......................................................................................................................................3

Data Analysis.........................................................................................................................................6

Biological Community Assessment ............................................................................................................6

Algae ....................................................................................................................................................7

Invertebrates .......................................................................................................................................12

Fish ..................................................................................................................................................19

Comparative Bioassessment Among Algae, Invertebrates, and Fish........................................22

Toxicity and Chemical Assessment Using SPMDS................................................................................23

SPMD Toxicity Tests...........................................................................................................................24

SPMD Chemical Screening...............................................................................................................24

Summary and Conclusions.........................................................................................................................26

References Cited..........................................................................................................................................27

Figures

Figure 1. Map showing sites where biological assessments were completed in 

2004 and 2007 in the Milwaukee Metropolitan Sewerage planning area, 

Wisconsin .................................................................................... 4

Figure 2. Photographs showing Lincoln Creek at 47th Street above USGS gage, 

looking upstream at pedestrian bridge, (A) in November 2001 during channel 

restructuring, and (B) in June 2003 during recovery of riparian vegetation ......... 5

Figure 3. Photograph of passive-sampling devices (SPMDs) that were deployed 

for an average of 37 days at 6 of the 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area to evaluate potential 

toxicity and concentrations of selected constituents in stream water ............... 6

Figure 4. Graph showing diatom pollution class for 14 sites in the Milwaukee 

Metropolitan Sewerage District planning area, Wisconsin, in 2004 and 2007 ...... 12

Figure 5. Map showing Invertebrate Ephemeroptera-Plecoptera-Trichoptera (EPT) 

index values at 14 stream sites in the Milwaukee Metropolitan Sewerage 

District planning area, Wisconsin, 2004 and 2007 ....................................... 15

Figure 6. Map showing Invertebrate Hilsenhoff Biotic Index (HBI-10) values at 

14 stream sites in the Milwaukee Metropolitan Sewerage District planning 

area, Wisconsin, 2004 and 2007............................................................ 18

Figure 7. Map showing Fish Index of Biotic Integrity (IBI) scores at 14 stream sites in 

the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 

2004 and 2007................................................................................. 21
iv

Tables

Table 1. Stream sites where biological assessments were completed in 2004 and 

2007 in the Milwaukee Metropolitan Sewerage District planning area of 

Wisconsin, showing drainage area and annual mean discharge ..................... 5

Table 2. Algal assemblage information from one-time surveys conducted in 

September 2007 at 14 stream sites in the Milwaukee Metropolitan Sewerage 

District planning area, Wisconsin ......................................................... 8

Table 3. Comparison of algal-assemblage data from one-time surveys at 14 stream 

sites in the Milwaukee Metropolitan Sewerage District Planning area, 

Wisconsin, 2004 and 2007 .................................................................. 9

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

of Biotic Integrity for streams ............................................................ 12

Table 5. Invertebrate-assemblage information from one-time surveys conducted in 

September 2007 at 14 stream sites in the Milwaukee Metropolitan Sewerage 

District planning area, Wisconsin ......................................................... 13

Table 6. Comparison of invertebrate-assemblage data from one-time surveys at 

14 sites in the Milwaukee Metropolitan Sewerage District Planning area, 

Wisconsin, 2004 and 2007 .................................................................. 16

Table 7. Scores and ratings for the fish Index of Biotic Integrity for warmwater streams.... 19

Table 8. Comparison of fish-assemblage data from one-time surveys at 14 sites in 

the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 

2004 and 2007................................................................................. 20

Table 9. Average trophic-level rankings and aggregate bioassessment rankings for 

stream sites in the Milwaukee Metropolitan Sewerage District planning area, 

Wisconsin, in 2007 and 2004 ............................................................... 23

Table 10. Toxicity test results for passive sampling devices (SPMDs, semi-permeable 

membrane devices) deployed during July–August 2007, for a subset of six 

Phase III stream sites in the Milwaukee Metropolitan Sewerage District 

planning area, Wisconsin .................................................................. 24

Table 11. Estimated concentration in water, in nanograms per liter, of polycyclic 

aromatic hydrocarbons (PAHs) computed from results for passive sampling 

devices (SPMDs, semi-permeable membrane devices) deployed at 6 of 

14 stream sites in the Milwaukee Metropolitan Sewerage District planning 

area of Wisconsin, July–August, 2007. Values were estimated using 37 days, 

the average number of days all SPMDs were deployed. .............................. 25
v

Conversion Factors and Abbreviations

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2) 

Volume

liter (L) 1.057 quart (qt)

liter (L) 0.2642 gallon (gal)

cubic meter (m3) 264.2 gallon (gal) 

Flow rate

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

Mass

ounce, avoirdupois (oz) 28.35 gram (g) 

pound, avoirdupois (lb) 0.4536 kilogram (kg) 

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

°F=(1.8×°C)+32

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 either in milligrams per liter (mg/L) 

or micrograms per liter (μg/L).
vi

Other Abbreviations

BOD Biological Oxygen Demand

EPT Ephemeroptera-Plecoptera-Trichoptera taxa

GIS Geographic Information System

HBI Hilsenhoff Biotic Index

HBI-10 Hilsenhoff Biotic Index, 10-Max modification

IBI Index of Biotic Integrity

MMSD Milwaukee Metropolitan Sewerage District

P450RGS Cytochrome-P450 Reporter Gene System

PAH Polycyclic aromatic hydrocarbon

PCB Polychlorinated biphenyl

PEC Probable effects concentration

PRA Percent relative abundance

SEWRPC Southeastern Wisconsin Regional Planning Commission

SPMD Semipermeable membrane device (type of passive-sampling device)

TEC Threshold effect concentration

TEQ Toxic equivalents, from the SPMD P450RGS toxicity test

TU50 Toxicity units for the Microtox toxicity test

USGS U.S. Geological Survey

WDNR Wisconsin Department of Natural Resources
vii

Acknowledgments

Technical Reviewers

Elisabeth A. Graffy, Economist, U.S. Geological Survey, Middleton, Wis.

Mitchell A. Harris, Ecologist, U.S. Geological Survey, Urbana, Ill.

Editorial and Graphics

Alice Koller, Editor, Greymont –Koller Group, Lincoln, Mass.

Michelle Greenwood, Geographer, U.S. Geological Survey, Middleton, Wis.

Data Collection, 2007

Austin K. Baldwin, Hydrologist, U.S. Geological Survey, Middleton, Wis.

David J. Graczyk, Hydrologist, U.S. Geological Survey, Middleton, Wis.

Ryan T. Jirik, Hydrologic Technician, U.S. Geological Survey, Rhinelander, Wis.

Kevin D. Richards, Hydrologist, U.S. Geological Survey, Middleton, Wis.

Approving Official

Rip S. Shively, Bureau Reports Approving Official-Biology, Central Region, U.S. Geological 

Survey, Columbia, Mo.
viii

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Biological Water-Quality Assessment of Selected 

Streams in the Milwaukee Metropolitan Sewerage 

District Planning Area of Wisconsin, 2007

By Barbara C. Scudder Eikenberry, Amanda H. Bell, Daniel J. Sullivan, Michelle A. Lutz, and David A. Alvarez

Abstract

Changes in the water quality of stream ecosystems in 

an urban area may manifest in conspicuous ways, such as in 

murky or smelly streamwater, or in less conspicuous ways, 

such as fewer native or pollution-sensitive organisms. In 2004, 

and again in 2007, the U.S. Geological Survey sampled stream 

organisms—algae, invertebrates, and fish—in 14 Milwaukee 

area streams to assess water quality as part of the ongoing 

Milwaukee Metropolitan Sewerage District (MMSD) Corridor 

Study. In addition, passive-sampling devices (SPMDs, 

“semipermeable membrane devices”) were deployed at a 

subset of sites in order to evaluate the potential exposure of 

stream organisms to certain toxic chemicals. Results of the 

2007 sampling effort are the focus of this report. Results of 

sampling from 2007 are compared with results from 2004. 

The water quality of sampled streams was assessed by 

evaluating biological-assemblage data, metrics computed from 

assemblage data, and an aggregate bioassessment ranking 

method that combined data for algae, invertebrates, and fish. 

These data contain information about the abundance (number) 

of different species in each group of stream organisms and the 

balance between species that can or cannot tolerate polluted 

or disturbed conditions. In 2007, the highest numbers of algal, 

invertebrate, and fish species were found at the Milwaukee 

River at Milwaukee, the largest sampled site. Algal results 

indicated water quality concerns at 10 of the 14 sampled sites 

due to the occurrence of nuisance algae or low percentages of 

pollution-sensitive algae. When compared to 2004, total algal 

biovolume was higher in 2007 at 12 of 14 sites, due mostly 

to more nuisance green algae from unknown causes. Results 

of several metrics, including the Hilsenhoff Biotic Index 

(HBI-10), suggest that invertebrate assemblages in the Little 

Menomonee River, Underwood Creek, and Honey Creek were 

poorer quality in 2007 compared to 2004. Six sites received 

“very poor” quality ratings for fish in 2007, mostly because 

inadequate numbers of fish were collected at five sites to 

allow computation of an Index of Biotic Integrity (IBI); this 

resulted in three additional sites receiving “very poor” ratings 

compared to 2004. Some signs of potential improvement in 

the fish assemblage were evident at Lincoln Creek, possibly 

reflecting delayed effects of the restoration of stream habitat, 

completed in 2002; however, algae and invertebrates did not 

show signs of improvement. 

Aggregate bioassessment rankings across all groups of 

organisms for 2004 and 2007 indicated that water quality 

at the two Milwaukee River main stem sites (at Milwaukee 

and near Cedarburg), Jewel Creek, and the Menomonee 

River at Menomonee Falls was the least-degraded among all 

sampled sites. Rankings for Oak Creek and Little Menomonee 

suggested water quality was worse in 2007 compared to 2004 

and placed these two sites together with Kinnickinnic River 

and Underwood Creek, two concrete-line sites, indicating 

the most-degraded water quality among all sampled sites. 

The aggregate ranking for Lincoln Creek in 2007 would 

have placed it in the most-degraded category but for the 

positive influence of the fish ranking when compared to 

poor algal and invertebrate rankings. Potential toxicity due 

to certain manmade chemicals, such as polycyclic aromatic 

hydrocarbons (PAHs), was found at all six sites where 

SPMDs were deployed. As was found in 2004, the highest 

potential toxicity in 2007 was observed at Lincoln Creek 

where chemical screening in 2007 also showed the highest 

total PAHs of all six sites; however, potential toxicity at Little 

Menomonee River, Honey Creek, and Kinnickinnic River was 

relatively high compared to Milwaukee River near Cedarburg. 

Although toxicity and chemical results in 2007 did not agree 

with aggregate rankings for Lincoln Creek because of fish, 

nor for Honey Creek, the results did agree with aggregate 

rankings at four of the six sites. In addition to toxicological 

and chemical influences, the more urbanized sites have high 

percentages of impervious surface area, resulting in frequent 

high stream flows that can adversely affect algal, invertebrate, 

and fish assemblages. Assessments of the ecological status 

of different groups of organisms and of potential chemical 

and physical stressors to organisms are important tools in 

evaluating streamwater quality. 
2 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

Introduction

The Milwaukee Metropolitan Sewerage District (MMSD) 

Corridor Study is designed to improve the understanding of 

water resources in the MMSD planning area by evaluating 

the quality of water resources and of biological communities 

of stream corridors within the MMSD planning area and by 

providing information for assessing the potential success 

of current and future management efforts. The study is a 

collaborative effort by MMSD, the Wisconsin Department 

of Natural Resources (WDNR), the Southeastern Wisconsin 

Regional Planning Commission (SEWRPC), University of 

Wisconsin-Milwaukee, Marquette University, Wisconsin 

Lutheran College, and the U.S. Geological Survey (USGS). 

Biological data, in combination with water chemistry and 

hydrologic data, provide multiple lines of evidence to assist 

scientists and managers in the assessment of water quality 

conditions. In the MMSD planning area, watersheds are 

generally becoming more urbanized, and the resulting changes 

in habitat, flow, and water chemistry can have major effects on 

organisms (biota) living in the streams. Because biota differ 

in their response to changes in water quality, data collected as 

part of this study included distribution and number of algal, 

invertebrate, and fish taxa (species, genus, family, phylum, or 

other grouping based on taxonomy of biota). 

Benthic algae, also known as periphyton, are algae that 

attach to streambed materials such as rocks, logs, and other 

substrates. The most common benthic algae in most streams 

are diatoms. Blue-green and green algae may be found in 

greater abundance than diatoms in stream ecosystems that are 

subject to greater disturbance from human (anthropogenic) 

activities, such as nutrient enrichment and sedimentation 

carried in storm runoff from lawn fertilizers, construction, 

streets, etc. Because algae reproduce quickly and thus respond 

to short-term environmental changes, benthic algae were 

collected as water-quality indicators of short-term effects.

Benthic (attached) invertebrates include snails, mussels 

or clams, worms, leeches, and the larvae of many insects; 

aquatic insect larvae were targeted in this study. Invertebrates 

were collected as indicators of water-quality conditions of a 

slightly longer period than algae due to their relatively longer 

life spans: many invertebrates have life cycles of about a 

year. In addition, invertebrates are relatively stationary, and 

therefore are good indicators of conditions at a particular site. 

Some invertebrates are tolerant of a wide variety of water 

quality conditions, and others have a very narrow range of 

conditions they can tolerate.

Fish also were collected as part of the MMSD 

water‐quality assessment. Fish generally live longer than 

algae or invertebrates and thus the fish assemblage may reflect 

water quality integrated over multiple years. However, fish 

are also mobile, and in some cases move great distances up 

and down rivers and streams. Thus, the fish assemblage at 

a particular site must be assessed within the larger context 

of the watershed (Allen and others, 1999; Fitzpatrick and 

others, 2001; Fore and others, 2003; Hambrook Berkman and 

others, 2010). Fish data also are useful from the standpoint of 

public interest for sport and recreational fishing, and results of 

fish studies can be applied to the fishable waters mandate of 

Congress as part of the Clean Water Act. 

While the health of in-stream biological communities 

is a useful indicator of ecosystem health, another aspect 

of pollution that is of concern to resource managers is the 

accumulation of potentially toxic chemicals in the tissues 

of fish and other stream biota. However, it is sometimes 

difficult or impossible to find sufficient numbers of the 

same taxa and size (or age) of biota across multiple sites for 

tissue analyses. Therefore, passive-sampling devices called 

“semipermeable membrane devices” (SPMDs) that mimic 

biological membranes, such as the gills of fish, can be used to 

predict exposure and accumulation of selected chemicals in 

fish and other aquatic biota (Alvarez and others, 2008; Bryant 

and Goodbred, 2009; Goodbred and others, 2009). SPMDs 

contain a manmade substance that is similar to lipids, or fats, 

found in fish tissues where waterborne chemicals accumulate. 

Chemicals commonly assessed by use of SPMDs are 

polycyclic aromatic hydrocarbons (PAHs), the largest group 

of suspected chemical carcinogens, which are formed mostly 

during incomplete combustion of fuel (Van Metre and others, 

2000 and 2009). Together with assessment of the quality of 

aquatic assemblages at a site, use of SPMDs allow for a more 

complete picture of the overall health of each stream site 

examined (Bryant and Goodbred, 2009; Goodbred and others, 

2009).

Purpose and Scope

Data collection was part of a larger water-quality study 

that began in 2000 to assess the water quality of selected 

stream sites in the Milwaukee area for the MMSD. The present 

report describes the results of biological and SPMD toxicity 

data collected in 2007 (“Phase III”) in streams of the MMSD 

planning area, and includes comparisons to data collected in 

2004 (referred to as “Phase II”) and to a retrospective analysis 

of data (referred to as “Phase I”) collected prior to Phase II 

(Schneider, Lutz, and others, 2004; Thomas, Lutz, and others, 

2007). 

Biotic integrity and water quality were assessed at 

selected stream sites based on the biological assemblage data 

as well as on selected biological measures (metrics) that were 

computed based on these data. Effects of stream flows on 

biota at a subset of sites are described elsewhere (Richards 

and others, 2010; Steuer and others, 2010). The potential level 

of toxicity to stream biota from certain manmade chemicals 

was estimated at a subset of six sites based on analysis of 

data from SPMDs. Additional analysis of extracts for selected 

chemical concentrations allowed for a time-integrated 

concentration of the bioavailable fraction of these chemicals, 

thus supplementing single-sample measurements of total 

concentrations in water-column samples. The SPMD results 

were also compared to biological assemblage data at sampled 

sites, and together with the biological data provide multiple 

lines of evidence in an assessment of water quality.
Methods 3

Methods

Biological samples were collected once in 2004 and 

once in 2007 from early July through early October, generally 

during periods of stable low flow when conditions were 

relatively stable and problems with access were minimized. 

Methods were in accordance with the USGS National WaterQuality Assessment Program (NAWQA) protocols detailed 

below. 

Study Area

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 both discharge directly into Lake Michigan south 

of the Milwaukee Harbor. Jewel Creek discharges into the 

Mississippi River by way of the Fox and Illinois Rivers. The 

Underwood Creek and Kinnickinnic River sampled reaches 

are mostly or entirely concrete-lined. Aquatic biological 

assemblages were sampled at the same 14 sites that were 

sampled in 2004 (Phase II) for numbers and types of algal, 

invertebrate, and fish taxa.

At the Lincoln Creek site, a major stream-restoration 

project was completed in 2002, about 2 years before this study 

began (fig. 2). The project included restructuring the channel 

together with removal and replacement of the streambed; 

all riparian vegetation was removed to allow for the major 

channel restructuring and streambank replacement. These 

dramatic modifications to the aquatic habitat will lead to 

ongoing ecological changes at this site, independently of direct 

water-quality changes, as biological assemblages adapt to the 

changed environment and approach equilibrium. 

Data Collection

Algal, invertebrate, and fish samples were collected in a 

defined stream reach (150–300 m in length) according to the 

methods documented in Moulton and others (2002). Algal 

and invertebrate samples were collected during late August 

or early September 2004 and 2007. Fish were collected July 

through October in 2004 and only September in 2007. Areawide storms and resulting high stream flows that occurred 

August 18–20, 2007, may have reduced the number of some 

stream biota for sampling. In addition to biological sampling, 

surface-water field parameters, including water temperature, 

pH, and specific electrical conductance (conductivity), were 

collected at the time of sampling. 

Algal and invertebrate assemblages were sampled using 

USGS protocols for quantitative Richest-Targeted Habitat 

(RTH) samples (Moulton and others, 2002). The RTH 

sample was intended to represent the habitat with the greatest 

diversity of biota in a given stream reach, and was usually a 

riffle. Willow Creek is a sand-bottomed stream with no riffles; 

therefore, woody snags were sampled as the richest habitat. 

Collection of algal and invertebrate samples was done at the 

same time in the same general area of the reach. Water depth 

and velocity were recorded at sampling locations during 

collection of algal and invertebrate samples. 

Algal assemblage samples were collected using standard 

USGS methods (Moulton and others, 2002). Most samples 

were collected from cobble in riffle areas, except for the 

Willow Creek sample, which was collected from woody snags. 

At each site, five discrete collections in five riffle or snag 

areas were combined into a single composited algal sample 

to represent that site. The Academy of Natural Sciences in 

Philadelphia identified and counted algal taxa (generally 

species or genus) in all samples. 

Invertebrate assemblage samples were collected using 

standard USGS methods (Moulton and others, 2002). Five 

discrete invertebrate collections were made from cobble 

at all but one site, using a modified Surber sampler with 

500-micron-mesh net, and then combined into a single sample 

for each site (Moulton and others, 2002). At Willow Creek, 

where woody snags were sampled, discrete invertebrate 

collections from two snags were made at each of five locations 

and combined into a single sample. Identification and 

enumeration of invertebrate taxa (generally species or genus) 

were done by the Benthic Invertebrate Laboratory at the 

University of Wisconsin-Stevens Point (Stevens Point, Wis.).

A representative fish assemblage sample was collected 

at each site using backpack-mounted or towed-barge 

electrofishing units, as applicable, as well as seines (Moulton 

and others, 2002). Two electrofishing passes of the sampling 

reach were supplemented with three seine hauls per site. 

Fish were identified as to taxa (generally species), counted, 

weighed, and measured in the field, and then released to the 

stream. In the few cases where a fish could not be identified 

with certainty in the field, a few representative individuals 

were preserved for later identification. 

SPMDs were deployed in duplicate at 6 of the 14 sites. 

SPMDs were in streams for 33–44 days (average of 37 days) 

during July–August 2007. One additional SPMD per site 

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

and was never deployed into the stream. SPMDs were 

15.2-cm “mini-unit” devices of ultra-high-pure triolein, 

inside protective metal containers, and were purchased 

from Environmental Sampling Technologies (EST Labs; St. 

Joseph, MO) (fig. 3). Following deployment, SPMDs were 

returned to EST Labs for processing and dialysis to obtain 

chemical extracts. Extracts were sent to the USGS Columbia 

Environmental Research Center (CERC; Columbia, Mo.) for 

Microtox toxicity testing and PAH screening. The Microtox 

test screens for acute toxicity from certain manmade chemicals 

using strains of bioluminescent bacteria (Strategic Diagnostics, 

Inc.; Newark, DE). Extracts were sent to the U.S. Army 

Corps of Engineers, Engineer Research and Development 

Center—Waterways Experiment Station (Vicksburg, Miss.) 

for Cytochrome-P450 Reporter Gene System (P450RGS) 
4 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

EXPLANATION

Water

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

Stream

Phase III biologysampling site

Oak Creek

at South Milwaukee

(OCSM)

Jewel Creek

at Muskego

(JCM)

Honey Creek at Wauwatosa (HCW)

Willow Creek at Maple Road

near Germantown

(WCG)

Lincoln Creek

at 47th Street

at Milwaukee

(LCM)

Underwood Creek

at Wauwatosa

(UCW)

Kinnickinnic River

at S. 11th Street at Milwaukee

(KRM)

Little Menomonee River

at Milwaukee

(LMM)

Root River

near Franklin

(RRF)

Root River

at Grange Avenue

at Greenfield

(RRG)

Menomonee River

at Wauwatosa

(MRW)

Milwaukee River

at Milwaukee

(MRM

Milwaukee River

near Cedarburg

(MRC)

Menomonee River

at Menomonee Falls

(MRMF)

Oak Creek

at South Milwaukee

(OCSM)

Jewel Creek

at Muskego

(JCM)

Honey Creek at Wauwatosa (HCW)

Willow Creek at Maple Road

near Germantown

(WCG)

Lincoln Creek

at 47th Street

at Milwaukee

(LCM)

Underwood Creek

at Wauwatosa

(UCW)

Kinnickinnic River

at S. 11th Street at Milwaukee

(KRM)

Little Menomonee River

at Milwaukee

(LMM)

Root River

near Franklin

(RRF)

Root River

at Grange Avenue

at Greenfield

(RRG)

Menomonee River

at Wauwatosa

(MRW)

Milwaukee River

at Milwaukee

(MRM)

Milwaukee River

near Cedarburg

(MRC)

Menomonee River

at Menomonee Falls

(MRMF)

FOX RIVE FOX RIVER

ROOT RIVER ROOT RIVER

MILWAUKEE RIVE MILWAUKEE RIVER

MENOMONEE

RIVER

ROCK RIVER ROCK RIVER

OAK CREEK OAK CREEK

KINNICKINNIC

RIVER

DIRECT

TRIBUTARY TRIBUTARY

DIRECT

TRIBUTARY TRIBUTARY

LAKE

MICHIGAN

DIRECT

88°10' 87°50'

42°50' 43°10'

Lake Michigan

0 42 Miles

0 42 Kilometers

Base composited 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.

Figure 1. Sites where biological assessments were completed in 2004 and 2007 in the 

Milwaukee Metropolitan Sewerage planning area, Wisconsin.

WISCONSIN

MICHIGAN

ILLINOIS

IOWA

MINNESOTA

MMSD

planning area

Figure 1. Sites where biological assessments were completed in 2004 and 2007 in the Milwaukee Metropolitan Sewerage 

planning area, Wisconsin.
Methods 5

Figure 2. Lincoln Creek at 47th Street above USGS gage, 

looking upstream at pedestrian bridge, 

(A) in November 2001 during channel restructuring, and 

(B) in June 2003 during recovery of riparian vegetation.

Table 1. Stream sites where biological assessments were completed in 2004 and 2007 in the Milwaukee 

Metropolitan Sewerage District planning area of Wisconsin, showing drainage area and annual mean discharge.

[Site locations are shown in figure 1. *, site at which semi-permeable membrane devices were deployed in 2007; mi2, square mile; 

ft3/s, cubic foot per second; ND, no data]

USGS site name Site

abbreviation

USGS 

gaging

station 

No.

Drainage 

area

(mi2

)

Annual mean 

discharge 

(ft3/s)

Milwaukee River near Cedarburg * MRC 04086600 607 453

Lincoln Creek at 47th Street, at Milwaukee * LCM 040869416 9.56 13.2

Milwaukee River at Milwaukee MRM 04087000 696 442

Willow Creek at Maple Road, near Germantown WCG 040870195 6.33 ND

Menomonee River at Menomonee Falls MRMF 04087030 34.7 31.1

Little Menomonee River at Milwaukee * LMM 04087070 19.7 18.0

Underwood Creek at Wauwatosa UCW 04087088 18.2 15.2

Honey Creek at Wauwatosa * HCW 04087119 10.3 15.2

Menomonee River at Wauwatosa MRW 04087120 123 107

Kinnickinnic River at S. 11th Street, at Milwaukee * KRM 04087159 18.8 25.3

Oak Creek at South Milwaukee * OCSM 04087204 25 23.9

Root River at Grange Avenue, at Greenfield RRG 04087214 14.7 17.3

Root River near Franklin RRF 04087220 49.2 44.8

Jewel Creek at Muskego JCM 05544371 8.16 5.58

B

A
6 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

testing. The P450RGS test detects the presence of and potential 

biological response to PAHs, polychlorinated biphenyls (PCBs), 

dioxins, and furans, and was performed according to USEPA 

Method 4425 using strains of bioluminescent hepatoma cells 

(Ang and others, 2000). 

SPMDs were deployed in 2004 at some of these same sites 

as part of a USGS NAWQA study, and results can be found in 

the Phase II report (Thomas, Lutz, and others, 2007) as well as 

in Bryant and others (2007), Bryant and Goodbred (2009), and 

Richards and others (2010). Where possible, results for 2004 

and 2007 are compared in the present report. The 2004 SPMD 

sites included Little Menomonee River, Lincoln Creek, and Oak 

Creek; SPMDs also were deployed at two additional sites that 

were near MMSD sites: Underwood Creek at Watertown Plank 

Road, at Elm Grove (040870856, about 3 mi upstream of the 

Underwood Creek at Wauwatosa, Phase II site), and Honey Creek 

near Portland Avenue, at Wauwatosa (04087118, about 1 mi 

upstream of the Honey Creek at Wauwatosa, Phase II site).

Data Analysis

Water quality was assessed at the 14 sites by examining the 

biological communities and their characteristics, such as number 

of individuals, number and types of taxa, pollution tolerance, 

and other traits. Algal metrics computed included the number 

of taxa, the relative proportion of each algal group (including 

diatoms), and percent pollution-sensitive and pollution-tolerant 

taxa. Computed metrics for invertebrate samples included the 

number of invertebrate taxa, Shannon Diversity Index, the 

percentage of invertebrate individuals or genera in the orders 

Ephemeroptera-Plecoptera-Trichoptera (EPT), the 

Hilsenhoff Biotic Index (HBI-10; Hilsenhoff, 1987, 

1998), and Index of Biotic Integrity (IBI; Weigel, 2003). 

Assemblage information and metrics for invertebrate 

samples were provided in the BUG database from the 

Benthic Invertebrate Laboratory at the University of 

Wisconsin-Stevens Point (Stevens Point, Wis.). Metrics 

computed for fish assemblages included the number of 

species and individuals; native species; predator fish; 

number of fish in certain groups such as sunfishes, 

suckers; pollution sensitive and pollution tolerant fish; and 

Fish IBI for Wisconsin warmwater streams (Lyons, 1992). 

For SPMD results, values 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 average number of days deployed (37). Total PAH 

water concentrations were estimated using pyrene as a 

representative common PAH. Pyrene is produced during 

incomplete fossil-fuel combustion, for example, by cars 

and power plants, and it is also found in coal tar and 

coal-tar sealants (Mahler and others, 2005; Van Metre and 

others, 2009). 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, 

as well as graphing and Spearman Rank correlation (Data 

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

Biological Community Assessment

The following discussion includes results from the 

Phase III sampling conducted in 2007 and compares 

these results from the Phase II sampling conducted in 

2004. In addition, maps showing the distribution of 

biological indexes from earlier reporting on the 2004 

sampling results (Thomas, Lutz, and others, 2007) have 

been updated with Phase III data. It should be noted 

that differences between single samples taken in 2004 

and 2007 are provided for comparison; however, these 

results may not represent statistically significant trends. 

Actual long-term trends in water quality and biological 

communities can be determined only from additional 

samples collected during ensuing years. Some degree 

of year-to-year variation in the structure of biotic 

communities is expected to occur in all streams and may 

not by itself be indicative of a trend. Variation may be 

greater in urban-affected streams because of increased 

disturbance from physical and chemical stressors, for 

example, impervious land cover leading to more stream 

Figure 3. Passive-sampling devices (SPMDs) that were deployed 

for an average of 37 days at 6 of the 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area to evaluate potential 

toxicity and concentrations of selected constituents in stream water.
Biological Community Assessment 7

flows of higher magnitude and shorter duration that have 

adverse effects on stream biota (Paul and Meyer, 2001; 

Kennen and others, 2010; Poff and Zimmerman, 2010). 

Although an evaluation of flow effects on biota is beyond the 

scope of this report, an increase in these so-called “flashy” 

high flows is common in many of the study streams with high 

percentages of developed land and impervious urban surfaces 

(Richards and others, 2010; Steuer and others, 2010)

Algae

In small to medium-sized rivers, benthic algae are the 

most common type of algae. As primary producers, they 

use photosynthesis to convert sunlight, water, nutrients, and 

carbon dioxide into plant matter, sugars, and oils that are the 

basis of all food for other stream biota. The close interaction 

of algae and surface water can allow for the assessment 

of water quality based on the abundance and diversity 

of algae found in a particular stream. Metrics have been 

developed to characterize water quality based on the algal 

assemblage. These indexes included the number of taxa, the 

relative proportion of each algal group (including diatoms), 

and percent pollution-sensitive and pollution-tolerant taxa 

(table 2; Porter, 2008). The percentage of eutrophic diatoms, 

a group of diatoms found in greater abundance in waters 

enriched by nutrients (nitrogen and phosphorus), is a based on 

classifications from van Dam and others (1994). 

A total of 118 algal taxa were collected from at least 1 of 

the 14 sites in 2007, compared to 177 taxa collected in 2004. 

The median number of taxa per site was similar as between 

2007 (37.5 taxa per site) and 2004 (37 taxa per site). The 

fewest taxa (26) collected from any site in 2007 were from the 

Kinnickinnic River; in 2004, the fewest (24) were collected at 

the Root River at Greenfield (table 2). The samples containing 

the most taxa from a site in 2007 (70) and in 2004 (57) were 

both from the Milwaukee River at Milwaukee, the largest 

stream. In 2007, five diatom taxa were collected at all 14 

sites. Three of these taxa (Amphora pediculus, Nitzschia 

inconspicua, and Rhoicosphenia abbreviata) also were 

observed at all sites in 2004; the two additional taxa observed 

in 2007 were Navicula minima and Nitzschia frustulum, the 

latter of which was found only at a single site (Menomonee 

River at Menomonee Falls) in 2004. There did not appear to 

be any similarity in the characteristics of these taxa to explain 

the year-to-year variation in abundance.

Four algal groups (phyla) were identified at the MMSD 

sites: diatoms, as well as green, blue-green, and red algae. 

In 2004, all four algal phyla were present at only two sites 

(Honey Creek and Menomonee River at Wauwatosa), and the 

phylum missing at other sites was either red or green algae. 

In 2007, all four phyla were present at 8 of the 14 sites; the 

phylum missing at the remaining 6 sites was red algae. In 

2004, unidentifiable algal taxa were found at Oak Creek, 

Menomonee River at Menomonee Falls, and Honey Creek that 

were not found in 2007 and therefore are not discussed further. 

The percent relative abundance (PRA) of each algal phylum is 

the number of cells from that algal phylum divided by the total 

number of algal cells. In general, there was little difference 

between 2004 and 2007 in the PRA of algal phyla at any of the 

sites (table 3), with only two sites showing PRA differences 

equal to or greater than 10 percent: diatoms were 13 percent 

higher and red algae were 11 percent lower at Root River at 

Franklin and diatoms were 10 percent higher while blue-green 

algae were 9.1 percent lower at Lincoln Creek. 

Biovolume can be described as the physical area 

(volume) that an algal cell occupies. Together with the 

lower overall number of taxa in 2007 compared to 2004, 

the total biovolume of algae at all 14 sites combined was 

lower by almost half—from 208 billion to 136 billion 

cubic microliters per square centimeter (μL3/cm2) in 2007. 

This difference was primarily related to lower biovolume 

observed at Milwaukee River at Milwaukee in 2007 (from 

167 billion μL3/cm2 in 2004 to 3 billion μL3/cm2 in 2007), 

even though biovolume at 12 of the 14 sites was actually 

higher in 2007 (data not shown). Biovolume also can be 

expressed as a percentage of the total. At each site, percent 

biovolume was calculated for each phylum by multiplying 

the number of algal cells in that phylum by the volume of 

space each cell occupies, then dividing by the total biovolume 

of all algal cells in all phyla. Using this measure, we found 

that the most dramatic difference in the Milwaukee River at 

Milwaukee algal assemblage was 94 percent lower biovolume 

for the blue‐green alga Pleurocapsa minor in 2007 compared 

with 2004 (163 billion μL3/cm2 and 36 million μL3/cm2, 

respectively). Blooms of potential toxin-producing algal taxa, 

primarily certain kinds of blue-green algae, were not found in 

any samples from the 14 stream sites in 2004 or 2007. 

Overall, the most notable differences in percent 

biovolume were due to green algae, which was more than 

10 percent higher in 2007 at 12 of the 14 sites (Milwaukee 

River near Cedarburg was 8.9 percent lower and Root 

River was 5.7 percent lower). The largest difference in 

percent biovolume at a site was at Lincoln Creek: in 2004 

early-colonizing species of blue-green algae accounted for 

99.5 percent biovolume and in 2007 green algae accounted for 

98.9 percent. The green alga that may be largely responsible 

for this change is the mid- to late-colonizer Cladophora 

glomerata; percent biovolume changed from 0 to 96 percent 

between 2004 and 2007 at Lincoln Creek and from 2.1 to 

78 percent during this same time for all sites. Cladophora 

glomerata is a large-cell filamentous green alga that is several 

orders of magnitude larger than many other algal taxa. This 

taxa also is known to be a bloom-producing nuisance alga 

that can clog streams and pipes, and it may be indicative of 

nutrient enrichment (Prescott, 1962; Wehr and Sheath, 2003). 
8 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007 Table 2. Algal assemblage information from one-time surveys conducted in September 2007 at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin. [Percent of eutrophic diatoms is the sum of mesotrophic-eutrophic, eutrophic, polytrophic, and eurytrophic; μL, microliters; cm2, square centimeter] Site Number of taxa Biovolume (μL/cm2 * 106

)

Cell density 

(cells/cm2 * 

106

)

Shannon 

index of 

diversity

Percent of 

nuisance 

algae

Percent diatoms

Eutrophic Pollution- tolerant Pollution- moderate Pollution- sensitive

Milwaukee River near Cedarburg 50 29,944 81 3.02 0.02 83.4 20.9 33.5 29.0

Lincoln Creek at 47th Street at Milwaukee 40 53,118 16 2.58 0.6 71.8 21.5 35.8 15.1

Milwaukee River at Milwaukee 57 2,607.5 6.9 3.09 0.4 82.5 10.4 41.2 31.9

Willow Creek at Maple Road near Germantown 43 4,170.4 1.5 2.69 0.1 85.8 14.7 32.2 38.7

Menomonee River at Menomonee Falls 32 506.6 3.0 2.37 0 81.8 1.96 5.17 73.6

Little Menomonee River at Milwaukee 30 3,307.2 16 2.52 0 81.8 22.3 26.7 33.2

Underwood Creek at Wauwatosa 35 1,148.1 13 2.61 0 82.0 9.28 58.8 13.8

Honey Creek at Wauwatosa 29 21,965 8.6 2.38 0.3 86.3 7.38 61.9 17.0

Menomonee River at Wauwatosa 32 3,751.6 12 1.88 1 87.1 10.0 68.7 8.48

Kinnickinnic River at S. 11th Street at Milwaukee 26 4,417.0 2.4 1.96 0.1 86.6 13.9 19.8 52.6

Oak Creek at South Milwaukee 48 3,565.1 2.7 3.06 0 89.0 14.7 42.3 23.3

Root River at Grange Avenue at Greenfield 30 1,476.0 3.2 2.55 0 88.0 3.35 21.7 49.9

Root River near Franklin 49 2,690.4 6.1 3.00 0 85.7 9.71 28.1 44.8

Jewel Creek at Muskego 50 4,074.9 8.5 2.95 0 72.3 1.54 14.7 55.2
Biological Community Assessment

9

Table 3. Comparison of algal-assemblage data from one-time surveys at 14 stream sites in the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 2004 and 2007.[Highlighted values represent a difference of 10 percent or greater between the two sampling events]

Site Collection 

year

Percent relative abundance of algae Percent biovolume of algae Percent relative abundance of diatoms

Diatom Green Blue- Green Red Diatom Green Blue- Green Red Pollution- tolerant Pollution- moderate Pollution- sensitive Unknown tolerance

Milwaukee River near Cedarburg 2004 90.1 0.6 9.31 0.0 11.8 86.5 1.8 0.0 1.2 14.9 56.9 27.0

2007 89.7 1.0 9.30 0.0 14.7 77.6 7.7 0.0 20.9 33.5 29.0 16.6

Difference -0.4 0.4 -0.01 0.0 2.9 -8.9 6.0 0.0 19.7 18.6 -27.9 -10.5

Lincoln Creek at 47th Street at Milwaukee 2004 87.8 5.2 7.1 0.0 0.5 0.1 99.5 0.0 7.8 62.4 11.1 18.7

2007 77.7 6.1 16.2 0.0 0.5 99.0 0.5 0.0 21.5 35.8 15.1 27.6

Difference -10.0 0.9 9.1 0.0 -0.0 98.9 -98.9 0.0 13.7 -26.6 4.0 8.9

Milwaukee River at Milwaukee 2004 87.5 0.9 11.6 0.0 1.7 0.0 98.3 0.0 5.0 33.3 39.1 22.6

2007 89.3 2.9 7.8 0.0 15.9 79.9 4.2 0.0 10.4 41.2 31.9 16.5

Difference 1.8 2.0 -3.8 0.0 14.2 79.8 -94.0 0.0 5.4 7.8 -7.2 -6.0

Willow Creek at Maple Road near Germantown 2004 97.9 0.3 1.8 0.0 53.5 43.7 2.8 0.0 12.9 13.5 63.8 9.8

2007 91.0 1.8 6.0 1.2 2.6 95.3 1.2 1.0 14.7 32.2 38.7 14.4

Difference 6.9 1.5 4.2 1.2 -50.9 51.5 -1.6 1.0 1.8 18.7 -25.1 4.6

Menomonee River at Menomonee Falls 2004 89.9 0.0 6.8 3.3 40.4 0.0 2.4 41.6 4.3 26.5 42.0 27.3

2007 85.9 2.5 10.1 1.5 50.6 23.9 13.3 12.2 2.0 5.2 73.6 19.3

Difference -4.1 2.5 3.3 -1.7 10.2 23.9 11.0 -29.4 -2.3 -21.3 31.6 -8.0

Little Menomonee River at Milwaukee 2004 80.4 0.0 17.5 2.1 55.1 0.0 5.4 39.5 4.6 42.8 26.8 25.8

2007 85.1 1.8 11.4 1.7 9.7 62.4 16.9 11.0 22.3 26.7 33.2 17.8

Difference 4.7 1.8 -6.1 -0.4 -45.4 62.4 11.5 -28.5 17.7 -16.1 6.4 -8.0

Underwood Creek at Wauwatosa 2004 81.5 1.0 17.5 0.0 47.1 4.9 47.9 0.0 7.6 33.8 36.7 21.9

2007 87.8 1.6 10.6 0.0 23.6 19.0 57.4 0.0 9.3 58.8 13.8 18.1

Difference 6.3 0.6 -6.9 0.0 -23.6 14.1 9.5 0.0 1.7 25.0 -22.9 -3.8

Honey Creek at Wauwatosa 2004 86.3 0.1 7.6 5.9 73.0 0.8 0.8 27.0 6.2 44.8 21.4 27.6

2007 87.8 1.6 10.6 0.0 1.1 98.3 0.6 0.0 7.4 61.9 17.0 13.7

Difference 1.5 1.5 3.0 -5.9 -71.9 97.5 -0.1 -27.0 1.2 17.1 -4.3 -13.9

Menomonee River at Wauwatosa 2004 84.5 0.1 15.0 0.4 47.5 0.1 47.9 4.6 7.1 49.6 23.5 19.8

2007 90.0 1.0 8.8 0.3 6.4 84.5 6.4 2.8 10.0 68.7 8.5 12.9

Difference 5.5 0.8 -6.2 -0.1 -41.1 84.4 -41.5 -1.8 2.9 19.1 -15.1 -6.9
10 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007 Site Collection year Percent relative abundance of algae Percent biovolume of algae Percent relative abundance of diatoms Diatom Green Blue- Green Red Diatom Green Blue- Green Red Pollution- tolerant Pollution- moderate Pollution- sensitive Unknown tolerance Kinnickinnic River at S. 11th Street at Milwaukee 2004 92.3 0.5 7.2 0.0 68.0 0.6 31.4 0.0 26.1 38.1 17.8 18.0 2007 87.5 2.3 10.1 0.0 4.6 94.5 0.9 0.0 13.9 19.8 52.6 13.7 Difference -4.8 1.9 2.9 0.0 -63.4 93.9 -30.5 0.0 -12.2 -18.3 34.8 -4.3 Oak Creek at South Milwaukee 2004 89.0 0.0 7.5 3.5 59.0 0.0 5.8 33.7 7.5 44.7 26.5 21.3 2007 93.7 1.9 2.8 1.7 46.7 47.6 1.0 4.8 14.7 42.3 23.3 19.6 Difference 4.6 1.9 -4.7 -1.8 -12.3 47.6 -4.9 -28.9 7.2 -2.4 -3.2 -1.6 Root River at Grange Avenue at Greenfield 2004 83.6 0.0 0.8 15.6 10.8 0.0 0.3 88.9 4.9 32.3 36.2 26.6 2007 89.1 3.6 1.0 6.3 19.9 37.5 0.2 42.5 3.4 21.7 49.9 25.1 Difference 5.5 3.6 0.2 -9.3 9.1 37.5 -0.1 -46.4 -1.5 -10.6 13.6 -1.5 Root River near Franklin 2004 81.9 0.0 4.9 13.2 17.3 0.0 4.4 78.3 13.9 13.0 49.5 23.6 2007 94.4 0.8 3.0 1.8 71.1 5.7 5.7 17.5 9.7 28.1 44.8 17.5 Difference 12.5 0.8 -1.9 -11.4 53.8 5.7 1.3 -60.8 -4.2 15.1 -4.8 -6.2 Jewel Creek at Muskego 2004 92.6 0.0 1.9 5.6 63.6 0.0 1.3 35.1 2.8 10.8 62.2 24.2 2007 84.2 2.4 7.3 6.1 35.8 21.2 1.8 41.2 1.5 14.7 55.2 28.6 Difference -8.4 2.4 5.4 0.6 -27.8 21.2 0.5 6.1 -1.2 3.9 -7.0 4.4 Table 3. Comparison of algal-assemblage data from one-time surveys at 14 stream sites in the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 2004 and 2007.—Continued [Highlighted values represent a difference of 10 percent or greater between the two sampling events]
Biological Community Assessment 11

In 2004, this taxa was collected only at Milwaukee River 

near Cedarburg (0.83 percent biovolume) even though its 

presence was mentioned in field notes for four other sites; 

however, in 2007, it was collected in samples at six additional 

sites (Lincoln Creek, Milwaukee River at Milwaukee, Willow 

Creek, Honey Creek, Menomonee River at Wauwatosa, and 

Kinnickinnic River), and represented 32 percent of the total 

biovolume across all sites. Biovolume of green algae at all six 

of these additional sites was more than 50 percent higher in 

2007. Increases in temperature, light, and (or) nutrients could 

be responsible for these higher percentages of green algae 

but evaluation of these factors is beyond the scope of this 

report. Other nuisance algae present in 2007 samples included 

Stigeoclonium lubricum. Like C. glomerata, this taxa is a 

green alga that is common in streams and lakes receiving high 

loads of nutrients, especially phosphorus, in the Great Lakes 

area (Prescott, 1962; Wehr and Sheath, 2003). S. lubricum was 

collected at three sites (Lincoln Creek, Milwaukee River at 

Milwaukee, and Menomonee River at Wauwatosa), but was 

not found at Underwood Creek, as it had been in 2004.

The relative abundance of diatoms classified as 

pollution tolerant or pollution sensitive in a stream may 

be an indicator of water quality (Lange-Bertalot, 1979; 

Bahls, 1993). In streams with impaired water quality, a 

greater proportion of diatom taxa would be expected to be 

comprised of taxa that are tolerant to pollution, with the 

opposite being true in more pristine streams. For example, 

fewer pollution-sensitive taxa at a site indicate that, for a 

given stream, at least one of the variables that make up the 

pollution-tolerance classes—such as nutrient concentration, 

saprobic conditions (providing nutrients for nuisance algae), 

biological oxygen demand (BOD), and toxic chemicals—is 

elevated and not suited for pollution-sensitive taxa (Bahls, 

1993). Most streams have some level of pollution-tolerant 

taxa, which are usually relatively common and cosmopolitan. 

However, pollution tolerant taxa that begin to dominate the 

algal assemblage indicate that water quality is degrading to 

a point at which the pollution-sensitive taxa cannot survive. 

Therefore, a difference in the relative proportion of pollutiontolerant or pollution-sensitive taxa can indicate that water 

quality is better (increased number of sensitive taxa) or worse 

(increased number of tolerant taxa). 

Substantial differences in pollution-tolerant and 

pollution-sensitive diatoms were noted between 2004 and 

2007 for some sites (table 3). Pollution-tolerant diatom 

abundance in 2007 was 20 percent higher at Milwaukee 

River near Cedarburg compared to the abundance in 2004; 

pollution-sensitive diatom abundance in 2007 was 28 percent 

lower (fig. 4). The percentages of pollution-tolerant taxa at 

Lincoln Creek and Little Menomonee River were higher in 

2007 (14 and 18 percent higher, respectively). The only stream 

to have a relatively large negative difference in pollutiontolerant diatoms was the Kinnickinnic River, from 26 percent 

in 2004 to 14 percent in 2007. Additionally, the proportion 

of pollution-sensitive diatoms was 18 percent in 2004 and 

53 percent in 2007 at Kinnickinnic River; 42 and 74 percent 

at Menomonee River at Menomonee Falls; and 36 and 

50 percent at the Root River at Greenfield. The proportions 

of pollution-sensitive diatoms were 64 percent in 2004 and 

39 percent in 2007 at Willow Creek, 37 and 14 percent at 

Underwood Creek, and 24 and 8.5 percent at Menomonee 

River at Wauwatosa. 

Several streams, including the Milwaukee River near 

Cedarburg and Underwood Creek, indicate high nutrient 

loading and high concentrations of other pollutants based 

on the occurrence of nuisance algae and the proportion of 

diatoms in various pollution classes. Samples from these 

sites contained taxa that could develop into large blooms 

of nuisance algae, creating issues of aesthetics, odor, and 

water quality as they die and begin to decay. Streams with 

low percentages of pollution-sensitive diatoms indicate 

that at least one of the variables that are used to determine 

pollution‐sensitivity is elevated and that those rivers cannot 

sustain a large percentage of pollution-sensitive taxa. The 

Milwaukee River near Cedarburg, Lincoln Creek, Underwood 

Creek, Honey Creek, Menomonee River at Wauwatosa, Oak 

Creek, and Root River at Greenfield have less than 30 percent 

pollution-sensitive diatoms. Ten of the 14 sites sampled in the 

MMSD planning area are of concern for water quality, based 

on either the occurrence of nuisance algae or a low abundance 

of pollution-sensitive diatoms. Four streams do not fall into 

this class: Milwaukee River at Milwaukee, Willow Creek, 

Root River at Franklin, and Jewel Creek.
12 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

Invertebrates

Invertebrate assemblages were evaluated by the 

number of their taxa, Shannon Diversity Index, percentage 

of taxa or individuals in the aquatic insect orders 

Ephemeroptera‐Plecoptera-Trichoptera (EPT; also known as 

mayflies, stoneflies, and caddisflies), the Hilsenhoff Biotic 

Index (HBI-10), and the Index of Biotic Integrity (table 4). 

The number of taxa and Shannon Diversity Index scores 

generally decrease with degrading water quality. The highest 

numbers of invertebrate taxa (42 species and 36 genera) 

and the highest Shannon diversity score (4.14) in 2007 

were found at the Milwaukee River at Milwaukee (table 5). 

0

20

40

60

80

 100

 2004 2007

20042007200420072004200720042007200420072004200720042007200420072004200720042007200420072004200720042007

MRC

LCM

MRM

WCG

MRMF

LMM

UCWHCW

MRW

KRM

OCSM

RRG

RRF

JCM

SITES, ARRANGED IN DOWNSTREAM ORDER

RELATIVE ABUNDANCE OF DIATOMS

IN EACH POLLUTION-TOLERANCE CLASS, IN PERCENT

Most-tolerant Moderately tolerant Sensitive Unknown

Figure 4. Diatom pollution class for 14 sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, in 2004 and in 2007.

Figure 4. Diatom pollution class for 14 sites in the Milwaukee Metropolitan Sewerage District planning area, 

Wisconsin, in 2004 and 2007.

Table 4. Water-quality ratings for the invertebrate Hilsenhoff 

Biotic Index and Index of Biotic Integrity for streams.

[(HBI, Hilsenhoff Biotic Index (Hilsenhoff, 1987); HBI-10, modified HBI 

(Hilsenhoff, 1998); IBI, Index of Biotic Integrity (Weigel, 2003); >, greater 

than; <, less than; ≤, less than or equal to]

HBI/HBI-10

value

Water-quality 

rating

Invertebrate

IBI value

≤3.50 Excellent >8

3.51–4.50 Very good

4.51–5.50 Good 6– 8

5.51–6.50 Fair 4– 6

6.51–7.50 Fairly poor

7.51–8.50 Poor 2– 4

 8.51–10.00 Very poor <2
Biological Community Assessment

13

Table 5. Invertebrate-assemblage information from one-time surveys conducted in September 2007 at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin.[EPT, Ephemeroptera (Mayflies), Plecoptera (Stoneflies), and Trichoptera (Caddisflies); HBI-10, modified Hilsenhoff Biotic Index; IBI, Index of Biotic Integrity]

Site Number of species Number of genera Shannon index of diversity Percent of EPT individuals Percent of EPT taxa HBI-101 IBI2 Value Rating Value Rating

Milwaukee River near Cedarburg 26 23 3.55 62 48 4.79 Good 6.25 Good

Lincoln Creek at 47th Street at Milwaukee 32 24 2.60 27 21 6.46 Fair 3.78 Poor

Milwaukee River at Milwaukee 42 36 4.14 58 39 5.52 Fair 7.94 Good

Willow Creek at Maple Road near Germantown 33 29 3.94 26 21 5.61 Fair 4.99 Fair

Menomonee River at Menomonee Falls 24 22 3.27 70 32 4.77 Good 3.91 Poor

Little Menomonee River at Milwaukee 22 18 2.58 15 17 6.57 Fairly Poor 3.44 Poor

Underwood Creek at Wauwatosa 21 17 2.64 1 12 6.66 Fairly Poor 3.78 Poor

Honey Creek at Wauwatosa 17 14 2.96 47 36 5.81 Fair 4.12 Fair

Menomonee River at Wauwatosa 22 17 2.21 27 29 5.85 Fair 4.54 Fair

Kinnickinnic River at S. 11th Street at Milwaukee 21 16 2.04 47 31 6.09 Fair 4.13 Fair

Oak Creek at South Milwaukee 32 26 3.61 38 19 5.77 Fair 4.34 Fair

Root River at Grange Avenue at Greenfield 25 21 3.38 30 19 5.73 Fair 3.75 Poor

Root River near Franklin 27 24 2.86 67 25 5.73 Fair 3.56 Poor

Jewel Creek at Muskego 37 29 3.31 59 17 5.79 Fair 2.87 Poor

1 Hilsenhoff, 1987 and 1998.2 Weigel, 2003.
14 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

All else being equal, higher numbers of taxa and higher 

diversity are expected at larger streams compared to smaller 

streams; however, this may not be the case in disturbed 

streams. Willow Creek, a much smaller stream, ranked next 

highest for diversity score (3.94). The lowest numbers of 

invertebrate taxa (17 species and 14 genera) were found at 

Honey Creek; however, Underwood Creek (21 species and 

17 genera), Kinnickinnic River (21 species and 16 genera), 

Little Menomonee River (22 species and 18 genera), and 

Menomonee River at Wauwatosa (22 species and 17 genera) 

also ranked similarly in number of taxa, underscoring the poor 

quality invertebrate assemblages at these sites. These findings 

suggest that the water quality at these sites was more degraded 

than at other sampled sites. 

EPT invertebrates generally are considered to be 

relatively intolerant of degraded water quality (Lenat, 1988). 

Intolerant organisms tend to dominate in streams with good 

water quality, whereas tolerant organisms dominate in streams 

with degraded water quality; therefore, the percentages 

of EPT individuals and of EPT genera tend to decrease as 

water quality degrades. The highest percentages of EPT 

taxa in samples collected in 2007 were from the Milwaukee 

River sites near Cedarburg (48 percent) and at Milwaukee 

(39 percent). Invertebrate assemblages at Underwood Creek 

and Little Menomonee River had the lowest percentages of 

EPT taxa (12 and 17 percent, respectively) and individuals 

(1 and 15 individuals, respectively). The high value for 

percent EPT taxa at Honey Creek may be misleading because 

the EPT taxa at this site are known to be relatively pollutiontolerant (Barbour and others, 1999). Historically, the Middle 

and Lower Root River Phase I subwatersheds had much 

higher median EPT percentages than the Upper Root River 

or East Branch Root River subwatersheds, suggesting that 

water quality was less degraded at the lower subwatersheds 

(Schneider, Lutz, and others, 2004). The 2004 and 2007 

samples for Root River near Franklin (Middle Root River 

subwatershed) had much lower percentages of EPT taxa 

(28 and 25 percent, respectively) compared to historical 

percentages (median of 50 percent EPT taxa) (fig. 5). 

However, although historical data indicated that EPT taxa 

were few or absent from the Lincoln Creek subwatershed, 

samples from 2004 and 2007 indicated a higher percentage 

of EPT taxa (18 and 21 percent, respectively), suggesting that 

water quality was better (Lenz and Rheaume, 2000; Schneider, 

Lutz, and others, 2004). 

The two biotic indexes used to assess invertebrate 

assemblages were the HBI-10 (Hilsenhoff 1987, 1998) and 

an invertebrate Index of Biotic Integrity (IBI; Weigel, 2003). 

The original Hilsenhoff Biotic Index (HBI) was designed to 

assess oxygen depletion in streams resulting from an excess 

of organic matter such as manure or sewage (Hilsenhoff, 

1987); however, the index also may be sensitive to other 

types of pollution, such as that from metals or some manmade 

chemicals. The HBI represents the number of arthropod 

invertebrates in certain families or species, multiplied by 

their respective pollution-tolerance score, divided by the 

number of arthropods in the sample. HBI values can range 

from 0.00 (“excellent” water quality) to 10.00 (“very poor” 

water quality). A modification of the HBI, the HBI-10, was 

used in the Phase II and Phase III analyses because it limits 

the number of individuals per taxa to 10 for computation of 

the index. The HBI-10 is thought to be more accurate than the 

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

(Hilsenhoff, 1998). Invertebrate IBI values also can range 

from 0.00 to 10.00, but its ratings are opposite to those of 

the HBI (Weigel, 2003). HBI-10 scores for 2007 invertebrate 

samples ranged from values indicating “fairly poor” water 

quality at Little Menomonee River and at Underwood Creek, 

to “good” at two sites (Menomonee River at Menomonee 

Falls and Milwaukee River near Cedarburg); all other sampled 

sites had a value indicating “fair” water quality (table 5). The 

Milwaukee River near Cedarburg was rated “good” using both 

the HBI-10 and the IBI; however, the Menomonee River at 

Menomonee Falls dropped from “good” using the HBI-10 to 

“poor” using the IBI. The reason for the difference in ratings 

between these two metrics is unclear but could perhaps be due 

to the fact that the IBI weights the percentage of EPT taxa. IBI 

ratings at only six sites agreed with HBI ratings; seven sites 

rated lower for the IBI and received “poor” ratings. However, 

the HBI-10 rated Milwaukee River at Milwaukee “fair”, 

while the IBI rated it “good”, and other measures that showed 

relatively high number of taxa, diversity, and EPT measures 

for this site supported the “good” IBI rating.

When 2004 and 2007 data are compared, results across 

invertebrate measures were not entirely consistent for a 

given site (table 6). Even so, relatively consistent negative 

differences were found for the Little Menomonee River, for 

Underwood Creek, and for Honey Creek (fig. 6). Within‐site 

differences in invertebrates and in water quality were not 

consistent at Menomonee River at Menomonee Falls, despite 

a higher number of taxa, diversity, and the HBI-10 rating. 

Additional sampling at these sites could help establish whether 

these differences reflect improvements in the invertebrate 

assemblages at these sites. Lincoln Creek received a “fair” 

rating in 2004 and in 2007, based on the HBI-10. Although 

Lincoln Creek showed a higher number of taxa in 2007, 

diversity was lower due to dominance by individuals of only a 

few species; percent EPT showed no notable difference.
Biological Community Assessment 15

88°10' 87°50'

42°50' 43°10'

Lake Michigan

0 42 Miles

0 42 Kilometers

Base composited 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.

EXPLANATION

Water

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

Stream

7–17

18–43

EPT index values, percentages

2004 2007

44–51

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

MRC

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

Figure 5. Invertebrate Ephemeroptera-Plecoptera-Trichoptera (EPT) index values at 14 stream 

sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004 and 2007.

Figure 5. Invertebrate Ephemeroptera-Plecoptera-Trichoptera (EPT) index values at 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area, Wisconsin, 2004 and 2007.
16 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007 Table 6. Comparison of invertebrate-assemblage data from one-time surveys at 14 sites in the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 2004 and 2007. [Highlighted values represent a difference of 10 percent or greater between the two sampling events; EPT, Ephemeroptera (Mayflies), Plecoptera (Stoneflies), and Trichoptera (Caddisflies); HBI-10, modified Hilsenhoff Biotic Index] Site Collection year Number of species Number of genera Shannon index of diversity1 Percent of EPT taxa HBI-102 Value Rating Milwaukee River near Cedarburg 2004 45 39 3.86 51 5.01 Good 2007 26 23 3.55 48 4.79 Good Difference -42.2 -41.0 -8.0 -3.0 -4.39 No difference Lincoln Creek at 47th Street at Milwaukee 2004 20 17 3.06 18 6.30 Fair 2007 32 24 2.60 21 6.46 Fair Difference 60.0 41.2 -15.0 3.0 2.54 No difference Milwaukee River at Milwaukee 2004 46 41 3.70 39 5.20 Good 2007 42 36 4.14 39 5.52 Fair Difference -8.7 -12.2 12.0 0.0 6.15 Lower Willow Creek at Maple Road near Germantown 2004 32 29 3.94 17 5.45 Good 2007 33 29 3.94 21 5.61 Fair Difference 3.1 0.0 0.1 4.0 2.94 Lower Menomonee River at Menomonee Falls 2004 18 16 2.29 44 5.56 Fair 2007 24 22 3.27 32 4.77 Good Difference 33.3 37.5 42.8 -12 -14.2 Higher Little Menomonee River at Milwaukee 2004 23 22 2.28 23 5.33 Good 2007 22 18 2.58 17 6.57 Fairly poor Difference -4.3 -18.2 13.5 -6.0 23.3 Lower Underwood Creek at Wauwatosa 2004 33 28 2.71 18 5.96 Fair 2007 21 17 2.64 12 6.66 Fairly poor Difference -36.4 -39.3 -2.6 -6.0 11.7 Lower Honey Creek at Wauwatosa 2004 24 24 2.73 17 5.28 Good 2007 17 14 2.96 36 5.81 Fair Difference -29.2 -41.7 8.42 19.0 10.0 Lower Menomonee River at Wauwatosa 2004 20 16 2.68 31 5.86 Fair 2007 22 17 2.21 29 5.85 Fair Difference 10.0 6.3 -17.5 -2.0 -0.17 No difference Kinnickinnic River at S. 11th Street at Milwaukee 2004 34 27 3.02 7.0 6.52 Fairly poor 2007 21 16 2.04 31 6.09 Fair Difference -38.2 -40.7 -32.5 24 -6.60 Higher
Biological Community Assessment

17

Site Collection

year

Number of 

species

Number of 

genera

Shannon 

index of 

diversity1

Percent of 

EPT taxa

HBI-102

 Value Rating

Oak Creek at South Milwaukee 2004 28 23 2.86 22 5.55 Fair

2007 32 26 3.61 19 5.77 Fair

Difference 14.3 13.0 26.5 -3.0 3.96 No difference

Root River at Grange Avenue at Greenfield 2004 23 22 2.69 18 6.15 Fair

2007 25 21 3.38 19 5.73 Fair

Difference 8.7 -4.5 26.0 1.0 -6.83 No difference

Root River near Franklin 2004 31 25 3.35 28 5.92 Fair

2007 27 24 2.86 25 5.73 Fair

Difference -12.9 -4.0 -14.6 -3.0 -3.21 No difference

Jewel Creek at Muskego 2004 28 24 3.07 29 5.58 Fair

2007 37 29 3.31 17 5.79 Fair

Difference 32.1 20.8 7.88 -12 3.76 No difference

1 Odum, 1971.2 Hilsenhoff, 1987 and 1998.

Table 6. Comparison of invertebrate-assemblage data from one-time surveys at 14 sites in the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 2004 and 2007.—Continueder[Highlighted values represent a difference of 10 percent or greater between the two sampling events; EPT, Ephemeroptera (Mayflies), Plecoptera (Stoneflies), and Trichoptera (Caddisflies); HBI-10, modified Hilsenhoff Biotic Index]
18 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

88°10' 87°50'

42°50' 43°10'

Lake Michigan

0 42 Miles

0 42 Kilometers

Base composited 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.

EXPLANATION

Water

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

Stream

5.51–6.50 (fair)

HBI–10 scores and categories

4.77–5.50 (good)

2004 2007

6.51–6.66 (fairly poor)

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

MRC

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

Figure 6. Invertebrate Hilsenhoff Biotic Index (HBI-10) values at 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area, Wisconsin, 2004 and 2007. Figure 6. Invertebrate Hilsenhoff Biotic Index (HBI-10) values at 14 stream sites in the Milwaukee Metropolitan Sewerage 

District planning area, Wisconsin, 2004 and 2007.
Biological Community Assessment 19

Fish

Biological integrity is commonly defined as “the 

capability of supporting and maintaining a balanced, 

integrated, adaptive community of organisms having a 

species composition, diversity, and functional organization 

comparable to that of natural habitat of the region” (Karr 

and Dudley, 1981; also see Frey, 1977). The use of attributes 

of fish assemblages has been shown to be a useful means to 

assess biotic integrity and environmental quality of streams 

(Karr, 1981; Karr and others, 1986; Lyons, 1992). Fish 

Index of Biotic Integrity (IBI) scores, which were computed 

according to Lyons (1992) and can range from 65 or greater 

(“excellent”) to 0 (“very poor”), are shown in table 7. 

A total of 31 fish species were collected at at least 1 of 

the 14 sites in 2007, compared to 38 species collected in 2004. 

However, five of the species not collected in 2007 were from 

the Milwaukee River near Cedarburg, where sampling was 

limited to a single pass due to weather conditions and thus the 

sample may be biased low. The most species collected at a 

single site in 2007 was 19 at Milwaukee River at Milwaukee, 

compared to 21 species collected in 2004 at the Milwaukee 

River near Cedarburg (table 8). The largest negative difference 

in species number was at the Root River where only 4 species 

were captured in 2007, compared to 12 in 2004. The largest 

positive difference was at Willow Creek, where the number of 

species collected in 2007 (12) was twice that collected in 2004 

(6). The number of species collected in 2007 was the same 

or higher at seven sites and lower at seven sites, compared to 

2004 results. 

The median number of individual fish collected per site 

in 2007 was 157, compared to a median of 200 fish collected 

per site in 2004. In 2007, the most individual fish (1,051) 

were collected at Underwood Creek and the fewest (2) at 

Kinnickinnic River (table 8). In 2004, the most individual fish 

(511) were collected at Jewel Creek and the fewest (11) were 

again collected at Kinnickinnic River. The abundance of fish 

collected in 2007 was lower at eight sites compared to 2004 

sampling efforts. At several sites, the number of fish captured 

in 2007 was considerably lower than the number captured 

in 2004. In 2004 at Root River at Greenfield, 179 fish were 

captured, and near Franklin, 183 fish were captured; in 2007, 

only 10 fish were captured at the first Root River site, and only 

7 fish were caught at the second. At Oak Creek, 218 fish were 

captured in 2004, while only 35 fish were captured in 2007. 

Catch also was lower at Jewel Creek from 2004 (511 fish) 

to 2007 (144 fish). Without additional information, it is not 

possible to discern whether lower fish abundances at these 

sites in 2007 were due to degradation or due to area wide 

storms previously mentioned, that occurred about two and a 

half weeks prior to sampling of these sites. However, a similar 

pattern was not seen for algae or invertebrates, which were 

Table 7. 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

collected about a week and a half after fish were collected 

in September. Root River, Jewel Creek, Kinnickinnic River, 

and Oak Creek are all the sampled basins in the southern 

part of the MMSD planning area and these streams were 

consecutively sampled for fish. Captures of individual fish 

were dramatically higher at several sites, including the 

Menomonee River at Wauwatosa (119 in 2004, and 449 in 

2007); Honey Creek (135 in 2004, and 521 in 2007); and 

Underwood Creek (256 in 2004, and 1,051 in 2007). 

Fish IBI ratings based on 2007 sampling ranged from 

“excellent” (1 site) to “very poor” (6 sites). Two sites scored 

“good,” five sites were “fair,” and there were no sites rated 

“poor.” Compared to 2004 results, the 2007 results are slightly 

better: 7 sites received “very poor” ratings, 2 rated “poor,” 3 

were “fair,” 1 was rated “good,” and 1 was rated “excellent” 

in 2004 (fig. 7). In 2007, not enough fish were collected at 5 of 

the 14 sites to compute a fish IBI score (table 8). A minimum 

of 50 fish must be collected in order for a valid IBI rating 

(Lyons, 1992); indeed, sites with fewer than the minimum 

number of individuals receive the IBI rating “very poor”. In 

2004 sampling as part of Phase II, at only two sites were fewer 

than 50 fish collected. Fish IBI scores were worse at 3 sites 

and were better at 6.

The two Milwaukee River sites had the highest IBI scores 

for fish of the 14 study sites. The large size, diverse habitats, 

and good water quality of these sites provide suitable living 

space for a large number and variety of species, including 

desirable game fish such as smallmouth bass, northern pike, 

walleye, and pan fish. The upstream Milwaukee River site, 

located near the city of Cedarburg, scored an “excellent” IBI 

rating based samples of its fish population in both 2004 and 

2007. At this site the Milwaukee River is a scenic, meandering 

stream with clear waters, a rocky substrate and habitat that 

supports a diverse variety of fish species including many sport 

fish—approximately 28 percent of the fish collected in 2007 

were top carnivores such as northern pike, smallmouth bass, 

rock bass, and bluegill. The Milwaukee River at Milwaukee 

site had the greatest percentage of fish that were top carnivores 

(40 percent of the total number of fish captured). 
20 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007 Table 8. Comparison of fish-assemblage data from one-time surveys at 14 sites in the Milwaukee Metropolitan Sewerage District Planning area, Wisconsin, 2004 and 2007. [ND, no data; *, the Wisconsin warmwater Index of Biotic Integrity (Lyons, 1992) was not used because fewer than 50 individual fish were collected] Site Total number of fish species Total number of fish Index of Biotic Integrity Percent intolerant species Percent tolerant species Score Rating 2004 2007 2004 2007 Phase I 2004 2007 Phase I 2004 2007 2004 2007 2004 2007 Milwaukee River near Cedarburg 21 14 320 173 ND 70 65 ND Excellent Excellent 10 14 8 4 Lincoln Creek at 47th Street at Milwaukee 8 11 59 170 10 12 57 Very poor Very poor Good 14 0 66 19 Milwaukee River at Milwaukee 18 19 240 295 62 60 57 Good Good Good 12 11 13 7 Willow Creek at Maple Road near Germantown

6 12 238 142 ND 29 39 ND Poor Fair 0 0 38 76

Menomonee River at Menomonee Falls 13 9 296 212 ND 29 15 ND Poor Very poor 8 0 79 55

Little Menomonee River at Milwaukee 5 4 14 14 ND * * ND Very poor Very poor 6 5 79 86

Underwood Creek at Wauwatosa 8 11 256 1,051 15 17 37 Very poor Very poor Fair 0 0 99 37

Honey Creek at Wauwatosa 6 11 135 521 20 16 39 Very poor Very poor Fair 0 0 98 60

Menomonee River at Wauwatosa 8 8 119 449 ND 10 40 ND Very poor Fair 0 0 97 8

Kinnickinnic River at S. 11th Street at 

Milwaukee

1 2 11 2 20 * * Very poor Very poor Very poor 0 0 100 50

Oak Creek at South Milwaukee 7 5 218 35 17 10 * Very poor Very poor Very poor 0 0 94 97

Root River at Grange Avenue at Greenfield 9 4 179 10 ND 36 * ND Fair Very poor 0 0 83 50

Root River near Franklin 12 4 183 7 ND 32 * ND Fair Very poor 0 0 69 43

Jewel Creek at Muskego 16 10 511 144 ND 31 42 ND Fair Fair 7 0 53 42
Biological Community Assessment 21

88°10' 87°50'

42°50' 43°10'

Lake Michigan

0 42 Miles

0 42 Kilometers

Base composited 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.

EXPLANATION

Water

Area within the MMSD

planning area

Watershed boundary

Subwatershed boundary

Stream

Excellent

Good

Fish IBI score

Fair

2004 2007

Very Poor

Poor

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

MRC

OCSM

MRW

HCW

UCW

LMM

WCG

LCM MRM

MRMF

RRF

RRG

KRM

JCM

Figure 7. Fish Index of Biotic Integrity (IBI) scores at 14 stream sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, 2004 and 2007. Figure 7. Fish Index of Biotic Integrity (IBI) scores at 14 stream sites in the Milwaukee Metropolitan Sewerage District 

planning area, Wisconsin, 2004 and 2007.
22 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

The largest positive difference in IBI score was found 

at Lincoln Creek, with 12 (“very poor”) in 2004 and 57 

(“good”) in 2007. Lincoln Creek was the only site other than 

the two Milwaukee River sites to score at least a “good” fish 

IBI rating in 2007, a marked difference compared to its “very 

poor” rating in 2004. The number of fish collected at Lincoln 

Creek was 59 in 2004 and 170 in 2007, and the number of 

species also was higher, with 8 in 2004 and 11 in 2007. The 

2004 sample was dominated by golden shiner (26 of 59, or 

44 percent), a species tolerant of low dissolved oxygen. In 

2007, only 12 golden shiner were collected, or 7 percent of 

the total. The higher number of fish collected in 2007 was in 

spite of problems with fish collection at this site because of a 

large and deep pool and high water conductivity that reduced 

fish capture efficiency. As noted earlier, channel reconstruction 

prior to the 2004 sampling year could have contributed to 

major changes in fish assemblage, independently of any 

potential effects on water quality. This re-engineering of 

the entire floodplain has resulted in an increase in suitable 

habitat for a diversity of fishes. In addition, the removal of 

shoreline vegetation opened up the canopy, thereby increasing 

sunlight and increasing algal abundance. Fish-assemblage 

samples collected at Lincoln Creek during 1992–95 as part of 

the USGS’s National Water-Quality Assessment (NAWQA) 

Program scored “very poor” IBI ratings for each of the three 

years of sampling (Sullivan, 1997). In 1993, five species were 

collected, in 1994 only two species were collected, and in 

1995 a single species was found. Efforts to improve water 

quality, together with flow and fish habitat, will hopefully lead 

to a more diverse and abundant fish assemblage in this urban 

stream in future years. 

Comparative Bioassessment Among Algae, 

Invertebrates, and Fish

Data for selected biological metrics were used to 

divide the 14 stream sites into groups in order to compare 

results among algal, invertebrate, and fish assemblages and 

to ensure a more complete assessment of water quality at 

sites. Metric values were chosen to be most representative 

of water quality for each biotic assemblage. Values for each 

metric were standardized (ranked, lowest rank indicating best 

water quality) and averaged for each biotic assemblage. The 

averages of these ranks were taken across all biota to yield 

aggregate bioassessment rankings for each site. Based on 

these aggregate bioassessment rankings, sites were divided 

into four groups: (1) less than the 25th percentile; (2) between 

the 25th and 49th percentiles; (3) between the 50th and 

74th percentiles; and (4) greater than 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. 

Results of aggregate bioassessment rankings placed four 

sites in Group 1 for 2007, suggesting that the water quality 

at these sites is among the least degraded of all 14 sampled 

sites: Milwaukee River at Milwaukee, Milwaukee River 

near Cedarburg, Jewel Creek, and Menomonee River at 

Menomonee Falls (table 9). These sites were the same ones 

in the least degraded group for 2004 (Thomas, Lutz, and 

others, 2007). These rankings are averages for the three biotic 

assemblages, and as such, results for each assemblage may 

vary. For example, although the aggregate assessment for 

the Milwaukee River near Cedarburg placed it in Group 1, 

the 2007 results for algae alone would have placed it in the 

most-degraded category. 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 show improvement 

or degradation in the water quality at a site. The aggregate 

assessment rankings for Oak Creek and Little Menomonee 

suggests that water quality was worse in 2007 than in 2004 

and place these two sites together with Kinnickinnic River and 

Underwood Creek in Group 4, indicating the most degraded 

water quality. Rankings for Honey Creek and Lincoln Creek 

suggest that water quality at these sites was better in 2007 

than in 2004; however, the difference in ranking at Lincoln 

Creek in 2007 primarily was due to a better fish IBI ranking 

that countered algal and invertebrate rankings that, without 

including the fish ranking, would have indicated degraded 

water quality. As was mentioned earlier, improvements for 

Lincoln Creek fish may be the result of restoration of the 

habitat completed in 2002.
Toxicity and Chemical Assessment Using SPMDS 23

Toxicity and Chemical Assessment 

Using SPMDS

Toxicity and chemical assessment using SPMDs provided 

valuable information about potential chemical stressors 

on stream biota at a subset of six sites: Milwaukee River 

near Cedarburg, Lincoln Creek, Little Menomonee, Honey 

Creek, Kinnickinnic River, and Oak Creek. Replicate SPMD 

samples from each site were evaluated using two toxicity tests, 

Microtox and P450RGS, and also by using a chemical screen 

for PAHs and for selected other manmade chemicals. PAHs 

represent 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 (Björseth and Ramdahl, 1985; Van Metre and 

others, 2000, 2009). Urban sources include not only emissions 

and wastes from these processes but also commonly used 

pavement sealants (Mahler and others, 2005; Van Metre and 

others, 2009). Many PAHs are persistent in the environment. 

Some animals, including human beings, metabolize PAHs 

very slowly or not at all and can accumulate them to toxic 

levels in their tissues from low levels in food, sediment, and 

water (Neff, 1985). Most fish tend to rapidly metabolize and 

excrete PAHs; for this reason, fish tissues may be inadequate 

for characterizing concentrations of PAHs in streams. Thomas, 

Lutz, and others (2007), Bryant and Goodbred (2009), and 

Richards and others (2010) describe USGS studies on the 

effects of urbanization on stream ecosystems, including the 

results for SPMDs deployed in the Milwaukee area during 

2004. 

Table 9. Average trophic-level rankings and aggregate bioassessment rankings for stream sites in the Milwaukee Metropolitan 

Sewerage District planning area, Wisconsin, in 2007 and 2004.

[IBI, Index of Biotic Integrity; EPT, Ephemeroptera, Plecoptera, and Trichoptera; HBI, Hilsenhoff Biotic Index; fill color indicates the quartile based on 

percentiles of the ranked data (blue, less than the 25th percentile, least degraded; light blue, between the 25th and 49th percentile/median; yellow, between 

the 50th to 74th percentile; orange, greater than the 75th percentile, most degraded; each average bioassessment ranking is assessed independently)]

Site

2007 Average bioassessment ranking 2007 2004

Algae1 Invertebrates2 Fish33

Aggregate 

bioassessment 

ranking

Aggregate 

bioassessment 

ranking

Group 1

Milwaukee River at Milwaukee 8.00 2.00 2.5 4.17 3.56

Milwaukee River near Cedarburg 10.50 2.33 1 4.61 1.44

Jewel Creek at Muskego 1.50 8.83 4 4.78 4.17

Menomonee River at Menomonee Falls 1.50 4.00 9 4.83 4.78

Group 2

<—Better water quality 

Willow Creek at Maple Road near Germantown 8.50 4.83 6.5 6.61 5.72

Honey Creek at Wauwatosa 7.50 6.67 6.5 6.89 9.39

Root River at Grange Avenue at Greenfield 3.50 7.00 12 7.50 8.50

Group 3

Root River near Franklin 5.50 7.17 12 8.22 7.06

Menomonee River at Wauwatosa 10.50 9.67 5 8.39 8.61

Lincoln Creek at 47th Street at Milwaukee 12.50 10.50 2.5 8.50 11.56

Group 4

Kinnickinnic River at S. 11th Street at Milwaukee 6.00 10.00 12 9.33 12.72

Oak Creek at South Milwaukee 10.00 6.83 12 9.61 8.78

Underwood Creek at Wauwatosa 9.00 12.67 8 9.89 9.44

Little Menomonee River at Milwaukee 10.50 12.50 12 11.67 9.28

1

 Averaged bioassessment rankings for algae included percent of most-tolerant diatoms and percent of sensitive diatoms.

2

 Averaged bioassessment rankings for invertebrates included Shannon index of diversity scores, percent of EPT taxa, and HBI-10 scores.

3

 Averaged bioassessment rankings for fish included only IBI scores.
24 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

SPMD Toxicity Tests

There was little to no Microtox 

toxicity at the six streams where 

SPMDs were deployed in 2007. 

Results are given in terms of 

toxicity units (TU50), computed by 

dividing 100 by the concentration 

at which the production of 

light is reduced by one-half for 

photoluminescent test bacteria; the 

larger the calculated TU50 value, the 

more toxic the sample. Only SPMD 

replicate sample A from Lincoln 

Creek had a TU50 value that was 

higher than the reporting limit for 

that set; replicate sample B also had 

the highest TU50 among that set but 

it was still slightly lower than the 

reporting limit (table 10).

Based on results from 

P450RGS tests, potential toxicity 

from certain manmade chemicals, 

such PCBs, PAHs, dioxins, and furans, was indicated at all 

six sites (table 10). Results are given as toxic equivalents 

(TEQs); the higher the TEQ, the higher the potential toxicity 

of these chemicals in the stream water. As was found with 

Microtox tests, the highest potential toxicity for the P450RGS 

tests was found at Lincoln Creek; however, P450RGS tests 

also found that potential toxicity at Little Menomonee River, 

Honey Creek, and Kinnickinnic River also was relatively high 

compared to Milwaukee River at Cedarburg and Oak Creek. 

Cedar Creek at Cedarburg, a tributary to the Milwaukee River 

upstream of the MMSD Cedarburg site, is a Superfund site 

due mostly to PCBs in bed sediment (U.S. Environmental 

Protection Agency, 2006b). For SPMDs deployed at seven 

sites in 2004, Thomas, Lutz, and others (2007) reported that 

the P450RGS tests indicated the highest potential toxicity 

at Lincoln Creek, Little Menomonee River, Honey Creek, 

Oak Creek, and Root River at Greenfield when compared 

to Menomonee River at Menomonee Falls and Underwood 

Creek.

SPMD Chemical Screening

The patterns of total PAH concentrations in SPMDs 

correlated positively with Microtox test results for those sites 

where the TU50 values were greater than estimated analytical 

detection limits. The highest TU50 values and total PAH 

concentrations were from Lincoln Creek for both SPMD 

replicate extracts (table 11). Total PAH concentrations for 

Lincoln Creek were 520 and 560 ng/L from replicate sets A 

and B, respectively. SPMDs from the Milwaukee River near 

Table 10. Toxicity test results for passive sampling devices (SPMDs, semi-permeable 

membrane devices) deployed during July–August 2007, for a subset of six Phase III stream 

sites in the Milwaukee Metropolitan Sewerage District planning area, Wisconsin.

[A, B, replicate sample sets; TU50, toxicity units for Microtox toxicity tests; TEQ, toxic equivalents for 

Cytochrome-P450 tests; P450RGS, Cytochrome P450 tests; each value represents the average of three sample 

analyses that has been standardized to 30-day exposure times (higher values indicate greater potential toxicity); 

pg TEQ/mL, picograms TEQ per milliliter; <, less than minimum detection limits of 1.2 for set A and 5.2 for 

set B]

Site

Microtox P450RGS

Sample sets Sample sets

A B A B

TU50 TU50 TEQ TEQ 

(pg TEQ/mL)

Milwaukee River near Cedarburg <1.2 < 5.2 491 547

Lincoln Creek at 47th Street, at Milwaukee 5.5 12.2 2,430 2,490

Little Menomonee River at Milwaukee <1.2 < 5.2 1,980 2,660

Honey Creek at Wauwatosa <1.2 < 5.2 2,280 1,900

Kinnickinnic River at S. 11th Street, at Milwaukee <1.2 < 5.2 970 3,360

Oak Creek at South Milwaukee <1.2 < 5.2 457 2,000

Cedarburg had the lowest concentrations in both sets (35 ng/L 

for A and 44 ng/L for B). In 2004, concentrations of PAHs 

in SPMDs from Lincoln Creek, Honey Creek, Oak Creek, 

and Root River at Greenfield were high compared to other 

sampled sites (Thomas, Lutz, and others, 2007). However, the 

highest concentrations of PAHs found in 2004 were at Little 

Menomonee River and Menomonee River at Menomonee 

Falls, with concentrations at Little Menomonee River nearly 

twice those found at the Menomonee River at Menomonee 

Falls. PAHs and volatile organic compounds in bed sediment 

are the reason for a Superfund site upstream of the Little 

Menomonee River site (U.S. Environmental Protection 

Agency, 2006a; Thomas, Lutz, and others, 2007). 

Van Metre and others (2000) measured PAHs in sediment 

cores from lakes and reservoirs in the United States, and 

they found a positive relation between PAH concentrations 

and automobile use. In the 2004 Milwaukee area study, 

Richards and others (2010) found that results for P450RGS 

toxicity tests and concentrations of PAHs in SPMDs were 

correlated positively with measures of urbanization, such as 

road infrastructure and the percentage of impervious surface 

and developed urban land in a stream’s watershed. The 

use of coal‐tar sealants (also known as sealcoats) on roads, 

driveways, and parking lots has been identified as a significant 

source of PAHs to urban areas (Mahler and others, 2005; 

Van Metre and others, 2009). The PAHs benzo(a)pyrene, 

fluoranthene, phenanthrene, and pyrene are components of 

coal-tar sealants. The results of these studies suggest that 

that automobiles and their supporting infrastructure are a 

significant source of PAHs to streams.
Toxicity and Chemical Assessment Using SPMDS 25

Table 11. Estimated concentration in water, in nanograms per liter, of polycyclic aromatic hydrocarbons (PAHs) computed from 

results for passive sampling devices (SPMDs, semi-permeable membrane devices) deployed at 6 of 14 stream sites in the Milwaukee 

Metropolitan Sewerage District planning area of Wisconsin, July–August, 2007. Values were estimated using 37 days, the average 

number of days all SPMDs were deployed. 

[ng/L, nanograms per liter; bracketed value is greater than the method detection limit (varies according to compound) but below the reporting limit (varies 

according to compound), indicating that the compound was detected but the exact value of the measurement is uncertain; concentrations of total PAHs were 

computed , based on the sum of all measured PAH concentrations in replicate sample sets of SPMDs and SPMD uptake kinetics for pyrene]

Site name Milwaukee River 

near Cedarburg 

Lincoln Creek at 

Milwaukee 

Little Menominee 

River, at 

Milwaukee 

Honey Creek at 

Wauwatosa

Oak Creek at 

South Milwaukee

Kinnickinnic 

River at 

Milwaukee

Chemical compound1 Set A Set B Set A Set B Set A Set B Set A Set B Set A Set B Set A Set B

(ng/L) (ng/L) (ng/L) (ng/L) (ng/L) (ng/L)

Acenaphthene <0.23 <0.23 15 <0.23 2.5 13 <0.23 <0.23 <0.23 <0.23 <0.23 <0.23

Anthracene <0.12 1.2 <0.12 100 1.3 3.7 <0.12 <0.12 1.3 <0.12 <0.12 <0.12

Benz[a]anthracene 0.23 0.28 3.2 <0.01 1.6 3.1 1.6 <0.01 0.82 <0.01 1.1 <0.01

Benzo[a]pyrene 0.09 0.13 0.36 <0.01 0.47 0.89 0.35 <0.01 0.36 <0.01 0.34 <0.01

Benzo[b]fluoranthene 0.49 0.35 2.8 <0.01 2.7 4 2.6 <0.01 1.4 <0.01 2.3 <0.01

Benzo[g,h,i]perylene 0.2 0.19 1.1 <0.02 1.3 1.7 0.78 <0.02 0.53 <0.02 1 <0.02

Benzo[k]fluoranthene 0.32 0.31 2.1 <0.01 1 1.3 1.8 <0.01 1.1 <0.01 1.6 <0.01

Chrysene 2.4 2.5 26 <0.20 17 24 18 <0.20 8.8 <0.20 14 <0.20

Dibenz[a,h]anthracene <0.02 <0.02 0.21 <0.02 0.17 [0.08] 0.21 <0.02 <0.02 <0.02 0.2 <0.02

Fluoranthene 14 15 220 250 76 120 115 <2.4 47 34 70 76

Fluorene <0.16 1.7 25 34 1.8 9.3 3.6 0.85 1.8 <0.16 <0.16 <0.16

Indeno[1,2,3-c,d]pyrene 0.1 [0.05] 0.42 <0.01 0.33 0.42 0.54 <0.01 0.14 <0.01 0.39 0.56

Naphthalene <24 [42] <24 2,000 <24 [35] <24 <16 <24 1,500 <24 69

Phenanthrene [15] [25] 370 560 33 86 81 <25 29 [38] 33 [54]

Pyrene 7.6 <18 130 130 56 86 60 <18 32 [26] 45 [45]

1,2-dimethylnaphthalene <0.17 0.87 <0.17 <0.17 <0.17 1.7 1.8 0.87 <0.17 <0.17 <0.17 <0.17

1-methylfluorene <0.05 <0.05 <0.05 <0.05 <0.05 <0.05 2.4 <0.05 1.8 <0.05 2.4 <0.05

1-methylnaphthalene <6.5 [13] <6.5 [23] <6.5 [16] <6.5 <13 <6.5 [26] <6.5 <13

2-methylfluoranthene 0.15 0.22 1.8 2.7 1.1 1.6 0.96 <0.01 0.54 <0.01 0.84 0.73

2-methylnaphthalene <8.9 [26] <8.9 [39] <8.9 [34] [11] <26 <8.9 [49] <8.9 <26

2-methylphenanthrene 0.89 <1.3 18 <1.3 2.2 4.9 8 <1.3 2.7 <1.3 4 4.2

3,6-dimethylphenanthrene <0.02 <0.02 <0.02 <0.02 <0.02 1.1 <0.02 <0.02 <0.02 <0.02 <0.02 <0.02

Benzo[e]pyrene 0.79 0.75 6 <0.03 5.8 7.3 4.8 <0.03 3.2 <0.03 4.6 <0.03

Dibenzothiophene 1.8 [1.7] 21 <1.4 1.8 6.8 5.4 <1.4 1.8 <1.4 1.8 4.2

Total PAHs 35 [44] 520 560 200 320 260 260 120 105 170 140

1

Analyzed for but not detected in any sample: acenaphthylene, benzo[b]naphtho[2,1-d]thiophene, benzo[b]thiophene, biphenyl, 4-methylbiphenyl, perylene, 

2,3,5-trimethylnaphthalene, 1-ethylnaphthalene, 9-methylanthracene.
26 Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007

Summary and Conclusions

Stream biota—algal, invertebrate, and fish assemblages—

were sampled at 14 stream sites in the Milwaukee area as part 

of the MMSD Corridor Study by the U.S. Geological Survey 

in 2004 and 2007. In addition, SPMDs were deployed at a 

subset of six sites to assess potential toxicity to biota from 

certain manmade chemicals. The objectives of biological 

community sampling were to assess the water quality of 

selected stream sites as part of a larger water-quality study that 

began in 2000.

In 2007, the highest numbers of algal, invertebrate, and 

fish taxa were found at the Milwaukee River at Milwaukee, the 

largest of all sampled sites. The small streams Jewel Creek and 

Willow Creek were second highest to the Milwaukee River at 

Milwaukee for number of invertebrate taxa. Milwaukee River 

near Cedarburg was second highest to the Milwaukee site 

in number of fish species. The fewest algal taxa were found 

at the Kinnickinnic River, and the fewest invertebrate taxa 

(all similar numbers of taxa) were collected at Honey Creek, 

Underwood Creek, Kinnickinnic River, Little Menomonee 

River, and Menomonee River at Wauwatosa. The sites with 

the fewest fish species (less than or equal to 5, starting with 

fewest) were: Kinnickinnic River, Root River (both sites), 

Little Menomonee River, and Oak Creek. 

Results from the 2007 biological sampling were 

compared to results of the 2004 biological sampling, and 

that comparison was evaluated together with historical data 

in Schneider, Lutz, and others (2004) and Thomas, Lutz, and 

others (2007); however, data are insufficient for assessment 

of the significance of these differences and may not represent 

statistically significant trends. Additional sampling would be 

required to evaluate any trends (or lack of trends). Comparing 

2004 to 2007, total algal biovolume was higher at 12 of the 

14 sites, primarily because of higher amounts of nuisance 

green algae. For algal assemblages, water quality at 10 of 

the 14 sites sampled was of concern based on the occurrence 

of nuisance algal species or less than 30 percent pollutionsensitive algal species. Four streams that did not have nuisance 

algae or less than 30 percent pollution sensitive algae include 

Milwaukee River at Milwaukee, Willow Creek, Root River 

at Franklin, and Jewel Creek. Invertebrate metrics suggest 

poorer quality invertebrate assemblages in 2007 than 2004 in 

the Little Menomonee River, Underwood Creek, and Honey 

Creek. Based on IBIs for invertebrates and fish, the highest 

rated sites were generally the two Milwaukee River mainstem 

sites, at Milwaukee and near Cedarburg; Cedarburg received 

a “good” HBI-10 rating for invertebrates in 2004 and 2007, 

despite a relatively large negative difference in invertebrate 

taxa compared to 2004. In 2007, the number of fish species 

was higher or the same at seven sites and lower at seven sites. 

The lowest fish IBI scores tended to be qualitatively lower, 

with six “very poor” fish IBI ratings compared to just two 

“fairly poor” invertebrate HBI-10 ratings. Fish IBI scores 

were the same in 2007 and 2004 at three sites; at 5 sites fish 

IBI scores were higher in 2007 than in 2004; and at 6 sites fish 

IBI scores were lower in 2007 than in 2004. Relatively large 

negative differences in fish abundance were seen between 

2004 and 2007 at both Root River sites, at Jewel Creek, and at 

Oak Creek. Some signs of improvement in the fish assemblage 

were found at Lincoln Creek (from “very poor” in 2004 to 

“good” in 2007), possibly reflecting recent changes from 

restoration of stream habitat completed in 2002. 

Aggregate bioassessment rankings across all groups of 

biota indicated least degraded water quality at Milwaukee 

River at Milwaukee and near Cedarburg, at Jewel Creek, 

and at Menomonee River at Menomonee Falls for 2004 and 

2007. The rankings for Oak Creek and Little Menomonee 

River suggest worse water quality in 2007 compared to 2004, 

thereby placing these two sites together with Kinnickinnic 

River and Underwood Creek as indicating the most degraded 

water quality among all sampled sites. The aggregate ranking 

for Lincoln Creek was higher in 2007, primarily due to 

improved higher fish IBI score.

Potential toxicity was found at all six SPMD sites. 

As was found in 2004, Lincoln Creek showed the highest 

potential toxicity in 2007, and subsequent chemical screening 

indicated the highest total PAH concentrations; however, 

toxicity at Little Menomonee River, Honey Creek, and 

Kinnickinnic River was also relatively high compared to 

Milwaukee near Cedarburg. The high PAHs at Lincoln Creek 

might help explain low rankings for algae and invertebrate 

assemblages despite apparent improvement in the quality 

of the fish assemblage, which may be able to relocate and 

recolonize from stream sites with less degraded water quality. 

Although toxicity and chemical results did not agree with 

aggregate rankings for Lincoln Creek or Honey Creek, the 

results did agree with aggregate rankings at four of the six 

sites.

Evaluation of the condition of algal, invertebrate, and fish 

assemblages together with toxicity and chemical screening 

using SPMDs provided an integrated assessment of the 

ecological condition and water quality at these 14 sites in the 

Milwaukee area. Despite somewhat variable results among 

the different assemblages, our evaluations suggest good water 

quality at some sites and degraded water quality at others. 

Some of the variability in the results may be attributable 

to frequent high stream flows (characterized by rapid rise 

and fall) that are known to have adverse effects on biota 

in many of these streams. Resampling that is planned for 

2010, together with physical and chemical assessments, will 

contribute toward our understanding of the overall integrity of 

these streams.
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Scudder Eikenberry and others— Biological Water-Quality Assessment, Milwaukee Metropolitan Sewerage District Planning Area, Wisconsin, 2007—SIR 2010–5166