U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2016–5090

Prepared in cooperation with the Wisconsin Department of Natural Resources and 

the U.S. Environmental Protection Agency—Great Lakes National Program Office

Comparison of Benthos and Plankton for Selected 

Areas of Concern and Non-Areas of Concern in 

Western Lake Michigan Rivers and Harbors in 2012
Cover. Posterized photograph of Lake Michigan coastline and Algoma Lighthouse by 

Barbara Scudder Eikenberry with color and effects added by Michelle Greenwood.
Comparison of Benthos and Plankton for 

Selected Areas of Concern and Non-Areas 

of Concern in Western Lake Michigan 

Rivers and Harbors in 2012

By Barbara C. Scudder Eikenberry, Amanda H. Bell, Hayley A. Templar, and 

Daniel J. Burns

Prepared in cooperation with the Wisconsin Department of Natural Resources and 

the U.S. Environmental Protection Agency—Great Lakes National Program Office

Scientific Investigations Report 2016–5090

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Director

U.S. Geological Survey, Reston, Virginia: 2016

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Suggested citation:

Scudder Eikenberry, B.C., Bell, A.H., Templar, H.A., and Burns, D.J., 2016, Comparison of benthos and plankton 

for selected Areas of Concern and non-Areas of Concern in Western Lake Michigan Rivers and Harbors in 2012: 

U.S. Geological Survey Scientific Investigations Report 2016–5090, 28 p., http://dx.doi.org/10.3133/sir20165090.

ISSN 2328-0328 (online)
iii

Contents

Acknowledgments .......................................................................................................................................vi

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

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

Purpose and Scope ..............................................................................................................................4

Methods...........................................................................................................................................................4

Sample Collection and Processing....................................................................................................4

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

Condition of the Benthos and Plankton Communities .............................................................................9

Overview of Benthos and Plankton Communities in Lower Green Bay 

and Milwaukee Harbor...........................................................................................................9

Comparison of Subsites for the Lower Green Bay and Fox River and the 

Milwaukee Estuary Areas of Concern...............................................................................12

Benthos Community Comparisons Between Areas of Concern and 

Non-Areas of Concern .........................................................................................................12

Plankton Community Comparisons between Areas of Concern and

 Non-Areas of Concern ........................................................................................................15

Invasive Species at Areas of Concern and Non-Areas of Concern...........................................22

Benthos Community Comparisons to Other Studies.....................................................................22

Phytoplankton Community Comparisons to Other Studies ..........................................................23

Summary and Conclusions.........................................................................................................................23

References....................................................................................................................................................24
iv

Figures

1. Map showing sampling sites and subsites investigated for the evaluation

of benthos and plankton communities at Wisconsin’s four Lake Michigan

Areas of Concern and six non-Area of Concern comparison sites in

Wisconsin and Michigan.............................................................................................................3

2. Diagram of the decision tree for comparing benthos and plankton community

metrics at four Lake Michigan Areas of Concern in Wisconsin and six

non-Area of Concern comparison sites in Wisconsin and Michigan..................................7

3. Boxplots of richness, diversity metric values for combined benthos, and 

Index of Biotic Integrity from four Lake Michigan Areas of Concern and 

six non-Area of Concern comparison sites ...........................................................................13

4. Multi-Dimensional Scaling ordination plots for the combined benthos at four 

Lake Michigan Areas of Concern, including subsites for the Milwaukee Estuary

Area of Concern, and non-Area of Concern comparison sites, based on relative

abundance with no rare or ambiguous taxa, with seasons combined and with

seasons separate .......................................................................................................................16

5. Plots of richness and diversity metric values for zooplankton at four

 Lake Michigan Areas of Concern and six non-Area of Concern comparison sites .......17

6. Multi-Dimensional Scaling ordination plots for zooplankton at four Lake Michigan 

Areas of Concern, including subsites for the Milwaukee Estuary Area of Concern,

and six non-Area of Concern comparison sites, based on relative abundance

with no rare or ambiguous taxa with seasons combined with seasons separate..........19

7. Plots of richness and diversity metric values for combined phytoplankton at four

Lake Michigan Areas of Concern and six non-Area of Concern comparison sites ........20

8. Multi-Dimensional Scaling ordination plots for the combined phytoplankton at

four Lake Michigan Areas of Concern, including subsites for the Milwaukee Estuary 

Area of concern, and six non-Area of Concern comparison sites, based on relative 

abundance with no rare or ambiguous taxa with seasons combined and with

seasons separate .......................................................................................................................21

Tables

1. U.S. Geological Survey sampling sites and subsites during 2012 at four 

Lake Michigan Areas of Concern in Wisconsin and six non-Area of Concern

comparison sites in Wisconsin and Michigan.........................................................................5

2. Richness, diversity, and Index of Biotic Integrity values for benthos samples

collected in 2012 by the U.S. Geological Survey at four Lake Michigan Areas

of Concern in Wisconsin and six non-Area of Concern comparison sites in

Wisconsin and Michigan...........................................................................................................10

3. Richness and diversity values for plankton samples collected in 2012 by 

the U.S. Geological Survey at four Lake Michigan Areas of Concern and 

six non-Area of Concern comparison sites in Wisconsin and Michigan..........................11

4. Significance values for Mann-Whitney tests and paired t-tests for metric

comparisons between each of the four Lake Michigan Areas of Concern

and the six non-Area of Concern comparison sites as a group or the specific

 non-Areas of Concern pair across the spring, summer, and fall seasons in 2012..........14

5. Summarized results of metric comparisons for benthos and plankton samples

collected in 2012 by the U.S. Geological Survey at four Lake Michigan Areas

of Concern and six non-Area of Concern comparison sites ...............................................14
v

Conversion Factors

International System of Units to Inch/Pound

Multiply By To obtain

Length

micrometer (μm) 0.00003937 inch (in)

meter (m) 3.281 foot (ft) 

meter (m) 1.094 yard (yd) 

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2

) 0.3861 square mile (mi2)

Volume

liter (L) 0.2642 gallon (gal)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

Concentrations of chemical constituents in water are given in either milligrams per liter 

(mg/L) or micrograms per liter (μg/L). The mesh opening size for the plankton net is given 

in micrometers (μm).

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Abbreviations

AOC Area of Concern

BUI Beneficial Use Impairment

HD Hester-Dendy (artificial substrate sampler)

IBI Index of Biotic Integrity

MMSD Milwaukee Metropolitan Sewerage District

PCBs polychlorinated biphenyl compounds

USGS U.S. Geological Survey

WDNR Wisconsin Department of Natural Resources

WSLH Wisconsin State Laboratory of Hygiene
vi

Acknowledgments

This study was done in cooperation with the Wisconsin Department of Natural Resources 

(WDNR), with Great Lakes Restoration Initiative funding from the Great Lakes National 

Program Office of the U.S. Environmental Protection Agency. Cheryl Bougie, Donalea Dinsmore, 

Andrew Fayram, Stacy Hron, Laurel Last, Victor Pappas, Benjamin Uvaas, and others of the 

WDNR assisted with study planning and sampling logistics. We also acknowledge Brian Weigel 

(WDNR) and Jeffrey Dimick (University of Wisconsin Stevens Point-Aquatic Biomonitoring 

Laboratory) for sharing their 2003 and 2005 Hester-Dendy sampler data and, together with 

Jason Knutson and James Hudson of the WDNR, for assistance with Index of Biotic Integrity 

calculations. Kurt Schmude (University of Wisconsin-Superior), Paul Garrison (WDNR), and 

Dawn Perkins (Wisconsin State Laboratory of Hygiene) identified and enumerated benthos 

and plankton. 

Nicolas Buer, U.S. Geological Survey (USGS), assisted with Hester-Dendy deployment and 

sampling. James Kennedy and Michelle Lutz (USGS) assisted with geographic information 

systems and creation of the figure 1 map; Mark Bonito (USGS) and Rosemary Stenback 

(USGS retired) assisted with finalization of figure 1. James F. Coles and Barry Baldigo (USGS) 

and Megan O’Shea (WDNR) provided technical comments on an earlier manuscript version. 

David Voelker (USGS retired), and Elizabeth Enright and David Craven (USGS) contributed to 

the editorial review, and Caryl J. Wipperfurth (USGS) completed the publication layout.
Comparison of Benthos and Plankton for Selected 

Areas of Concern and Non-Areas of Concern in 

Western Lake Michigan Rivers and Harbors in 2012

By Barbara C. Scudder Eikenberry, Amanda H. Bell, Hayley A. Templar, and Daniel J. Burns

Abstract 

Recent data are lacking to assess whether impairments 

still exist at four of Wisconsin’s largest Lake Michigan 

harbors that were designated as Areas of Concern (AOCs) in 

the late 1980s due to sediment contamination and multiple 

Beneficial Use Impairments (BUIs), such as those affecting 

benthos (macroinvertebrates) and plankton (zooplankton 

and phytoplankton) communities. During three seasonal 

sampling events (“seasons”) in May through August 2012, the 

U.S. Geological Survey collected sediment benthos and water 

plankton at the four AOCs as well as six less-degraded nonAOCs along the western Lake Michigan shoreline to assess 

whether AOC communities were degraded in comparison 

to non-AOC communities. The four AOCs are the Lower 

Menominee River, the Lower Green Bay and Fox River, the 

Sheboygan River, and the Milwaukee Estuary. Due to their 

size and complexity, multiple locations or “subsites” were 

sampled within the Lower Green Bay and Fox River AOC 

(Lower Green Bay, the Fox River near Allouez, and the 

Fox River near De Pere) and within the Milwaukee Estuary 

AOC (the Milwaukee River, the Menomonee River, and the 

Milwaukee Harbor) and single locations were sampled at 

the other AOCs and non-AOCs. The six non-AOCs are the 

Escanaba River in Michigan, and the Oconto River, Ahnapee 

River, Kewaunee River, Manitowoc River, and Root River 

in Wisconsin. Benthos samples were collected by using 

Hester-Dendy artificial substrates deployed for 30 days and 

by using a dredge sampler; zooplankton were collected by 

net and phytoplankton by whole-water sampler. Except for 

the Lower Green Bay and Milwaukee Harbor locations, 

communities at each AOC were compared to all non-AOCs 

as a group and to paired non-AOCs using taxa relative 

abundances and metrics, including richness, diversity, and 

an Index of Biotic Integrity (IBI, for Hester-Dendy samples 

only). Benthos samples collected during one or more seasons 

were rated as degraded for at least one metric at all AOCs. 

In the Milwaukee Estuary, benthos richness was lower in 

the Milwaukee River subsite spring and summer samples 

and in the Menomonee River subsite spring sample relative 

to the paired non-AOCs. Benthos diversity and IBIs at the 

Menomonee River subsite and IBIs at the Milwaukee River 

subsite and Sheboygan River were significantly lower than at 

all non-AOCs as a group across all seasons and therefore were 

rated as degraded. In addition, IBIs at the Lower Menominee 

River were significantly lower than those at the paired nonAOCs during all seasons and were therefore rated degraded. 

Benthos at both Fox River subsites and the Milwaukee River 

subsite were significantly different from their paired nonAOCs during all three seasons, based on a comparison of the 

relative abundances of taxa using multivariate testing. Metrics 

for plankton at AOCs were not significantly lower than those 

at the paired or group non-AOCs during all seasons; however, 

zooplankton richness in spring at the Sheboygan River and in 

fall at the Menomonee River subsite was rated as degraded in 

comparison to paired non-AOCs. Also, zooplankton richness 

in fall at the Fox River near Allouez subsite and in spring 

at the Milwaukee River subsite was rated degraded overall 

because values were lower than at all non-AOCs as a group 

and lower than at the paired non-AOCs. Zooplankton diversity 

in fall at the Fox River near Allouez subsite and the Lower 

Menominee River was rated degraded in comparison to paired 

non-AOC comparison sites. Zooplankton communities at the 

Fox River near Allouez subsite were significantly different 

from the paired non-AOCs when multivariate comparisons 

were made without rotifers other than A. priodonta. Overall, 

benthos and zooplankton BUIs remained at the AOCs in 2012 

but no AOCs with a phytoplankton BUI were rated degraded 

in comparison to non-AOCs. The use of a multiple ecological 

measures, structural and functional, and multiple statistical 

analyses, biological metrics and multivariate statistics, 

provided assessments that defined 2012 status of communities 

relative to less-impaired non-AOCs in the Great Lakes area. 
2 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Introduction

Within the Laurentian Great Lakes, certain sites were 

designated Areas of Concern (AOCs) under the United States 

and Canada Great Lakes Water Quality Agreement (International Joint Commission United States and Canada, 1987), 

because severe environmental degradation had affected the 

areas’ ability to support aquatic life. Along the Great Lakes 

shoreline, 43 AOCs were designated: 26 in U.S. waters 

and 17 in Canadian waters, and 5 AOCs are shared by the 

nations. The State of Wisconsin has jurisdiction over five 

AOCs contained entirely within the U.S. borders on two of 

the Great Lakes—one AOC along the Lake Superior shoreline 

and four AOCs along the Lake Michigan shoreline (fig. 1). 

The four AOCs along the Lake Michigan shoreline are the 

Lower Menominee River, Lower Green Bay and Fox River, 

Sheboygan River, and Milwaukee Estuary (Wisconsin 

Department of Natural Resources, 1990, 2013a). Each AOC is 

officially “listed” due to one or more Beneficial Use Impairments (BUIs); for example, degradation of fish and wildlife 

populations, degradation of benthos (bottom dwelling or 

benthic invertebrates), or degradation of plankton populations 

(free floating invertebrates and algae, or zooplankton and 

phytoplankton, respectively). Hereafter, unless otherwise 

specified, use of the term “plankton” in this report implies both 

zooplankton and phytoplankton. An AOC cannot be “delisted” 

until remediation has resulted in meeting set goals and 

objectives, thus allowing the removal of all BUI designations 

for the AOC except in cases where a beneficial use cannot be 

fully restored (U.S. Policy Committee, 2001). A BUI may be 

removed without a full recovery only in cases where: 1) the 

BUI is due to natural rather than human causes, 2) the BUI 

is not limited to the AOC but is instead typical of lakewide, 

regionwide, or areawide conditions, or 3) the impairment is 

caused by stressors outside of the AOC (Grapentine, 2009). 

The Great Lakes Water Quality Agreement (International 

Joint Commission United States and Canada, 1987) defines 

14 BUIs, and the four Lake Michigan AOCs in Wisconsin 

have most of them (Wisconsin Department of Natural 

Resources, 2011, 2012b, 2013b; Wisconsin Department of 

Natural Resources and Michigan Department of Environmental Quality, 2011). All four of Wisconsin’s Lake Michigan 

AOCs have the degraded benthos BUI designation, and the 

Lower Green Bay and Fox River, Sheboygan River, and 

Milwaukee Estuary AOCs have the degraded phytoplankton 

and zooplankton BUI, although few historical data are 

available for comparison of conditions at the time of listing to 

current conditions. Degradation of benthos is one of the most 

widespread BUIs in the United States, and it is most often 

related to sediment contamination; however, water chemistry, 

substrate type, inadequate food supply, and river flows may 

also be important (Reynoldson, 1987; U.S. Environmental 

Protection Agency, 1994; Wisconsin Department of Natural 

Resources, 2009, 2011). Degradation of plankton may be the 

result of poor water quality due to excessive nutrient enrichment or toxic chemicals, inadequate food supplies, high flows 

at river mouths, and other physical, chemical, and biological 

stresses (Gannon and Stemberger, 1978; Wisconsin Department of Natural Resources, 1994). 

The macroinvertebrate community of the benthos 

in nonwadable rivers and their harbors on large lakes is 

comprised of worms, insect larvae, crustaceans, clams, snails 

and other organisms. Many of these organisms are filter 

feeders on phytoplankton and detritus but some eat other 

animals (Merritt and Cummins, 1996). Oligochaete worms 

may be abundant and diverse in the soft sediments. Midges, 

the most common group of larval insects in the benthos, may 

also be abundant and diverse. Together, oligochaetes and 

midges may dominate this environment, especially in polluted 

rivers, though not all of these taxa are considered tolerant 

(Thorp and Covich, 1991; Canfield and others, 1996). In 

general, the dominant zooplankton taxa in freshwater environments are rotifers, microcrustaceans such as cladocerans and 

copepods, and protozoans. Rotifers and microcrustaceans may 

compete for food resources but in general, many rotifers are 

outcompeted by microcrustaceans because of lower clearance 

rates and smaller size requirements for food particles (Wallace 

and Snell, 1991). However, due to short development times 

and high population growth rates in response to increased 

temperatures, rotifers can take advantage of new environmental conditions more than many microcrustaceans can and 

so they may become more abundant. As secondary producers 

in aquatic food webs, benthos and zooplankton are important 

food sources for fish, aquatic birds, and other animals. As 

primary producers, phytoplankton form the basis of aquatic 

food chains in large rivers and lakes, and communities are 

usually dominated by diatoms and the percentage of diatoms 

tends to decrease with pollution (Flotemersch and others, 

2006). Changes in the phytoplankton community from a 

dominance by diatoms to a dominance by green or blue-green 

algae can have a cascading effect on secondary consumers and 

this in turn can have a cascading effect on organisms that feed 

on them (Wisconsin Department of Natural Resources, 1993). 

Lake Michigan’s water quality is greatly affected by 

development on its western shores in the State of Wisconsin. 

Each of Wisconsin’s four Lake Michigan AOCs has historical 

and ongoing practices that contribute to degraded benthos 

and plankton. High sediment concentrations of arsenic, coal 

tar, and paint sludge from historical pollution are listed as 

the reasons for degraded benthos in the Lower Menominee 

River AOC (Wisconsin Department of Natural Resources and 

Michigan Department of Environmental Quality, 2011); the 

Lower Green Bay and Fox River AOC received industrial 

discharge along the banks of the Fox River for many years 

(Wisconsin Department of Natural Resources, 2012a). Toxic 

substances from point source discharges, primarily polychlorinated biphenyls (PCBs), and nutrients, primarily phosphorus, 

from nonpoint runoff draining agricultural and urban lands, 

are responsible for degraded benthos and plankton BUIs 

(Wisconsin Department of Natural Resources, 2012a). The 

sediments of the Sheboygan River AOC are contaminated 

predominantly by PCBs and polycyclic aromatic hydrocarbons 
Introduction 3

Figure 1. Sampling sites and subsites investigated for the evaluation of benthos and plankton communities 

at Wisconsin’s four Lake Michigan Areas of Concern (AOCs) and six non-Area of Concern comparison sites 

in Wisconsin and Michigan.

Base map is the intellectual property of Esri and is used 

herein under license. ©2013 Esri, DeLorme, NAVTEQ

All rights reserved

WISCONSIN

MICHIGAN

MICHIGAN

L

A

K

E

M I C H I G A N

L A K E S U P E R I O R

6

7

5

2

1

8

9

3

4

10

90° 89° 88° 87° 86°

46°

45°

44°

43°

EXPLANATION

Type of sampling site

National Land Cover

Area of Concern

Map number

Non-Area of Concern

Water

Urban

Barren/shrubland

Forest

Grassland

Agriculture

Wetland

Drainage basin

County boundary

5

WISCONSIN

0 20 40 MILES

0 20 40 KILOMETERS
4 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

from industrial facilities and leaking landfills located on 

the shore of the river (Wisconsin Department of Natural 

Resources, 1995, 2012b). Contaminated sediment is listed as 

a source for degraded benthos, and contaminated sediment 

as well as point and nonpoint runoff pollution are listed as 

the sources for degraded plankton. The Milwaukee Estuary 

AOC is located at the confluence of three urban rivers: the 

Milwaukee, Menomonee, and Kinnickinnic Rivers. Toxic 

substances, such as PCBs and polycyclic aromatic hydrocarbons,

together with sewage overflows, thermal discharges, nonpoint 

runoff, and physical habitat alterations that include dams, 

drop structures, concrete lined channels, poorly sized culverts, 

and shoreline alterations are concerns in the Milwaukee 

Estuary AOC (Wisconsin Department of Natural Resources, 

2011; Wisconsin Department of Natural Resources and 

Milwaukee River Basin Land and Water Partners Team, 2001).

 Based on guidelines for benthos and plankton BUIs 

as stated in the U.S. Policy Committee report (U.S. Policy 

Committee, 2001), if the structure of the communities at 

an AOC are not found to differ significantly from one or 

more unimpacted control sites with comparable physical 

and chemical characteristics, then the target criteria are 

considered to have been met to remove that particular BUI. 

The International Joint Commission listing guideline states 

that an impairment will be listed when the community 

structure “significantly diverges from unimpacted control 

sites of comparable physical and chemical characteristics 

(Ohio Environmental Protection Agency, 2008).” 

In 2012, The U.S. Geological Survey (USGS), in 

cooperation with the Wisconsin Department of Natural 

Resources (WDNR) and the U.S. Environmental Protection 

Agency Great Lakes National Program Office conducted 

a study of the benthos and plankton at 10 sites in rivers 

and harbors along Wisconsin’s Lake Michigan shoreline. 

Four sampling sites were AOCs and six additional sites 

were relatively less-impacted comparison sites with similar 

physical and chemical characteristics (referred to hereafter 

as non-AOCs). Results were then compared to historical 

studies at the AOCs to provide context and evaluate potential 

progress in site remediation benefits. Sediment remediation 

was ongoing in 2012 at all four AOCs: the Lower Menominee 

River, Fox River, Sheboygan River, and Milwaukee Estuary. 

Purpose and Scope

The purpose of this study is to inform the decision process 

for removal of the BUI for degradation of benthos and the BUI 

for degradation of plankton population by determining whether 

or not the benthos or plankton community differed significantly 

from one or more less-impaired sites with comparable physical 

and chemical characteristics. The report presents an assessment 

of the status of aquatic communities at the four AOC and six 

non-AOC comparison sites in 2012. The results of the study 

are then compared to those of historical studies of the AOCs 

to provide context and evaluate potential progress in site 

remediation benefits in the four AOCs.

Methods

Four AOC sites and six non-AOC comparison sites 

were selected for this study (fig. 1, table 1). “Sites” refer to 

the geographic areas that were sampled; for example, the 

Lower Green Bay and Fox River AOC. The term “subsite” 

in this report is used when more than one area was sampled 

within an AOC site. Detailed site and location information 

is provided in Scudder Eikenberry, Bell, and others (2014). 

Although there are no rivermouths or harbors along the 

western Lake Michigan shoreline that are truly unimpacted, 

the six non-AOCs selected for comparison were not within 

any AOC and were representative of the region; therefore, 

they were assumed to have biological communities similar 

to those that would be present in the AOCs if the AOCs did 

not have the specific contamination that was identified during 

designation and listing. 

The selection of good comparison sites can be a challenge for making quantitative assessments of the degree to 

which aquatic communities at sites were impaired, and this 

is especially true of Great Lakes rivermouths and harbors. 

Aquatic communities in rivermouths and harbors are often 

quite different from either the upstream riverine communities 

or the downstream lake communities (Larson and others, 

2013). With the possible exception of remote northern 

sites, there are no unimpaired rivermouths or harbors in the 

Great Lakes for making comparisons to “unimpacted control” 

or reference sites as stated in the target criteria for AOCs 

(U.S. Policy Committee, 2001). Quantitative historical data 

also may be unavailable due to decades of pollution at a site. 

Comparison of sites within an AOC with those in unimpacted 

or less-impacted areas is an approach that has been used to 

delist BUIs in other Great Lakes states, such as Michigan and 

Ohio (Michigan Department of Environmental Quality, 2008; 

Ohio Environmental Protection Agency, 2008).

Sample Collection and Processing

Benthos and plankton assemblages were sampled at 

each of the four AOC sites and six non-AOC comparison 

sites during three visits approximately six weeks apart in late 

May and early June, mid-July, and late August. Hereafter for 

simplicity, the three sampling events are referred to as the 

“spring,” “summer,” and “fall “seasonal samples. All sites 

were nonwadable and samples were collected from a boat. 

During each sampling period, in situ water-quality samples 

were collected at each site for pH, specific conductance, and 

water temperature using a Hydrolab QuantaTM Sonde. All data 

and detailed method descriptions can be found in Scudder 

Eikenberry and others (2014). Many areas of the Midwest 

and Wisconsin were experiencing a stretch of high heat and 

drought during the summer and fall sampling periods that 

resulted in lower than average stream discharges to some 

sampling locations, most notably the Lower Menominee River 

(MENI), Menomonee River subsite (MENO), and Root River 
Methods 5

(ROOT) where annual mean discharge in 2012 was about 

two-thirds or less than the historical mean annual discharge at 

nearby stream gages (Scudder Eikenberry and others, 2014). 

Benthos samples were collected from bottom sediment 

at each site using two methods: dredge samples and HesterDendy (HD) artificial substrate samplers (U.S. Environmental 

Protection Agency, 1994; Weigel and Dimick, 2011). Three 

to five Ponar® dredge samples were composited into one 

sample per site (U.S. Environmental Protection Agency, 

2010a). A small amount of material (less than 50 grams) 

from each composited dredge sample was placed into two 

plastic bags: one for analysis of sediment size fractions 

for estimating substrate sizes and types and another for 

analysis of volatile-on-ignition for estimating the amount 

of organic matter. Size fraction samples were analyzed by 

the University of Wisconsin Soils Laboratory in Madison, 

Wisconsin, using the hydrometer method (Bouyoucos, 1962), 

and volatile-on-ignition samples were analyzed by the USGS 

using a combustion method (U.S. Geological Survey, 1989; 

Wentworth, 1922). Fine sediments were removed from the 

composite sample by sieving; large debris and empty shells 

were examined for any attached invertebrates before being 

discarded. The retained debris and organisms were stained 

with rose bengal dye and preserved with 10 percent buffered 

formalin for later sorting and identification of individual 

macroinvertebrates. With the exception of Green Bay, four 

individual HDs were deployed for 6 weeks at each site during 

each season (Weigel and Dimick, 2011). Once retrieved, three 

of the four HDs were randomly chosen to represent the site. 

Only two of the four HDs were available for analysis from 

the summer samples at the Oconto River (OCON) and ROOT

non-AOCs. All organisms were scraped off, composited into 

one sample per season for the site, stained with rose bengal 

dye, and preserved with 10 percent buffered formalin. All 

benthos samples were identified and counted by the Lake 

Superior Research Institute at the University of WisconsinSuperior (U.S. Environmental Protection Agency, 2010b). 

Zooplankton samples were collected using plankton nets 

towed from a depth of 5 meters (m), or just above the bottom 

if less than 5 m to the surface using a 63-micrometer (μm) 

mesh net (U.S. Environmental Protection Agency, 2010f). A 

KemmererTM vertical water sampler was used to collect a set 

of five whole water samples at 1-m depth intervals from 1 m 

below the surface to just above the bottom. Subsamples were 

collected from the whole water sample for chlorophyll a, total 

and volatile suspended solids, identification and enumeration 

Table 1. U.S. Geological Survey sampling sites and subsites during 2012 at four Lake Michigan Areas of Concern in Wisconsin and six 

non-Area of Concern comparison sites in Wisconsin and Michigan.

[A subsite, or additional sampling location within the geographic area of a site, is indicated by the addition of an alphabet letter to a site number. km2, square 

kilometer; Mich., Michigan; NA, not applicable]

Site or subsite name Abbreviated 

name

Site or

subsite 

number

Latitude Longitude Drainage

area

(km2

)

Comparison 

site or subsite 

(decimal degrees) number

Areas of Concern

Lower Menominee River MENI 1 45.09810 –87.60772 10,490 5, 6

Lower Green Bay-Fox River 2

 Lower Green Bay1 GREE 2a 44.57751 –87.98600 16,584 NA

 Fox River near Allouez FOXR 2b 44.49499 –88.02424 16,178 7, 8

 Fox River near De Pere2 FOXD 2c 44.46251 –88.05776 16,011 7, 8

Sheboygan River SHEB 3 43.74887 –87.70352 1,043 8, 9

Milwaukee Estuary 4

 Milwaukee River MILR 4a 43.04789 –87.91269 1,779 9, 10

 Menomonee River MENO 4b 43.03220 –87.92156 381 9, 10

 Milwaukee Harbor MILH 4c 43.02501 –87.89722 2,193 NA

Non-Areas of Concern

Escanaba River, Mich. ESCA 5 45.77845 –87.06325 2,393 1

Oconto River OCON 6 44.89198 –87.83678 2,502 1

Ahnapee River AHNA 7 44.60979 –87.43484 274 2b, 2c

Kewaunee River KEWA 8 44.46073 –87.50205 354 2b, 2c, 3

Manitowoc River MANI 9 44.09190 –87.66183 1,341 3, 4a, 4b

Root River ROOT 10 42.72866 –87.78827 514 4a, 4b

1

Benthos samples were not collected in Green Bay.

2

Plankton samples were not collected at the Fox River near De Pere.
6 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

of “soft” algae phytoplankton (blue-greens, cryptomonads, 

desmids, dinoflagellates, euglenoids, and greens), and 

identification and enumeration of diatom phytoplankton 

(U.S. Environmental Protection Agency, 2010d).

The samples for zooplankton and phytoplankton identification were preserved with glutaraldehyde to a 1 percent 

final solution. Identification and counting were done at the 

Wisconsin State Laboratory of Hygiene (WSLH) for soft algae 

and the WDNR for zooplankton and diatoms (Karner, 2005; 

U.S. Environmental Protection Agency, 2010c, e). Rotifers 

other than the large taxon Asplanchna priodonta were not 

identified and counted in the summer zooplankton samples 

from Lower Green Bay (GREE) and Ahnapee River (AHNA) 

nor for any seasons at the Fox River near Allouez (FOXR) 

due to interference from large amounts of algae in samples. 

Chlorophyll a and suspended solids (total suspended solids 

and volatile suspended solids) were determined at the WSLH 

(American Public Health Association, American Water Works 

Association, and Water Environment Federation, 2006; 

Kennedy-Parker, 2011).

Data Analysis

The benthos and plankton community data were compared 

among the sites using various metric analyses as well as 

multivariate nonmetric analyses of the relative abundance of 

each taxon, which is the abundance of each taxon compared to 

the total abundance of all taxa in a sample. Briefly, the metrics 

used for comparisons were taxa richness (the total number of 

taxa), the Shannon Diversity Index (Shannon, 1948), and, for 

HD sampler data only, a multi-metric macroinvertebrate Index 

of Biotic Integrity (IBI) designed for use with HD sampler 

data for large, nonwadable rivers of Wisconsin was calculated 

(Weigel and Dimick, 2011). 

The two largest AOCs, the Lower Green Bay and 

Fox River AOC and the Milwaukee Estuary AOC, are larger 

and far more complex systems than any other harbors or 

rivermouths along the western Lake Michigan shoreline. For 

the Lower Green Bay and Fox River AOC, samples were 

collected at three locations or subsites (table 1). Benthos 

and plankton samples were collected from the Fox River 

near Allouez (FOXR), and additional benthos samples 

were collected each season (spring, summer, and fall) 

from the Fox River near De Pere (FOXD); only plankton 

samples were collected in Lower Green Bay (GREE). The 

Milwaukee Estuary AOC was sampled at three locations or 

subsites: the Menomonee River (MENO), Milwaukee River 

(MILR), and the Milwaukee Harbor (MILH). Due to their size 

and complexity, it was assumed that GREE and MILH would 

likely have different community structures than the non-AOC 

comparison sites. Therefore, except for GREE and MILH, 

each AOC site and any associated subsites were matched 

to two non-AOC comparison sites (“paired non-AOCs”) as 

closely as possible, based on available environmental data and 

discussions between USGS and WDNR personnel who are 

familiar with the individual systems.

A multitiered analysis was used to compare metrics from 

AOCs and non-AOCs for evaluating community degradation 

(fig. 2). With the exception of the metric values for GREE and 

MILH, metric values were compared on three levels: 

• Level 1, between an AOC and all six non-AOCs as a 

group for each seasonal sample

• Level 2, between an AOC and its paired non-AOCs 

for each seasonal sample, and

• Level 3, between an AOC and its paired non-AOCs 

across all seasonal samples using median metric 

scores.

 Standard statistical tests could not be used for making 

comparisons within a single season because of small sample 

sizes. Therefore, for only single-season comparisons, one 

standard deviation or 10 percent of the mean was chosen by 

the WDNR as an acceptable, but still defensible, cutoff for 

comparison of single-season samples. The reasoning was 

that if the variation at non-AOCs was high, then the standard 

deviation also would be high; however, if there was little 

variability in metric values at non-AOCs, then the value(s) 

for an AOC should be within that range if the community was 

not degraded (Andrew Fayram, WDNR, Madison, Wis., oral 

communication, 2012). Hereafter, when the term “standard 

deviation” is used in seasonal metric comparisons, it refers 

to either the standard deviation of the non-AOC values or 

10 percent of the mean, whichever is greater. For Level 1, if 

a single seasonal metric value for an AOC site or subsite was 

more than one standard deviation below the range of all six 

non-AOC metric values, then the seasonal sample was rated 

to have a community more degraded than all non-AOCs as a 

group. For Level 2, if the seasonal metric value of an AOC site 

or subsite was below either of the seasonal metric values for 

the paired non-AOCs by one standard deviation of the mean 

of the paired seasonal metric values, then the seasonal sample 

was rated to have a community more degraded than the paired 

non-AOCs. For Level 3, if the median metric value of all 

seasons at an AOC site or subsite was more than one standard 

deviation below the median metric value for all seasons at 

the paired non-AOCs, then the AOC seasonal samples were 

rated to have communities more degraded than the paired 

non-AOCs. Also, if two or more seasonal samples were rated 

to be degraded, or if samples at two or more levels were rated 

to be degraded, then the AOC community overall was rated 

to be degraded. 

For additional statistical robustness, Mann-Whitney 

and paired t-tests were added to Level 1 and 3 to compare 

metrics across the three seasons. Except for single season 

metric comparisons where a higher significance level was 

used (see above), if the median metric value was significantly 

(p<0.05) below the median metric value of all non-AOCs as a 

group (Level 1) or below the median metric value of the two 

non-AOC comparison sites (Level 3), then the community 

in that AOC was rated more degraded than the communities 

of the selected non-AOCs. Unless otherwise stated, use of 

the term “significant” refers to values of p<0.05. Lack of a 
Methods 7

Figure 2. Diagram of the decision tree for comparing benthos and plankton community metrics at four Lake Michigan Areas of 

Concern in Wisconsin and six non-Area of Concern comparison sites in Wisconsin and Michigan.

The Wisconsin Department of Natural Resources (WDNR) 

evaluates results and consults the Stage II Remedial 

Action Plan for delisting targets. If targets are met, the 

WDNR consults the Area of Concern Technical Advisory 

Committee about recommendations for delisting.

LEVEL 1: Is the metric value for a seasonal sample at 

an Area of Concern more than one standard deviation or 

10 percent, whichever is greater, below the range of 

values for that season at all six non-Area of Concern 

comparison sites?

LEVEL 2: Is the metric value for a seasonal sample at 

an Area of Concern more than one standard deviation or 

10 percent, whichever is greater, below the metric 

values for that season at the two non-Area of Concern 

comparison sites?

No

The seasonal Area of Concern 

sample is DEGRADED.

No

LEVEL 3: Is the median metric value for all seasonal 

samples at an Area of Concern more than one standard 

deviation or 10 percent, whichever is greater, below 

the median metric values for all seasonal samples at 

the two non-Area of Concern comparison sites?

No

The seasonal Area of Concern 

samples are DEGRADED.

The seasonal Area of Concern sample(s) are NOT degraded.

Are two or more seasonal samples degraded at 

Level 2 or are two or more of the answers to the 

questions above YES?

No

The Area of Concern community 

is DEGRADED.

The Area of Concern community 

is NOT degraded.

Yes

The seasonal Area of Concern 

sample is DEGRADED.

Yes

Yes

Yes
8 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

significant difference does not infer that the AOC community 

is not degraded, but rather that it was not degraded in 

comparison to the selected non-AOCs in 2012. 

Five PRIMER software (Clarke and Gorley, 2006) 

routines were used for multivariate analyses of the relative 

abundance of taxa. The PRIMER routines used were: 

1. DIVERSE—to calculate diversity in loge, and 

2. SIMilarity PERcentage (SIMPER)—to assess differences in the relative abundance of taxa among each AOC 

and its paired nonAOCs, among primary and replicate 

samples collected each season at the Sheboygan River 

AOC and Manitowoc River non-AOC, and among 

subsites within the Lower Green Bay and Fox River 

AOC (benthos only) and the Milwaukee Estuary AOC,

3. Multi-Dimensional Scaling (MDS)—nonmetric method 

based on relative abundances of taxa—to derive benthos 

and plankton community site scores and create ordination plots of sites and (or) samples, and

4. ANalysis Of SIMilarity (ANOSIM)—to compare 

communities among sites and samples using similarity 

matrices in a procedure analogous to an analysis 

of variance.

5. Bio-Env+STepwise (BEST)—to discern the top five 

taxa for benthos, zooplankton, and phytoplankton that 

accounted for the most variability between AOCs as a 

group and non-AOCs as a group. 

For multivariate analyses in PRIMER routines, the relative 

abundance of each taxon was determined for each sample, and 

a Bray Curtis similarity matrix was calculated for the sample 

using a fourth root transformation of relative abundance 

data. These Bray Curtis similarity matrices formed the basis 

of MDS, SIMPER, and ANOSIM comparisons. A one-way 

ANOSIM, based on site-specific scores generated with MDS, 

was used to determine the extent to which relative abundances 

of taxa in benthos and plankton communities varied across sites 

by sampling event and across sampling seasons. A one-way 

ANOSIM also was used to compare HD data from the current 

study with one historical data set (Weigel and Dimick, 2011) 

that also used HD samplers. Site scores based on similarities 

between communities were used to determine whether the 

community composition of a sample or site was statistically 

different from other sites, with a 90 percent confidence limit. 

Taxa in a data set are ambiguous when some individuals 

cannot be classified to the species level due to immaturity or 

damage, and then abundances are reported for multiple, related 

taxonomic ranks. This can lead to erroneously high richness 

and diversity values. Ambiguous “parents” are taxa that are 

not identified to the species, while ambiguous “children” 

are the species that were identified and fall under the same 

classification of the “parent.” Ambiguous taxa were resolved 

prior to calculating metrics and prior to multivariate analyses 

by distributing counts for the parent to the children present 

within each site, taking into account the proportion of counts 

already assigned to each child and removing the counts for the 

parent (Cuffney and others, 2007). If no children were present 

in the sample, then counts were left with the parent as originally identified. This procedure for dealing with ambiguous 

data was applied to the benthos, zooplankton, and diatom taxa; 

there were no ambiguous soft algal taxa. For zooplankton, 

immature copepod taxa were distributed to the children when 

present within a sample; in samples without children, Calanoid 

and Cyclopoid copepodites were kept as distinct taxa when 

analyzing data. 

Rare taxa, or taxa that contributed less than 1 percent 

of the total abundance in a sample, were removed prior to 

multivariate analyses so that the total numbers of taxa would 

not exceed three times the total number of samples. Rare 

taxa are sometimes excluded in studies to reduce noise in 

the data analyses (Cao and others, 2001; Marchant, 2002). 

For the combined benthos samples (dredge and HD), a total 

of 203 benthic invertebrate taxa were identified across all 

sites and dates and, after removing rare taxa, 87 benthic taxa 

remained. Removal of rare taxa reduced the taxa list from 

164 to 85 for HDs and from 106 to 65 for dredge samples. 

A total of 95 zooplankton taxa were identified, including 

immature copepods (nauplii and copepodites); removal of 

rare taxa reduced this total number to 73. Removing rare taxa 

from soft algae reduced the taxa list from 48 to 43; a total of 

277 diatom taxa were identified across all sites and dates, and 

193 taxa remained after rare taxa were eliminated. 

Richness was computed by totaling the number of taxa 

with ambiguous taxa resolved and rare taxa included; diversity 

was calculated using the Shannon Diversity Index (loge) 

on raw abundances of taxa without data standardization or 

transformation, but with ambiguous taxa resolved and rare 

taxa included in loge. Richness and diversity were calculated 

separately for the two benthos sampling types—dredge and 

HDs—as well as for the combined benthos samples. Richness 

and diversity were also calculated separately for soft algae and 

diatom phytoplankton, as well as for combined phytoplankton 

(soft algae and diatoms together). An IBI was calculated for 

only the HD samples. IBI calculations followed the methods 

described by Weigel and Dimick (2011), with possible scores 

ranging from 0 (worst) to 100 (best). IBI calculations for 

benthos were designed by Weigel and Dimick (2011) for 

HD sampler data only; this metric ranges from 0 (worst) to 

100 (best) (Weigel and Dimick, 2011).

Benthos HD data collected in 2012 were compared 

quantitatively to historical benthos HD data from Weigel 

and Dimick (2011). In addition, the 2012 plankton data for 

the Milwaukee Estuary AOC were compared to plankton 

data from the Milwaukee Metropolitan Sewerage District 

(MMSD; Eric Waldmer, MMSD, electronic files accessed 

April 22, 2013). Although many studies of benthos and 

plankton have been done in Lake Michigan, few have been 

done at river mouths and harbors, and most of those do not 

conform to the standards required for quantitative comparison. 

Taxonomic resolution and changes in taxonomic classifications 

over time—especially for the phytoplankton community— 

posed the largest problems with using the historical data. 
Condition of the Benthos and Plankton Communities 9

Even when site locations match fairly closely, field collection 

methods can vary greatly between studies, and quality assurance and quality control procedures are not always reported. 

For the comparison to the study by Weigel and Dimick (2011), 

the metrics used were taxa richness; the IBI, and selected 

metrics that comprise the IBI: the number of insect taxa and 

the number of insect taxa that are Ephemeroptera (mayflies), 

Plecoptera (stoneflies), and Trichoptera (caddisflies) , and the 

percentages of total taxa comprised of insects, chironomids, 

and oligochaetes, and the combined percentage of individuals 

in the Orders Ephemeroptera, Plecoptera, and Trichoptera that 

is commonly known as the EPT index.

For quality assurance and quality control, the SIMPER 

routine was run on the replicate samples from the Sheboygan 

River (SHEB) AOC and Manitowoc River (MANI) non-AOC 

comparison site collected during each sampling event to evaluate the similarity between taxa and their relative abundances 

in the samples. Similarities greater than 60 percent were 

considered acceptable for quality assurance purposes (Kelly, 

2001). Except for diatoms, replicates within each seasonal 

sample at a site had similarities of 60 percent or greater. In 

general, diatom density was relatively low for all samples. For 

example, MANI summer samples had a similarity of 0, likely 

because less than 10 diatom taxa were identified in each of the 

two samples, and none of those taxa were identified in both 

samples. This demonstrates the difficulty of characterizing 

taxa at sites with low abundances and patchy distributions. 

By combining soft algae and diatom taxa and abundances in 

comparisons with AOCs, the effect of the diatom taxa on the 

overall phytoplankton comparisons was decreased.

Condition of the Benthos and Plankton 

Communities

Characterization of what taxa or abundances should 

comprise an unimpaired benthos or plankton community is a 

challenge for Great Lakes rivermouths and harbors. A study 

of benthos at 50 nearshore “reference” sites in lakes Superior, 

Huron, Erie, and Ontario by Bailey and others (1995) found 

that the top four taxa were chironomids, oligochaetes, 

bivalves, and sponges; however, that study found considerable 

variation in the benthos across sites and suggested that there 

was not a single, defined “healthy ecosystem.” Relatively 

diverse fauna with at least modest abundances of some taxa in 

a healthy, downstream community in a temperate rivermouth 

or harbor would be expected (Larson and others, 2013). 

In the present study, differences in benthos and plankton 

communities at AOCs were evaluated by comparing computed 

biological metrics as well as relative abundances of taxa 

comprising the aquatic communities at each site. Metrics 

for each site are shown graphically in figs. 3–5, and values 

are provided in tables 2 and 3 for the benthos and plankton, 

respectively. Invasive species and potentially harmful algal 

taxa were also characterized. 

Overview of Benthos and Plankton Communities 

in Lower Green Bay and Milwaukee Harbor

Although Lower Green Bay (GREE) and Milwaukee 

Harbor (MILH) were not included in direct comparisons with 

paired non-AOCs, results of this study provide an ecological 

assessment of the subsites for MILH benthos and plankton 

and GREE plankton that can be used for BUI evaluations and 

comparison to historical studies at the AOCs. 

In plankton samples from GREE, zooplankton richness 

was highest in spring at 28 and lowest in summer at 13; 

diversity was also highest in spring at 2.49 and lowest in 

summer at 1.55 (table 3). Summer richness and diversity 

values reflected the lack of data for rotifers in the summer 

samples because of interference from high algal counts; 

rotifers contributed at least half the richness in the spring and 

fall zooplankton samples at this site. The rotifer Conochilus 

unicornis was the dominant species in the spring zooplankton 

community, and the microcrustaceans Chydorus sphaericus

and immature Cyclopoid copepods were dominant in fall. 

Phytoplankton richness (soft algae and diatoms combined) 

was lowest in spring at 17 and highest in fall at 75; diversity 

ranged from 1.90 in spring to 3.14 in summer, and 3.12 in the 

fall, with blue-green algae dominant in spring, summer, and 

fall samples. 

In benthos samples from MILH, richness in dredge 

samples was lowest in spring at 10, and highest at 18 in the 

fall; benthos richness in HD samples ranged from 40 in spring 

to 11 in fall (table 2). Diversity was highest in fall for dredge 

samples (1.25), but highest in spring for HD samples (3.09). 

For combined benthos samples, the median richness and 

diversity values were 28 and 1.11, respectively. The IBIs for 

HD samples were lowest in summer at 10 and highest at 25 in 

the fall. In the spring and summer samples, oligochaetes were 

dominant in the dredge and HD samples; immature worms of 

the tubificids were dominant in dredge samples and Nais spp. 

were dominant in the HD samples. In the fall samples, zebra 

mussels were dominant in both sample types. Midges were 

also important members of the benthos community in the 

MILH samples. Oligochaetes and midges are considered to be 

relatively tolerant in general and some taxa can be abundant 

in degraded waters (Brinkhurst and Gelder, 1991; Kennedy, 

1966; Lenat, 1993; Rodriguez and Reynoldson, 2011). A 

study of other AOCs in New York, Indiana, and Michigan by 

Canfield and others (1996) determined that the absence of 

midges was indicative of a grossly contaminated sample. 

For plankton at MILH, zooplankton richness was lower 

in spring (18) than fall (27) samples (table 3). Rotifers and 

zebra mussel veligers were the dominant species in the 

zooplankton community, with rotifers primary in spring and 

fall but secondary in summer samples. Phytoplankton richness 

ranged from 11 in summer to 30 in fall and diversity ranged 

from 1.79 in summer to 2.90 in fall. Diatoms were dominant 

in the spring, cryptophytes and diatoms were dominant in 

summer, and green and blue-green algae were dominant in 

fall as diatoms dropped to third in abundance.
10 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Table 2. Richness, diversity, and Index of Biotic Integrity values for benthos samples collected in 2012 by the U.S. Geological Survey 

at four Lake Michigan Areas of Concern in Wisconsin and six non-Area of Concern comparison sites in Wisconsin and Michigan.

[Site abbreviations: MENI–Lower Menominee River; Lower Green Bay and Fox River subsites: GREE–Lower Green Bay, FOXR–Fox River near 

Allouez, and FOXD–Fox River near De Pere; SHEB–Sheboygan River; Milwaukee Estuary subsites: MILR–Milwaukee River; MENO–Menomonee 

River; and MILH–Milwaukee Harbor; ESCA–Escanaba River, Mich.; OCON–Oconto River; AHNA–Ahnapee River; KEWA–Kewaunee River; MANI–

Manitowoc River; and ROOT–Root River]

Site Season Dredge Hester-Dendy Combined benthos

Richness1 Diversity2 Richness Diversity IBI3 Richness Diversity

Areas of Concern4

MENI Spring 14 2.20 30 2.21 15 40 2.73

Summer 17 2.34 36 2.64 20 51 3.10

Fall 9 1.80 17 0.99 20 25 1.37

FOXR Spring 12 1.54 45 2.97 10 49 2.15

Summer 8 0.71 14 0.37 20 18 0.94

Fall 12 1.10 12 0.70 20 21 1.53

FOXD Spring 25 2.14 23 2.25 15 41 2.63

Summer 16 1.80 13 1.09 20 26 1.86

Fall 11 1.74 16 1.51 10 26 2.30

SHEB Spring 20 0.95 30 2.68 10 48 1.72

Summer 12 0.42 29 2.36 5 38 0.61

Fall 7 0.28 18 1.05 10 20 1.01

MILR Spring 14 0.63 25 2.13 10 36 1.07

Summer 8 0.32 18 1.26 10 23 0.67

Fall 15 0.98 13 1.88 0 24 1.41

MENO Spring 13 1.08 26 2.52 10 36 1.16

Summer 12 0.76 27 1.69 0 32 0.99

Fall 16 1.01 10 1.30 5 26 1.32

MILH Spring 10 0.84 40 3.09 20 45 1.11

Summer 11 0.65 20 1.64 10 28 0.72

Fall 18 1.25 11 0.49 25 21 1.15

Non-Areas of Concern

AHNA Spring 5 1.30 29 2.58 10 32 1.96

Summer 2 0.21 32 2.36 15 33 1.75

Fall 4 0.84 13 1.51 10 18 1.92

ESCA Spring 19 2.48 27 2.55 25 43 3.03

Summer 11 2.07 22 2.35 25 28 2.73

Fall 20 1.61 21 2.13 30 33 2.09

KEWA Spring 10 0.91 20 2.09 10 29 2.26

Summer 10 0.51 13 1.29 0 21 1.45

Fall 7 0.49 5 0.59 15 12 1.14

MANI Spring 8 0.46 41 1.92 15 47 0.65

Summer 7 0.64 37 2.42 10 41 0.96

Fall 7 0.64 23 2.05 0 27 1.44

OCON Spring 21 1.30 40 2.19 25 51 1.80

Summer 16 2.26 24 2.35 30 36 2.68

Fall 23 2.36 45 3.14 50 60 2.70

ROOT Spring 15 0.76 35 2.32 20 43 2.16

Summer 8 0.81 28 2.64 15 32 1.40

Fall 9 1.03 9 0.76 5 18 1.16

1

Richness computed as the number of unique taxa in the sample. 

2

Shannon Diversity, calculated as loge. 

3

Index of Biotic Integrity designed for use with Hester-Dendy artificial substrates in nonwadable rivers, calculated as in Weigel and Dimick (2011). 

The Index of Biotic Integrity ranges from 0 (worst) to 100 (best).

4

Benthos samples were not collected in Green Bay. 
Condition of the Benthos and Plankton Communities 11

Table 3. Richness and diversity values for plankton samples collected in 2012 by the U.S. Geological Survey at four Lake Michigan 

Areas of Concern and six non-Area of Concern comparison sites in Wisconsin and Michigan.

[Site abbreviations: MENI–Lower Menominee River; Lower Green Bay and Fox River subsites: GREE–Lower Green Bay, FOXR–Fox River near Allouez, 

and FOXD–Fox River near De Pere; SHEB–Sheboygan River; Milwaukee Estuary subsites: MILR–Milwaukee River; MENO–Menomonee River; and MILH–

Milwaukee Harbor; ESCA–Escanaba River, Mich.; OCON–Oconto River; AHNA–Ahnapee River; KEWA–Kewaunee River; MANI–Manitowoc River; and 

ROOT–Root River]

Site Season Zooplankton1 Soft algae Diatoms Combined phytoplankton4

Richness2 Diversity3 Richness Diversity Richness Diversity Richness Diversity

Areas of Concern5

MENI Spring 27 2.51 13 1.86 28 2.67 41 2.96

Summer 35 2.92 8 1.09 8 1.28 16 1.88

Fall 25 1.81 15 1.22 14 2.53 29 2.57

GREE Spring 28 2.49 12 1.60 5 0.81 17 1.90

Summer 13 1.55 22 1.91 36 2.99 58 3.14

Fall 23 2.14 18 1.67 57 3.18 75 3.12

FOXR Spring 10 1.50 12 1.42 55 3.01 67 2.91

Summer 8 1.22 14 1.46 65 3.11 79 2.98

Fall 5 0.98 13 0.68 50 2.77 63 2.42

SHEB Spring 18 1.87 14 1.71 29 1.61 43 2.35

Summer 19 2.25 13 1.50 37 2.66 50 2.78

Fall 24 2.08 8 1.21 70 3.16 78 2.89

MILR Spring 13 1.97 15 1.87 38 3.22 53 3.24

Summer 21 1.90 8 0.73 35 3.11 43 2.61

Fall 27 2.32 19 1.96 56 3.26 75 3.30

MENO Spring 24 2.18 8 1.53 47 3.26 55 3.09

Summer 14 2.25 12 1.90 33 3.19 45 3.24

Fall 20 2.28 19 2.11 10 2.22 29 2.86

MILH Spring 18 1.27 8 1.59 20 2.69 28 2.83

Summer 18 1.81 8 1.11 3 1.08 11 1.79

Fall 27 1.48 15 2.04 15 2.37 30 2.90

Non-Areas of Concern

AHNA Spring 19 1.36 14 0.83 24 2.52 38 2.37

Summer 7 1.26 15 0.81 24 2.83 39 2.51

Fall 20 2.15 18 0.94 19 2.12 37 2.22

ESCA Spring 24 2.35 9 1.27 32 3.00 41 2.83

Summer 21 1.62 13 1.95 12 2.25 25 2.79

Fall 27 2.64 11 1.31 12 2.30 23 2.50

KEWA Spring 27 1.71 13 2.15 2 0.64 15 2.09

Summer 14 1.66 17 1.71 45 2.64 62 2.87

Fall 22 1.93 17 1.86 55 2.71 72 2.98

MANI Spring 23 2.40 6 1.08 30 2.25 36 2.36

Summer 14 1.25 16 0.90 9 2.01 25 2.15

Fall 25 1.00 16 1.38 23 2.79 39 2.78

OCON Spring 18 2.21 6 0.82 10 2.27 16 2.34

Summer 25 2.04 16 2.08 28 2.84 44 3.16

Fall 23 2.40 8 1.28 32 2.82 40 2.75

ROOT Spring 20 1.49 15 1.99 71 3.67 86 3.52

Summer 15 0.54 14 1.44 24 2.19 38 2.51

Fall 24 1.34 14 1.64 15 2.46 29 2.74

1

For zooplankton, high algal counts precluded identification of rotifers other than Asplanchna priodonta in summer samples for Ahnapee River and 

Green Bay and all Fox River samples; therefore, comparison sites for these sites excluded other rotifers. 

2

Richness computed as the number of unique taxa in the sample. 

3

Shannon Diversity, calculated as loge.

4

Phytoplankton richness and diversity comparisons in this table were calculated for combined soft algae and diatoms. 

5

Plankton samples were not collected at the FOXD.
12 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Comparison of Subsites for the Lower Green Bay 

and Fox River and the Milwaukee Estuary Areas 

of Concern

Sampling was done at separate subsites in the Lower 

Green Bay and Fox River AOC (Fox River near De Pere 

[FOXD] and Fox River near Allouez [FOXR]) and the 

Milwaukee Estuary AOC (Milwaukee River [MILR], 

Menomonee River [MENO], and Milwaukee Harbor [MILH]) 

due to concerns about potential differences in environmental 

conditions at those sites. Similarity analyses of relative 

abundance with no ambiguous or rare taxa confirmed that 

community compositions at subsites within each AOC were 

sufficiently dissimilar to warrant separate analysis in order to 

properly characterize the AOCs.

For the combined benthos samples, SIMPER results 

showed that similarities in community composition between 

the two Fox River subsites (FOXR and FOXD) in the 

Lower Green Bay and Fox River AOC were 50.0 percent 

for spring, 61.1 percent for summer, and 57.6 percent for 

fall; because two of the three similarities were below the 

60 percent threshold, benthos data for these AOC subsites 

were kept separate in metric comparisons and multivariate 

analyses. For the three Milwaukee Estuary AOC subsites 

(MILR, MENO, and MILH), similarities were 60.0 percent 

for spring, 55.1 percent for summer, and 49.0 percent for 

fall, which indicated that these subsites were also dissimilar; 

therefore, these sites were also kept separate in the analyses. 

The relative abundance of immature oligochaetes (Tubificinae) 

was important for defining these dissimilarities for the two 

Fox River and three Milwaukee Estuary AOC subsites; 

however, immature oligochaetes dropped to second in number 

to zebra mussels (Dreissena polymorpha) in the summer 

sample at the Fox River subsites.

Similarities in zooplankton community composition 

between the MILR and MENO subsites in the Milwaukee 

Estuary AOC were 48.8 percent for spring, 60.0 percent 

for summer, and 54.9 percent for fall. Because not all three 

similarities were 60 percent or more, the MILR and MENO

communities were considered to be distinct and were kept 

separate in metric and multivariate comparisons with nonAOCs. The relative abundance of zebra mussels and several 

rotifer taxa (especially Pompholyx sulcata, Gastropus stylifer, 

Brachionus calyciflorus, and Synchaeta oblonga) was important in defining spring dissimilarities between these subsites. 

Another rotifer, Keratella crassa, became fourth and then first 

in importance in summer and fall dissimilarities, respectively, 

and Brachionus calyciflorus was second in importance. As 

mentioned earlier, plankton were collected from the FOXR but 

not from FOXD in the Lower Green Bay and Fox River AOC, 

so similarities could not be compared between these two 

subsites for zooplankton or phytoplankton. 

For combined phytoplankton, similarities in community 

composition among MILR and MENO in the Milwaukee 

Estuary AOC were 44.6 percent for spring, 24.1 percent for 

summer, and 43.4 percent for fall. Because all similarities 

were less than 60 percent, phytoplankton communities in 

MILR and MENO were considered to be distinct from each 

other and therefore were kept separate in metric comparisons 

and multivariate analyses. The colonial green alga of the genus 

Scenedesmus was determined to be important in defining 

these dissimilarities; peak abundance occurred in spring, and 

decreased in summer when the colonial blue-green alga of the 

genus Merismopedia became primary, with both taxa contributing fairly equally in the fall sample. 

Benthos Community Comparisons Between 

Areas of Concern and Non-Areas of Concern

Benthos taxa richness was generally lower for dredge 

samples than for HDs at all sites, possibly reflecting the 

greater suitability of the hard, artificial substrate of HDs in 

comparison to the soft, natural substrates collected in dredge 

samples (table 2). Dredge samples represent the habitat that 

is most affected by contaminants. For combined benthos, 

mean richness across seasonal samples at AOCs ranged from 

27.7±7.2 (mean±standard deviation) for the Milwaukee 

River (MILR) to 38.7±13.1 for the Lower Menominee River 

(MENI); mean taxa richness at non-AOCs ranged from 

20.7±8.5 for the Kewaunee River (KEWA) to 49.0±12.1 

for the Oconto River (OCON) (fig. 3A). Combined benthos 

richness for all seasons at each AOC was not significantly 

different from richness at non-AOCs as a group at Level 

1, based on Mann-Whitney tests (p<0.05) (table 4), and 

it was not different within seasons. However, at Level 2, 

seasonal richness values at two subsites in the Milwaukee 

Estuary AOC—spring and summer at MILR and spring at the 

Menomonee River (MENO)—were below a seasonal value 

for the paired non-AOCs by more than one standard deviation 

of the mean of seasonal values for the paired sites (table 5). 

At Level 3, Mann-Whitney tests showed that combined 

benthos richness at each AOC was not significantly lower than 

their paired non-AOCs across all seasons, so no sites were 

rated as degraded. However, because two seasonal samples 

were rated as degraded at Level 2 for richness, the benthos 

community for MILR was rated as degraded overall. Sand 

that was relatively low in organic matter was dominant in the 

substrate at MILR and may not have been suitable for many 

invertebrates. Although sand was dominant in most samples 

from MENO, silt made up a greater proportion of the substrate 

at MENO than at MILR.

Diversity in benthos samples also tended to be lower for 

dredge samples than for HDs overall. For combined benthos, 

mean diversity for AOCs ranged from 1.1±0.4 at MILR to 

2.4±0.9 at MENI; mean diversity at non-AOCs ranged from 

1.0±0.4 at the Manitowoc River (MANI) to 2.4±0.5 at OCON

(fig. 3B). Mann-Whitney tests showed that the diversity for 

combined benthos across all seasons at the MENO subsite 

in the Milwaukee Estuary AOC was significantly lower than 

diversity at non-AOCs as a group and therefore was rated 
Condition of the Benthos and Plankton Communities 13

Figure 3. Boxplots of A, richness, B, diversity metric values for combined benthos (dredge and Hester-Dendy data 

combined), and C, Index of Biotic Integrity (Hester-Dendy samples) from four Lake Michigan Areas of Concern and

six non-Area of Concern comparison sites. Site abbreviations: MENI–Lower Menominee River; Lower Green Bay

and Fox River subsites: FOXR–Fox River near Allouez and FOXD–Fox River near De Pere; SHEB–Sheboygan River; 

Milwaukee Estuary subsites: MILR–Milwaukee River, MENO–Menomonee River, and MILH–Milwaukee Harbor; 

ESCA–Escanaba River, Mich.; OCON–Oconto River; AHNA–Ahnapee River; KEWA–Kewaunee River; MANI–

Manitowoc River; and ROOT–Root River.

0

10

20

30

40

50

60

Combined benthos richness Combined benthos diversity Hester−Dendy sampler Index of Biotic Integrity

Areas of Concern Non-Areas of Concern

0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

0

10

20

30

40

50

EXPLANATION Range

Standard deviation

Standard deviation

Mean

MENI FOXR FOXD SHEB MILR MENO MILH ESCA

SITE

OCON AHNA KEWA MANI ROOT
14 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Table 4. Significance values (p) for Mann-Whitney tests and paired t-tests for metric comparisons between each of the four Lake 

Michigan Areas of Concern and the six non-Area of Concern comparison sites as a group or the specific non-Areas of Concern pair

across the spring, summer, and fall seasons in 2012.

[Site abbreviations: MENI–Lower Menominee River; Lower Green Bay and Fox River subsites: FOXR–Fox River near Allouez and FOXD–Fox River near 

De Pere; SHEB–Sheboygan River; Milwaukee Estuary subsites: MILR–Milwaukee River and MENO–Menomonee River; ESCA–Escanaba River, Mich.; 

OCON–Oconto River; AHNA–Ahnapee River; KEWA–Kewaunee River; MANI–Manitowoc River; and ROOT–Root River. Bold values indicate that Area of 

Concern metric values were significantly lower at p< 0.05. Benthos samples were not collected in Green Bay; AOC, Area of Concern; nc, plankton samples 

were not collected at the Fox River near De Pere; IBI, Index of Biotic Integrity computed as in Weigel and Dimick (2011); richness computed as the number 

of unique taxa in sample; Shannon diversity calculated as loge ]

Area of 

Concern site 

or subsite

Comparison

sites

Combined benthos Hester-Dendy 

benthos Zooplankton Combinedphytoplankton

Richness Diversity IBI3 Richness Diversity Richness Diversity

MENI NonAOCs 1.000 0.507 0.507 0.111 0.268 1.000 1.000

ESCA; OCON 1.000 0.667 0.046 0.400 0.737 1.000 1.000

FOXR Non-AOCs 0.667 0.667 0.507 0.053 0.121 0.111 0.507

AHNA; KEWA 1.000 1.000 0.102 0.111 0.281 0.111 0.444

FOXD Non-AOCs 0.507 0.222 0.667 nc nc nc nc

AHNA; KEWA 0.825 0.222 0.400 nc nc nc nc

SHEB Non-AOCs 1.000 0.400 0.046 1.000 0.311 0.111 0.507

KEWA; MANI 0.800 0.667 1.000 1.000 0.102 0.667 0.800

MILR Non-AOCs 0.444 0.111 0.046 1.000 0.109 0.111 0.102

MANI; ROOT 0.667 0.400 0.268 1.000 0.400 0.444 0.444

MENO Non-AOCs 1.000 0.038 0.038 1.000 (

1

) 0.667 (

1

)

MANI; ROOT 0.667 0.184 0.444 0.667 (

1

) 1.000 0.400

1

MENO values significantly higher, not lower, than comparison sites (p< 0.05).

Table 5. Summarized results of metric comparisons for benthos and plankton samples collected in 2012 by the U.S. Geological Survey 

at four Lake Michigan Areas of Concern and six non-Area of Concern comparison sites. 

[Site abbreviations: MENI–Lower Menominee River; Lower Green Bay and Fox River subsite: FOXR–Fox River near Allouez; SHEB–Sheboygan River; 

Milwaukee Estuary subsites: MILR–Milwaukee River and MENO–Menomonee River; and AHNA–Ahnapee River. Sites in bold italics were significantly lower 

in richness, diversity, or the IBI than non-AOCs for all seasons (Mann Whitney test or paired t test, p < 0.05); sites not in bold italics were evaluated for single 

seasons based on comparison of standard deviations and ranges because of the small sample numbers; AOC, Area of Concern; IBI, Index of Biotic Integrity]

Community Metric Degraded at Level 1

(AOC:nonAOC group)

Degraded at Level 2

(AOC:nonAOC pair, 

per season)

Degraded at Level 3

(AOC:nonAOC pair, 

all seasons)

Degraded 

overall

Combined benthos Richness None MILR Spring, Summer

MENO Spring

None MILR

Diversity MENO MENI Fall

FOXR Summer

SHEB Summer

None None

Hester-Dendy

benthos

IBI SHEB

MILR

MENO

MENI Spring, Summer

MILR Spring

MENO Spring, Summer

MENI MENI

MENO

Zooplankton1 Richness FOXR Fall

MILR Spring

FOXR Fall

SHEB Spring

MILR Spring

MENO Fall

None FOXR

MILR

Diversity None FOXR Fall

MENI Fall

None None

Combined 

phytoplankton

Richness None None None None

Diversity None MENI Summer None None

1

High algal counts precluded identification of rotifers other than Asplanchna priodonta in zooplankton for AHNA summer samples and all FOXR samples. 

Therefore, zooplankton comparisons FOXR excluded all other rotifers at non-AOCs.
Condition of the Benthos and Plankton Communities 15

as degraded at Level 1. Diversity in fall at MENI, summer 

at the Fox River near Allouez (FOXR), and summer at the 

Sheboygan River (SHEB) AOC were rated as degraded at 

Level 2 in comparison to their paired non-AOCs. No AOCs 

were rated as degraded at Level 3, based on results for Levels 

comparisons, Mann-Whitney tests, or paired t-tests, and so 

none were rated as degraded overall with regard to diversity 

when compared to the non-AOC sites. 

Mean IBIs at AOCs ranged from 5.0±5 at the MENO

subsite to 18±2.9 at MENI; mean IBIs at non-AOCs ranged 

from 8.3±7.6 at both KEWA and MANI to 35±13 at OCON

(fig. 3C ). Mann-Whitney or paired t-tests showed that the IBIs 

at SHEB, MILR, and MENO were significantly lower than 

non-AOCs as a group across all seasons and so were rated 

as degraded at Level 1 (tables 4 and 5). IBIs in spring and 

summer at MENI, spring at MILR, and spring and summer 

at MENO were rated as degraded at Level 2. Mann-Whitney 

tests showed that the IBIs across all seasons at MENI were 

also significantly lower than the paired non-AOCs for Level 3. 

Because two seasonal samples were rated as degraded at 

Level 2, the benthos communities for MENI and the MENO

subsite were rated as degraded overall with regard to benthos 

IBIs. Similar to its paired non-AOCs—ESCA and OCON, the 

substrate at MENI was primarily hard sand (84–91 percent), 

making dredge grabs difficult to obtain; volatile-on-ignition 

analyses indicated low amounts of organic matter in the 

samples. Multiple independent studies during the 1970s and 

1980s characterized the benthos of the Lower Menominee 

River AOC as predominantly pollution-tolerant oligochaetes 

and midges which were low in abundance or lacking in 

areas with high sediment chemical concentrations and poor 

substrate (Wisconsin Department of Natural Resources, 1996; 

Elwin Evans, unpub. data, July 1980, as cited in Wisconsin 

Department of Natural Resources and Michigan Department 

of Natural Resources, 1990). 

Nonmetric multidimensional scaling (MDS) is a 

multivariate method that represents objects, such as samples, 

in two or three dimensions where dissimilar objects plot far 

apart and similar objects plot close together. Stress values 

<0.2 are optimal with regard to how well relationships 

between objects are represented in an MDS plot. A small R 

(0.14) and moderate stress (0.21) in the two-dimensional MDS 

plot of benthos samples indicate that the relative relationships between samples are well represented in fig. 4. Based 

on ANOSIM tests with relative abundances of combined 

benthos taxa when seasons were treated separately, the 

differences between each AOC and all non-AOCs as a group 

were not significant. However, benthos at FOXR and FOXD

were significantly different from their paired non-AOCs 

(Ahnapee River [AHNA] and KEWA). Additional SIMPER 

testing showed that FOXD was 60 percent dissimilar, with 

zebra mussels, the caddisfly Cyrnellus fraternus, and the 

clam Sphaerium contributing most to distinguishing between 

the sites; FOXR was 64 percent dissimilar, and differences 

between the AOC and its non-AOC comparison sites were due 

mostly to differences in relative abundances of zebra mussels, 

the midge Procladius, and the oligochaete Limnodrilus cervix. 

The benthos community at MILR was significantly different 

when compared to the paired non-AOCs MANI and ROOT. 

The community at MILR was 48 percent dissimilar from the 

paired non-AOCs, with differences between the sites due 

mostly to differences in relative abundances of the oligochaete 

Aulodrilus pluriseta, the isopod Caecidotea intermedia, and 

the midge Procladius. ANOSIM tests indicated that relative 

abundances of combined benthos taxa at MENI, SHEB, and 

MENO were not significantly different than the paired nonAOCs across seasons.

For the combined benthos data, the taxon that accounted 

for most of the variability between AOCs as a group and 

non-AOCs as a group was immature tubificid oligochaete 

worms, Tubificinae (rs

=0.56). The five taxa that accounted 

for most of the variability between the two groups were 

immature tubificid oligochaetes as well as adult oligochaetes 

Limnodrilus hoffmeisteri and Nais pardalis, and chironomid 

midges Tanytarsus spp. and Ablabesmyia spp. (rs

=0.78). The 

tubificid oligochaete Limnodrilus hoffmeisteri has a worldwide 

distribution; it can be locally abundant and dominant because 

of its adaptable nature and high tolerance to pollution, salinity, 

and highly eutrophic conditions (Bode and others, 2002).

Plankton Community Comparisons between 

Areas of Concern and Non-Areas of Concern

Plankton communities at AOCs were compared using 

richness and diversity metrics. For zooplankton, rotifers made 

up at least half of the taxa in samples on average (Scudder 

Eikenberry and others, 2014), and this had a large effect on 

richness and diversity. With the exception of the large rotifer 

Asplanchna priodonta, data for the Fox River near Allouez 

(FOXR) and one of its paired non-AOCs, the Ahnapee River 

(AHNA), lacked rotifer data for the summer sample because 

large algal blooms obscured rotifer counts. For this reason, 

zooplankton comparisons for FOXR were made by excluding 

rotifers other than A. priodonta from metric comparisons. 

Mean zooplankton richness at AOCs ranged from 7.7±2.5 at 

FOXR (without rotifers) to 29.0±5.3 at the Lower Menominee 

River (MENI) (with rotifers); mean richness at non-AOCs 

ranged from 8.7±2.1 at AHNA (without rotifers) to 24.0±3.0 

at the Escanaba River (ESCA) (with rotifers) (fig. 5A). At 

Level 1, the FOXR fall and the Milwaukee River (MILR) 

spring samples for zooplankton richness were rated as 

degraded for richness (tables 4 and 5). At Level 1, zooplankton 

richness at FOXR was lower than non-AOCs as a group, 

but was not quite significantly lower (p=0.053). At Level 2, 

FOXR and MILR were also rated as degraded for richness, 

so the zooplankton communities at these AOCs were rated 

as degraded overall in comparison to their paired non-AOCs. 

The Sheboygan River (SHEB) AOC spring and Menomonee 

River (MENO) fall samples were rated as degraded at Level 2; 

no sites were rated as degraded at Level 3 with regard to 

zooplankton richness. 
16 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

SP

SP

SP

SP

SP

SP SP

SP

SP

SM

FL

SP

SP

SP SP

SP

SM

SM

SM

SM

SM

SM SM

SM

SM

SM

SM

SM

SM

FL

FL

FL

FL

FL

FL

FL

FL

FL

FL

FL

FL FL

A

B

AHNA

ESCA

FOXD

FOXR

KEWA

MANI

MENI

MENO

MILH

MILR

OCON

ROOT

SHEB

Two-dimensional stress=0.11

Two-dimensional stress=0.21

Area of Concern

Non-Area of Concern

EXPLANATION

Lower Menominee River 

(MENI)

Fox River near Allouez (FOXR)

Fox River near DePere (FOXD)

Sheboygan River (SHEB)

Milwaukee River (MILR)

Menomonee River (MENO)

Milkaukee Harbor (MILH)

Escanaba River, Mich. (ESCA)

Oconto River (OCON)

Ahnapee River (AHNA)

Kewaunee River (KEWA)

Manitowoc River (MANI)

Root River (ROOT)

Season

 Spring

 Summer

 Fall

Figure 4. Multi-Dimensional Scaling ordination plots for the combined benthos (dredge and Hester-Dendy samples) at 

four Lake Michigan Areas of Concern, including subsites for the Milwaukee Estuary Area of Concern, and non-Area of 

Concern comparison sites, based on relative abundance with no rare or ambiguous taxa, A, with seasons combined, and 

B, with seasons separate. Distances between sites are representative of their similarity or dissimilarity to each other. 
Condition of the Benthos and Plankton Communities 17

0

5

10

15

20

25

30

35

Zooplankton richness

0

0.5

1.0

1.5

2.0

2.5

3.0

Zooplankton diversity

Areas of Concern Non-Areas of Concern

MENI GREE FOXR SHEB MILR MENO MILH ESCA

SITE

OCON AHNA KEWA MANI ROOT

EXPLANATION

Range

Standard deviation

Standard deviation

Mean

Figure 5. Plots of A, richness, and B, diversity metric values for 

zooplankton at four Lake Michigan Areas of Concern and six non-Area of 

Concern comparison sites. Site abbreviations: MENI–Lower Menominee 

River; Lower Green Bay and Fox River subsites: GREE–Lower Green Bay 

and FOXR–Fox River near Allouez; SHEB–Sheboygan River; Milwaukee 

Estuary subsites: MILR–Milwaukee River, MENO–Menomonee River, and 

MILH–Milwaukee Harbor; ESCA–Escanaba River, Mich.; OCON–Oconto 

River; AHNA–Ahnapee River; KEWA–Kewaunee River; MANI–Manitowoc 

River; and ROOT–Root River.
18 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Zooplankton diversity at AOCs ranged from 1.23±0.26 

at FOXR (without rotifers) to 2.41±5.56 at MENI (with 

rotifers); diversity at non-AOCs ranged from 1.12±0.51 at 

the Root River (ROOT) with rotifers to 2.22±0.18 at the 

Oconto River (OCON) with rotifers (fig. 5B). No zooplankton 

samples were rated as degraded at Level 1 for diversity. The 

fall samples for the FOXR and MENI were rated as degraded 

for zooplankton diversity at Level 2 (table 5). No AOCs 

were rated as degraded at Level 3 or overall for zooplankton 

diversity in comparison to the non-AOCs.

One-way ANOSIM tests on relative abundances of 

zooplankton taxa were done with and without FOXR data 

because no rotifers, except Asplanchna priodonta, were 

counted at this site due to interference from high algal 

counts in the samples. In both cases, there was no significant 

difference (p>0.10) between zooplankton communities at all 

AOC and non-AOCs as a group (fig. 6A and B). However, 

zooplankton communities at FOXR were significantly different 

from the paired non-AOCs (AHNA and KEWA) when comparisons were made without rotifers other than A. priodonta. 

Additional SIMPER tests showed that FOXR was 57 percent 

dissimilar due in large part to differences in relative abundances of the rotifer A. priodonta, the copepod Diacyclops 

bicuspidatus thomasi, and cladoceran Chydorus sphaericus.

The zooplankton taxon that accounted for the most variability between AOCs as a group and non-AOCs as a group 

was the cladoceran Bosmina longirostris (rs

= 0.51) when only 

microcrustaceans were considered and the rotifer Brachionus 

calyciflorus when both microcrustaceans and rotifers were 

considered (rs= 0.51). The five taxa that accounted for most 

of the variability between the groups were the cladoceran 

Bosmina longirostris, and rotifers Brachionus calyciflorus, 

Ascomorpha saltans, Synchaeta oblonga, and Gastropus 

stylifer (rs= 0.77). 

Phytoplankton communities were compared between 

AOCs and non-AOCs using richness and diversity metrics 

calculated for soft algae and diatoms separately and combined. 

For combined phytoplankton, mean richness ranged from 

26.3±11.5 at MENI to 59.7±5.0 at FOXR; mean richness 

at non-AOCs ranged from 26.3±8.4 at ESCA to 45.0±26.3 

at Kewaunee River (KEWA) and 45.0±21.2 at ROOT

(fig. 7A). No AOC sites were rated as degraded for combined 

phytoplankton richness at any levels (table 5) in comparison 

to the sampled non-AOCs. Mann-Whitney tests showed 

no significant differences in chlorophyll-a concentration or 

total suspended solids and volatile suspended solids between 

AOCs and non-AOCs (p<0.05), indicating that phytoplankton 

biomass was not significantly different between AOCs and 

non-AOCs.

Mean diversity for combined phytoplankton at AOCs 

ranged from 2.42±0.5 at MENI to 3.00±0.20 at MENO, and at 

non-AOCs it ranged from 2.30±0.16 at AHNA to 2.88±0.48 

at ROOT (fig. 7B). Combined phytoplankton diversity for 

the MENI summer sample was rated as degraded at Level 2 

(tables 4 and 5). Combined phytoplankton communities were 

rated as not degraded at Level 3 or overall at any AOC sites 

in comparison to the sampled non-AOCs, possibly due to 

contributions of tolerant taxa to richness and diversity metrics 

for these sites. 

No significant difference between AOCs and non-AOCs 

were found for combined phytoplankton communities in a 

one way ANOSIM using transformed relative abundance 

with no ambiguous or rare taxa if seasons were combined 

(fig. 8A) or kept separate (p=0.40 and 0.07, respectively; 

fig. 8B). However, the combined phytoplankton community 

at FOXR was significantly different from its paired nonAOCs (AHNA and KEWA); SIMPER testing showed that 

the Fox River was 72 percent dissimilar, due mostly to the 

diatoms Aulacoseira granulata, Stephanodiscus hantzschii, 

and Stephanodiscus niagarae. 

The phytoplankton taxon that accounted for the most 

variability between AOCs as a group and non-AOCs as a 

group was Cocconeis placentula (rs

= 0.49). The five taxa that 

accounted for most of the variability between the groups 

were Cocconeis placentula, Amphora pediculus, Aulacoseira 

granulata, Rhoicosphenia abbreviata, and Staurosira 

construens (rs= 0.71). All five taxa are diatoms that are 

alkalophilous (occurring mostly at pH>7) and fresh brackish 

(chloride <500 milligrams per liter, salinity <0.9 percent) 

(Van Dam and others, 1994), tolerant of moderately polluted 

waters (ß-mesosaprobous) but relatively sensitive with regard 

to overall pollution class/tolerance (Bahls, 1993; LangeBertalot, 1979). 

Potentially harmful blue-green algae were identified in 

soft algae samples from three of four AOCs, including MENI

in fall, FOXR in all seasons, and all three Milwaukee Estuary 

subsites (MILR, MILH, and MENO) in fall. In addition, these 

taxa were found at two non-AOCs: KEWA in summer and 

fall, and ROOT in summer. Taxa of the blue-green algae 

were identified as Anabaena sp., Aphanizomenon flos aquae

and Aphanizomenon. issatschenkoi, Cylindrospermopsis 

raciborskii, Microcystis aeruginosa, and Microcystis sp. 

Aphanizomenon issatschenkoi was identified at six sites—

more than any other blue-green algae. Blue-green algae were 

dominant in all phytoplankton samples collected from Lower 

Green Bay (GREE) and FOXR, in part due to high densities 

of the harmful algal taxa Anabaena in spring and Microcystis

in summer and fall. Zebra mussels were first found in 

Green Bay in 1991 and are now (2012) very abundant. Their 

high densities and ability to filter large volumes of water in 

the Bay correlated with a change in dominance from green 

algae to blue-green algae, large increases in abundance of 

blue-green algae Anabaena and Microcystis, and an increase 

in phytoplankton biovolume and chlorophyll (De Stasio, Jr. 

and others, 2014). Microcystis is known to thrive in high 

nutrient conditions, such as those found at in 2012 samples 

at GREE and FOXR. These results may provide additional 

input to the BUI for excessive nutrients and undesirable 

algae in the Lower Green Bay and Fox River AOC and the 

Milwaukee Estuary AOC.
Condition of the Benthos and Plankton Communities 19

AHNA

ESCA

FOXR

KEWA

MANI

MENI

MILH MENO

MILR

OCON

ROOT

SHEB

SP

SP

SP

SP

SP

SP

SP

SP SP

SP

SP

SP

SM

SM

SM

SM

SM

SM

SM

SM

SM

SM

SM

SM

FL

FL

FL

FL

FL

FL

FL

FL

FL

FL

FL FL

A

B

Two-dimensional stress=0.07

Two-dimensional stress=0.19

Area of Concern

Non-Area of Concern

EXPLANATION

SP

SM

FL

Lower Menominee River 

(MENI)

Fox River near Allouez (FOXR)

Sheboygan River (SHEB)

Milwaukee River (MILR)

Menomonee River (MENO)

Milkaukee Harbor (MILH)

Escanaba River, Mich. (ESCA)

Oconto River (OCON)

Ahnapee River (AHNA)

Kewaunee River (KEWA)

Manitowoc River (MANI)

Root River (ROOT)

Season

 Spring

 Summer

 Fall

Figure 6. Multi-Dimensional Scaling ordination plots for zooplankton at four Lake Michigan Areas of Concern, 

including subsites for the Milwaukee Estuary Area of Concern, and six non-Area of Concern comparison sites, 

based on relative abundance (calculated by using fourth root transformation) with no rare or ambiguous taxa: 

A, with seasons combined, and B, with seasons separate. 
20 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

0

20

40

60

80

0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

Combined phytoplankton richness Combined phytoplankton diversity

Areas of Concern Non-Areas of Concern

MENI GREE FOXR SHEB MILR MENO MILH ESCA

SITE

OCON AHNA KEWA MANI ROOT

EXPLANATION

Range

Standard deviation

Standard deviation

Mean

Figure 7. Plots of A, richness and B, diversity metric values for combined 

phytoplankton (soft algae and diatoms) at four Lake Michigan Areas of 

Concern and six non-Area of Concern comparison sites. Site abbreviations: 

MENI–Lower Menominee River; Lower Green Bay and Fox River subsites: 

GREE–Lower Green Bay and FOXR–Fox River near Allouez; SHEB–Sheboygan 

River; Milwaukee Estuary subsites: MILR–Milwaukee River, MENO–

Menomonee River, and MILH–Milwaukee Harbor; ESCA–Escanaba River, 

Mich.; OCON–Oconto River; AHNA–Ahnapee River; KEWA–Kewaunee River; 

MANI–Manitowoc River; and ROOT–Root River.
Condition of the Benthos and Plankton Communities 21

SP

SM

FL

SP

SM

SP FL

SM

FL

SP

SM

FL

SP

SM

SP

SM

FL

SP

SM

FL

SP

SM

FL SP

SM

FL

FL

SP

SM

FL

SP

SM

FL

SP

SM

FL

AHNA

ESCA

FOXR

KEWA

MANI

MENI

MENO

MILH

MILR

OCON

ROOT

SHEB

A

B

Two-dimensional stress=0.14

Two-dimensional stress=0.23

Area of Concern

Non-Area of Concern

EXPLANATION

SP

SM

FL

Lower Menominee River 

(MENI)

Fox River near Allouez (FOXR)

Sheboygan River (SHEB)

Milwaukee River (MILR)

Menomonee River (MENO)

Milkaukee Harbor (MILH)

Escanaba River, Mich. (ESCA)

Oconto River (OCON)

Ahnapee River (AHNA)

Kewaunee River (KEWA)

Manitowoc River (MANI)

Root River (ROOT)

Season

 Spring

 Summer

 Fall

Figure 8. Multi-Dimensional Scaling ordination plots for the combined phytoplankton (soft algae and diatoms) 

at four Lake Michigan Areas of Concern, including subsites for the Milwaukee Estuary Area of concern, and 

six non-Area of Concern comparison sites, based on relative abundance (calculated by using fourth root 

transformation) with no rare or ambiguous taxa: A, with seasons combined, and B, with seasons separate. 
22 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

Invasive Species at Areas of Concern and 

Non-Areas of Concern

Invasive benthos species were found in some samples. 

Two live, large specimens of the invasive Asian clam 

Corbicula fluminea were identified in dredge samples in 

July and August at the Menomonee River (MENO) subsite 

in the Milwaukee Estuary AOC. Corbicula were not identified at any other sample in 2012. Corbicula is an aquatic 

invasive species that has been found at other locations in 

the Great Lakes and in rivers of the continental United 

States (Carlisle and others, 2013; Foster, 2013). Invasive 

zebra mussels were found in benthos and plankton samples 

from all sites and were considered abundant at some AOCs 

and non-AOCs. The highest abundances for adult zebra 

mussels were found in both Fox River subsites (FOXR and 

FOXD) summer HD and Sheboygan River (SHEB) fall HD 

samples. Overall, zebra mussels were more commonly found 

in HD samples than in dredge samples, possibly due to the 

preference of zebra mussels for hard substrate over the soft 

natural substrates. Lastly, the invasive benthic amphipod 

Echinogammarus ischnus has established populations in 

the Fox River (De Stasio, 2013), and populations have been 

documented elsewhere in the Great Lakes (Nalepa and others, 

2001; Witt and others, 1997). In our study, Echinogammarus sp. was identified in benthos samples—mostly in HD 

samples—from both Fox River subsites as well as from the 

Lower Menominee River (MENI) and SHEB, the Milwaukee 

Harbor (MILH) subsite, and the Escanaba River (ESCA), 

Ahnapee River (AHNA), and Manitowoc River (MANI) nonAOCs. However, because the identifications were not made 

past genus, we cannot confirm the presence of E. ischnus in 

any of our samples.

Benthos Community Comparisons to Other Studies

When values for eight invertebrate metrics from HD 

sampler data collected in the current study were compared 

quantitatively with values for data collected near the same 

AOC locations in 2003 through 2005 by Weigel and Dimick 

(2011), little difference was found between the two studies 

for these metrics as a group. Three sites, the Fox River near 

De Pere (FOXD), and the Lower Menominee (MENI) and 

Sheboygan River (SHEB) AOCs, had a single metric value 

that was significantly different between the studies. At FOXD, 

chironomids were dominant, making up 62 percent of the total 

taxa in 2005, and this was more than twice the highest value 

in 2012 (31.7 percent in spring, p=0.06). For MENI, the large 

river IBI scored 45 (fair) in 2005, and that was significantly 

higher (p=0.01) than the 2012 IBIs, which scored 15 (very 

poor) for spring and 20 (poor) in summer and fall. At SHEB, 

the percentage of Ephemeroptera-Plecoptera-Trichoptera taxa 

was 2.56, which was significantly (p<0.05) higher in 2003 

compared to all seasons in 2012, which scored <1. There were 

no significant differences in metric values between 2005 and 

2012 at the Milwaukee River (MILR). Although the large river 

IBI is designed for use in riverine sections with flows of at 

least 0.09 meters per second, this flow threshold may not have 

been met at times in our study, especially in the Milwaukee 

Estuary AOC; therefore values may not be comparable to 

other locations and studies.

Previous studies of the Lower Green Bay and Fox River 

AOC found the benthos to be low in diversity and predominantly tolerant tubificid oligochaete worms and chironomid 

midge larvae (Ankley and others, 1992; Balch and others, 

1956; Federal Water Pollution Control Administration, 1968; 

Howmiller and Beeton, 1971; Integrated Paper Services 

Inc., 2000; Surber and Cooley, 1952; Wisconsin Department 

of Natural Resources, 1993; Wisconsin State Committee 

on Water Pollution, State Board of Health, and Green Bay 

Metropolitan Sewerage Commission, 1939). A study by 

Canfield and others (1996) found that oligochaete worms 

and chironomid midge larvae made up over 90 percent of the 

benthos at three Great Lakes AOCs. The change from rocky to 

soft, silty bottom substrates along with toxins and low oxygen 

levels in the lower Fox River and into Lower Green Bay 

near the river’s mouth was accompanied by a change in the 

benthos from a mix of tolerant and intolerant taxa, to mostly 

tolerant taxa, to a lack of even tolerant taxa (Balch and others, 

1956). Burrowing mayfly larvae (Hexagenia sp.), which are 

referred to as “fish flies” or “Green Bay flies” when adults, 

were abundant in the 1930s although the larvae were found in 

low densities in dredge samples of Lower Green Bay in 1938 

and 1939 (Wisconsin State Committee on Water Pollution, 

State Board of Health, and Green Bay Metropolitan Sewerage 

Commission, 1939). The larvae also were collected at 

16 of 51 stations in surveys of Green Bay by Balch and others 

(1956), but rarely in later years (Ball and Patterson, 1985; 

Wisconsin Department of Natural Resources, 2013b). 

Studies in the late 1970s and early 1980s found low 

diversity and a dominance of pollution tolerant taxa—

primarily oligochaetes—in the Milwaukee and Menomonee 

rivers (Wisconsin Department of Natural Resources, 1991). 

River studies have been done of benthos in the Sheboygan 

River AOC (Wisconsin Department of Natural Resources, 

2012b) so historical comparisons are difficult to make. A 

study in 1997 using dredge grabs found immature tubificid 

oligochaetes made up over 90 percent of the benthos communities at most Sheboygan River sites sampled, and analyses 

of a subset of these sites determined that there were just two 

species present: Limnodrilus hoffmeisteri and Limnodrilus 

cervix (EVS Environment Consultants Inc. and National 

Oceanic and Atmospheric Administration, 1998). Our dredge 

samples at the Sheboygan River AOC in 2012 found degraded 

diversity and over 80 percent dominance by abundant 

immature tubificid oligochaetes and adult oligochaetes 

were primarily of the species Limnodrilus hoffmeisteri and 

L. cervix. These results suggest the Sheboygan River benthos 

community in 2012 had changed little since 1997.
Summary and Conclusions 23

Phytoplankton Community Comparisons to 

Other Studies

Historical studies in 1938 and 1939 in Lower Green Bay 

and the Fox River found zooplankton such as rotifers and 

microcrustaceans were usually present in low numbers 

(Wisconsin State Committee on Water Pollution, State Board 

of Health, and Green Bay Metropolitan Sewerage Commission, 1939). Later studies in the 1980s found rotifer abundance 

higher than that of microcrustaceans in the lower eutrophic 

portion of Green Bay (Richman, Bailiff, and others, 1984; 

Richman, Sager, and others, 1984). In a study of Green Bay 

and near the mouth of the Fox River, the phytoplankton 

found in 1938 and 1939 (Wisconsin State Committee on 

Water Pollution, State Board of Health, and Green Bay 

Metropolitan Sewerage Commission, 1939) included mostly 

diatoms and blue-green algae, with blooms of toxin-producer 

Aphanizomenon. Later surveys found plankton communities 

dominated by blue-green algae and small crustaceans, both 

with limited food value to consumer organisms. Studies of 

the plankton during the 1980s found green algae dominant 

(as much as 80 percent) in the lower eutrophic portion of 

Green Bay (Richman, Bailiff, and others, 1984; Richman, 

Sager, and others, 1984).

The MMSD collected zooplankton and phytoplankton 

periodically from 1980 through 1997 in the Milwaukee 

Estuary AOC using methods fairly similar to those used in this 

study. Zooplankton were collected using an 80-micrometer 

mesh plankton net with vertical hauls from 1 m off the bottom 

to the surface, and phytoplankton were collected using a 

whole water sampler, but depth was not specified. Most 

MMSD sites were in the outer harbor and nearshore areas of 

Lake Michigan near Milwaukee, but one site, NS 28 (also 

called OH 1), was near the Milwaukee Harbor (MILH) subsite 

sampled in 2012 for this study. At the MMSD site, rotifers and 

copepods were the dominant zooplankton present in samples 

during 1980–97. Rotifers were the dominant (59 to 75 percent) 

zooplankton in all seasons at MILH in 2012. However, zebra 

mussel veligers were subdominant (22 to 35 percent) in 2012, 

and copepods and cladocerans were only minor components 

of the community. For rotifers, Filinia longiseta was dominant 

during 1980–85, with species of Synchaeta, Keratella, 

and Brachionus subdominant; however, during 1988–97, 

F. longiseta was no longer a dominant rotifer and, instead, the 

previously subdominant taxa began to be dominant. Synchaeta 

oblonga was the dominant rotifer in the spring and summer of 

2012 at MILH, and Keratella crassa was dominant in the fall 

of 2012. The dominant copepod taxa during 1980 –94 were 

Cyclopoid copepods and unidentified immature copepods—

nauplii and copepodids or copepodites; during 1995–97, 

the copepods were predominantly nauplii and the taxon 

Diacyclops thomasi, a Cyclopoid copepod. The copepod taxa 

in 2012 appeared grossly similar to 1995–97, with nauplii and 

Cyclopoid copepodites dominant and Calanoid copepodites 

subdominant. Harpacticoid copepods, a benthic taxon, were 

reported first in the 1997 sample in low abundance, and 

these copepods were present in 2012 also in low abundance. 

For cladocerans, Bosmina longirostris was the dominant 

cladoceran species in all MMSD samples as well as in 2012 

at MILH, and Ceriodaphnia lacustris and Diaphanosoma 

birgei were subdominant in the summer and fall 2012 samples, 

respectively. 

In the MMSD phytoplankton samples collected near 

MILH, diatoms and green algae were generally the dominant 

algal group, followed by blue-green algae and (or) cryptophytes, depending on the season. In 2012, diatoms were the 

dominant group (58 percent) in spring, cryptophytes were 

dominant (50 percent) in summer, and green algae (37 percent) 

and blue-green algae (36 percent) were codominant in fall 

(fig. 8). Diatom taxa were identified beyond phylum in about 

one third of the MMSD samples and, in those cases, dominant 

taxa varied by season and year, so comparisons are difficult 

and not attempted here. Changes in dominance from diatoms 

to other algal groups can indicate short-term and long-term 

declines in water quality. 

Summary and Conclusions

The non-AOCs selected as comparison sites in this study 

were the best available with regard to being less impaired, 

having similar physical characteristics to the AOCs, and 

being located in the Great Lakes region. When the benthos or 

plankton community at an AOC is rated as more impaired than 

one of these non-AOC comparison sites, whether or not the 

non-AOC(s) have some impairment themselves, it emphasizes 

the finding of impairment at the AOC. Conversely, a finding of 

no statistical difference between a community or sample at an 

AOC community and selected non-AOCs does not mean that 

the benthos or plankton community at an AOC is unimpaired. 

It is critical to consider a variety of measures when 

comparing communities at an AOC with one or more less 

impaired sites because some measures address only a single 

aspect of the community. Use of both structural measures 

that relate to the relative numbers of different organisms (for 

example, richness, diversity, and relative abundance) and 

functional measures that relate to the role or preferences of 

different organisms (for example, environmental tolerances) 

is important in any complete assessment of ecological status. 

An aquatic community can change in many ways without a 

significant change in richness or structural diversity, such as 

when more tolerant taxa replace less tolerant taxa or when 

green or blue-green algae replace diatoms. Multivariate 

statistical analyses such as MDS and ANOSIM may be more 

sensitive at detecting community change than diversity or 

richness metrics because multivariate methods test differences 

based the specific taxa present at each site. However, in this 

study, the metric comparisons detected differences between 

AOCs and non-AOCs that the multivariate comparisons often 
24 Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan

did not, possibly because the multivariate tests highlight 

different aspects of these communities or because a metric 

may have had a lower variability and thus smaller differences 

could be detected statistically. An IBI combines structural and 

functional measures and may therefore be a more effective 

measure to use for defining differences or change. At present, 

there are no zooplankton or phytoplankton IBIs for use in 

rivermouths or harbors. The benthos IBI for rivermouths and 

harbors may be more valuable with the addition of functional 

and tolerance information for oligochaetes due to their importance in these ecosystems and the range in environmental 

preferences for this large and diverse group of organisms.

With regard to the BUI for benthos at the sampled 

AOCs, predominant taxa at sites were oligochaetes and 

chironomid midges. The benthos at the Lower Menominee 

and Milwaukee Estuary AOCs were rated as degraded overall 

because the metrics for more than one season or at more than 

one comparison level were rated as degraded. The Milwaukee 

Estuary AOC benthos samples were mostly comprised of 

immature tubificid oligochaetes at the three subsites (MILR, 

MENO, and MILH) except for the fall sample from MILH

which, as mentioned earlier, had zebra mussels in greater 

abundance than oligochaetes. Those oligochaete taxa that were 

identified to species included generally tolerant ones such as 

Limnodrilus hoffmeisteri. 

In the Lower Green Bay and Fox River AOC, the two 

Fox River subsites (FOXR and FOXD) sampled in this 

study were not rated as degraded for benthos in more than 

one season or event in comparison to non-AOCs. Although 

abundant in some historical samples, our study found 

Hexagenia sp. larvae only in dredge samples from the Lower 

Menominee River (MENI) and its paired non-AOCs, the 

Escanaba River (ESCA) and Oconto River (OCON). Sediment 

size fraction analyses showed that the substrates in those 

particular dredge samples had a high proportion of sand (at 

least 80 percent), unlike the substrate in the Lower Green Bay 

and Fox River samples collected as part of our study. 

AOC zooplankton communities appeared to be less 

impaired than benthos communities when compared to the 

non-AOC sites, which may be due to greater effects of historic 

sediment contamination on benthos communities. Zooplankton 

at the AOCs were not statistically different from non-AOCs 

as a group or from non-AOC pairs when compared across all 

seasons; FOXR and MILR were rated as degraded overall for 

zooplankton richness based on comparisons for one season to 

either non-AOCs as a group or to their non-AOC comparison 

sites. Zebra mussel veligers were in the top three dominant 

taxa of the zooplankton community in 2012 in the Milwaukee 

Estuary AOC for all seasons at MENO and for summer at MILR. 

No AOC was rated as degraded for phytoplankton in 

comparison to the non-AOCs but samples at some sites 

contained large percentages of nondiatoms, including 

blue-green algal taxa that are known to form toxins. Bluegreen algae dominated the phytoplankton communities 

at the Lower Green Bay and Fox River AOC, comprising 

over 50 percent of the total abundance in spring and up to 

87 and 92 percent, respectively, in fall samples. Although 

over 70 percent of the spring phytoplankton community in 

the Sheboygan River AOC was green algae, the community 

transitioned to increasing percentages of diatoms and eventual 

dominance by diatoms in the fall sample. Phytoplankton 

communities in the Milwaukee Estuary AOC were diverse, 

but nondiatoms were dominant at sites in two-thirds of the 

samples, indicating that the community is impaired. It is 

important to consider which groups of algal taxa are dominant 

in making assessments of site integrity because dominance 

by green or blue-green algae is indicative of water quality 

impairment due to eutrophication.

Further study after removal of historic sediment contamination at each of these AOCs should show improvements in 

benthos and plankton communities, although recovery may be 

complicated by other stresses such as excessive nutrients and 

invasive taxa. The magnitude of effort required to remediate 

these sites cannot be understated, and this report provides 

important information for evaluating the status of these 

communities in 2012.

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Manuscript approved June 17, 2016

Prepared by the USGS Science Publishing Network

Madison and Reston Publishing Service Centers

For more information concerning this report, 

please contact:

Director, Wisconsin Water Science Center

U.S. Geological Survey

8505 Research Way

Middleton, WI 53562

http://wi.water.usgs.gov
Scudder Eikenberry and others—Comparison of Benthos and Plankton for Selected Areas of Concern and Non-Areas of Concern in Western Lake Michigan—Scientific Investigations Report 2016–5090

ISSN 2328-0328 (online)

http://dx.doi.org/10.3133/sir20165090