A Product of the Great Lakes Restoration Initiative

Great Lakes Restoration Success through Science

U.S. Geological Survey Accomplishments 

 2010 through 2013

Circular 1404

U.S. Department of the Interior

U.S. Geological Survey

Great Lakes Restoration Success through Science

Great Lakes Restoration

Success through Science

U.S. Geological Survey Accomplishments 2010 through 2013

U.S. Geological Survey

A product of the Great Lakes Restoration Initiative

Circular 1404

U.S. Department of the Interior

U.S. Geological Survey
ii

U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2014

First Printing: 2015

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Suggested citation:

U.S. Geological Survey, 2014, Great Lakes restoration success through science—U.S. Geological Survey accomplishments 2010 through 2013: U.S. Geological Survey Circular 1404, 58 p, http://dx.doi.org/10.3133/cir1404.

ISSN 1067-084X (print)

ISSN 2330-5703 (online)
iii

Dear Reader, 

The Great Lakes Restoration Initiative (GLRI), implemented in 2010, brought 

together stakeholders from across the region in an effort to restore the Great Lakes 

and protect them for future generations. The U.S. Geological Survey (USGS) is 

proud to be a partner in this unprecedented restoration effort by providing 

scientific information and monitoring data needed to address many of the issues 

facing the Great Lakes. The USGS has a long history of conducting scientific 

research in the Great Lakes Basin, and the resulting knowledge and information is 

the foundation of our GLRI science strategy. 

We have structured our science to meet the goals and objectives of each of the five 

GLRI Focus Areas described in the GLRI Action Plan, and are working closely with 

our Tribal, Federal, State, and local agencies and other stakeholders to achieve 

these goals. We are also strategically looking ahead to ensure that we continue to 

meet the science needs of resource managers and advance the new GLRI Action 

Plan for 2015. As GLRI begins its sixth year of restoration work, the issues being 

addressed are becoming more complex and need greater input from the scientific 

community to achieve successful restoration.

Our scientists have been gathering data on the Great Lakes and the rivers and 

streams that flow into them to assess water quality and availability; providing 

the science to restore fish habitat in Areas of Concern to create healthier aquatic 

ecosystems; examining food web changes and effects on the health of the Great 

Lakes; developing cutting-edge technologies to control invasive species; and taking 

numerous other science actions to contribute to the restoration efforts.

We are excited to share this publication with you, which highlights many of our 

science accomplishments and describes how new science findings, data, tools, 

and technologies can help restore and revitalize the Great Lakes for the people of 

the Great Lakes region and the Nation!

— Leon Carl, 

Regional Director, Midwest Region, 

U.S. Geological Survey
iv
v

Contents

Introduction.....................................................................................................................................................1

Highlights—Cleaning Up Toxic Substances and Areas of Concern .....................................................3

Enhancing Fish Habitat in the Huron-Erie Corridor.........................................................................4

Identifying Sources of Toxic Contaminants......................................................................................8

Studying Mercury Processes ...........................................................................................................10

Using Birds as Indicators of Toxic Exposure..................................................................................13

Supporting Restoration of Beneficial Uses in Areas of Concern by Using Measures 

of Plankton and Benthos Conditions..................................................................................16

Highlights—Preventing and Controlling Invasive Species...................................................................19

Developing Innovative Control Strategies for Phragmites ..........................................................20

Developing Control Tools and Strategies for Asian Carp.............................................................22

Preventing Spread of Dreissenid Mussels.....................................................................................24

Highlights—Promoting Nearshore Health .............................................................................................27

Evaluating Best Management Practices in Targeted Geographic Watersheds ......................28

Estimating Real-Time and Forecasted Nutrient and Sediment Loads .......................................31

Enhancing Water-Quality Decision-Making at Great Lakes Beaches.......................................33

Highlights—Protecting and Restoring Habitat and Wildlife ................................................................37

Supporting Restoration of Native Fish in Lake Ontario ................................................................38

Supporting Restoration of Coastal Wetlands in the Ottawa National Wildlife 

Refuge and Adjacent Lake Erie...........................................................................................40

Developing Breakthroughs in the Prediction and Prevention of Botulism Outbreaks............42

Surveying Food Web Interactions within All Five Great Lakes ...................................................45

Highlights—Tracking Progress and Working with Partners ................................................................49

Supporting Lakewide Action and Management Plans.................................................................50

Characterizing Rivermouth Ecosystems .........................................................................................52

Watershed Modeling for Stream Ecosystem Management........................................................54

The Future of Communicating Science for GLRI ....................................................................................56

(Photo left) Collecting water samples from the Nemadji River in Wisconsin. Water samples have been collected from 

59 major tributaries to the Great Lakes, including the Nemadji River, to locate the sources of contaminants and to 

estimate the amount of the contaminants flowing into the Great Lakes. Photograph by Austin Baldwin, USGS.
Multitudes of prey fish are using the restored habitat at Crane Creek wetland (Lake Erie) now that they have access. Photograph by Kurt Kowalski, USGS.
 1

Introduction

The Great Lakes (Superior, Michigan, Huron, Erie, and Ontario) are the largest group of 

freshwater lakes on Earth and serve as an important source of drinking water, transportation, 

power, and recreational opportunities for the United States and Canada. They also support an 

abundant commercial and recreational fishery, are crucial for agriculture, and are essential to 

the economic vitality of the region. The Great Lakes support a wealth of biological diversity, 

including over 200 globally rare plants and animals and more than 40 species that are found 

nowhere else in the world. However, more than a century of environmental degradation has 

taken a substantial toll on the Great Lakes. To stimulate and promote the goal of a healthy 

Great Lakes region, President Obama and Congress created the Great Lakes Restoration 

Initiative (GLRI) in 2009. The GLRI is an interagency collaboration that seeks to address the 

most significant environmental problems in the Great Lakes ecosystem. The GLRI is 

composed of five focus areas that address these issues:

Cleaning up toxic substances and Areas of Concern,

Preventing and controlling invasive species,

Promoting nearshore health,

Protecting and restoring habitat and wildlife

Tracking progress and working with partners.

As of August 2013, the GLRI had funded more than 1,500 projects and programs of the 

highest priority to meet immediate cleanup, restoration, and protection needs. These projects 

use scientific analyses as the basis for identifying the restoration needs and priorities for the 

GLRI. Results from the science, monitoring, and other on-the-ground actions by the 

U.S. Geological Survey (USGS) provide the scientific information needed to help guide the 

Great Lakes restoration efforts. This document highlights a selection of USGS projects for each 

of the five focus areas through 2013, demonstrating the importance of science for restoration 

success. Additional information for these and other USGS projects that are important for 

Great Lakes restoration is available at http://cida.usgs.gov/glri/glri-catalog/.
Researchers inspect egg mats that had been placed in the St. Clair River to 

determine whether fish successfully used the new reefs for spawning. This 

buoy-less method for sampling fish eggs and spawning activity using egg 

mats deployed on the river bottom was developed by the USGS for sampling 

early life stages of lake sturgeon and other fish.
Cleaning Up Toxic Substances and Areas of Concern 3

Highlights

Cleaning Up Toxic Substances and Areas of Concern

Although many sources of contamination have been reduced, legacy contamination remains 

in the Great Lakes area. “Legacy contamination” is contamination largely left over from 

past practices but that continues to recirculate through the environment. These legacy 

contaminants often are persistent toxic substances, such as mercury, banned pesticides, 

polycyclic aromatic hydrocarbons (otherwise known as PAHs and are components in asphalt 

and coal tar), and polychlorinated biphenyls (otherwise known as PCBs). These legacy 

contaminants continue to be present in the environment at levels above those considered 

safe for humans and wildlife, sometimes warranting fish consumption advisories in the 

Great Lakes and connecting channels. In addition to the legacy contaminants, contaminants 

of emerging concern, such as pharmaceuticals, have been detected in the Great Lakes in 

recent years and also pose potential but unknown threats to the ecosystems. Altered or 

destroyed habitats in Areas of Concern—places in the Great Lakes with the largest legacies of 

toxic contamination—also affect Great Lakes ecosystems, causing degraded fish and wildlife 

populations, which is one of 14 Beneficial Use Impairments (BUIs) in Areas of Concern. 

A BUI is a change in the chemical, physical, or biological integrity of the Great Lakes system 

sufficient to cause any of 14 use impairments (http://epa.gov/greatlakes/lakeerie/buia/index.

html). Progress in cleaning up toxic substances and enhancing habitat in Areas of Concern is 

critical to public health, and to the health of fish and wildlife. Efforts to clean up toxic 

substances and to address BUIs are underway in the 30 U.S. Great Lakes Areas of Concern as 

part of the GLRI. As part of this effort, the USGS is working with others to improve the health 

of the Great Lakes fisheries by enhancing fish habitat for the Huron-Erie Corridor; identifying 

the types and locations of legacy contaminants and contaminants of emerging concern in 

major tributaries to the Great Lakes; examining mercury processes including how mercury 

enters the food chain, how it affects the fish, and how that affects public health; using birds 

as indicators of contaminant exposure in the Great Lakes; and supporting restoration of 

beneficial uses in Areas of Concern by using measures of plankton and benthos condition.
4 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Enhancing Fish Habitat in the Huron-Erie Corridor

The Huron-Erie Corridor is the international waterway that connects Lake Huron and Lake Erie, including the 

St. Clair River, Lake St. Clair, Detroit River, and western 

Lake Erie. The Huron-Erie Corridor supports more than 65 

species of fish, of which 16 are classified as threatened or 

endangered, and is one of the busiest navigation centers in 

the United States. Historically, the Huron-Erie Corridor supported a highly productive fishery, providing spawning and 

nursery habitat for 80 fish species including lake trout, lake 

sturgeon, lake whitefish, lake herring, walleye, and yellow 

perch. Fish productivity in the Huron-Erie Corridor was dramatically reduced over the last century due to construction 

of shipping channels, which has severely altered fish habitat, 

including spawning grounds and nursery habitats. The St. 

Clair River and Detroit River are Areas of Concern for the 

Great Lakes.

The USGS and partners are supporting restoration and 

enhancement of native fish habitat and populations in the 

Huron-Erie Corridor as part of the GLRI. The USGS and 

Huron-Erie Corridor Initiative partners (http://huron-erie.

org/) are developing science-based adaptive management 

strategies to help restore habitats and native fish in the corridor, ultimately providing societal, economic, and environmental benefits to the Great Lakes region. Adaptive management is a systematic approach for improving resource 

management by learning from management outcomes. 

Guided by a science-driven adaptive management framework, researchers are identifying, assessing, and prioritizing sites for fish spawning habitat construction and fish and 

nursery habitat restoration to address beneficial use impairments (BUIs) in the Detroit River and St. Clair River Areas 

of Concern and to help define what constitutes adequate 

restoration in the Areas of Concern. A BUI is a change in the 

chemical, physical, or biological integrity of the Great Lakes 

Lake St. Clair

Lake Erie

Lake Huron

ONTARIO

MICHIGAN St. Claire River

Detroit River

Restorations Sites 

Completed reefs

Planned reefs under construction 2013

Potential restoration sites 2014–2015

EXPLANATION

Lake St. Clair

Lake Erie

Lake Huron

ONTARIO

MICHIGAN St. Claire River

Detroit River

Restoration Sites 

Completed reefs

Planned reefs under construction 2013

Potential restoration sites 2014–2015

EXPLANATION

More than 14,000 samples of fish eggs and larvae have been collected at 

sites throughout the Huron-Erie Corridor (map, lower left) and across many 

habitat types. Pre- and post-construction monitoring near constructed 

spawning reefs (photo, upper left) demonstrated an immediate response by 

more than 14 native fish species, including lake sturgeon.
system sufficient to cause any of 14 use impairments (http://

epa.gov/greatlakes/lakeerie/buia/index.html). Restoration 

of functional spawning habitat in the Huron-Erie Corridor is 

critical to allowing fish populations to reproduce and maintain sustainable populations of sport and commercial fish.

The USGS is providing vital information to define restoration targets in Areas of Concern and is measuring restoration success through assessments of pre- and post-habitat 

construction. Monitoring information collected for this 

project indicate that restored habitats are attracting a variety 

of fish species, including multiple threatened species. Ongoing sampling is providing information on the timing and 

spatial distribution of fish spawning, abundance and survival 

of fish eggs, and production of larvae necessary for restoration efforts. Data gathered from this project also are used to 

validate and improve models used to predict spawning areas 

for lake sturgeon, walleye, and lake whitefish that would be 

suitable for spawning reef construction. Seven additional fish 

spawning habitat projects are planned for construction in the 

St. Clair and Detroit Rivers by 2015. With funding support 

from the GLRI, more than 20 acres of fish spawning habitat 

will be restored in the Huron-Erie Corridor by 2015. Habitat assessment and restoration techniques developed in the 

Huron-Erie Corridor through this project could be applied 

to other Great Lakes connecting channels, such as the St. 

Marys River (connecting Lakes Superior and Huron) and the 

Niagara River and Welland Canal (connecting Lakes Erie 

and Ontario). To ensure that information generated through 

this project is accessible by local communities, an outreach 

partnership with Michigan Sea Grant was developed. Ultimately, this project will enhance ecologically and economically valuable fish populations in the Huron-Erie Corridor, 

and contribute to the revitalization of the region.

Enhancing Fish Habitat in the Huron-Erie Corridor 5

Researchers sampling larval fish using bongo nets to collect larvae 

drifting along the river bottom (below) and lake whitefish sac fry larvae 

(above). Ongoing sampling provides information on the timing and 

spatial distribution of fish spawning, fish eggs, and larvae necessary for 

restoration efforts. 

Researchers capturing a lake sturgeon (lower right) and collecting a lake 

sturgeon on restored spawning grounds in the lower St. Clair River (page 6). 

Pre- and post-construction monitoring near constructed spawning reefs 

demonstrated an immediate response by more than 14 native fish species, 

including spawning by lake sturgeon, listed as a threatened species in both 

Michigan and Ontario.
“This work is assisting resource management agencies in developing 

science-based restoration criteria in the Areas of Concern. Both the 

restoration of important fish spawning habitat and evaluation of those 

projects are improving fish populations throughout the Huron-Erie 

Corridor, as well as improving future projects by using an adaptive 

approach.”

—Jim Francis, Lake Erie Basin Coordinator for the 

Michigan Department of Natural Resources, 

Fisheries Division 

6 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013
Enhancing Fish Habitat in the Huron-Erie Corridor 7

This northern madtom (Noturus stigmosus) was captured in a minnow trap near a constructed spawning reef in the Detroit River. 

Since 2010, nine northern madtoms, which are endangered in Michigan and Ontario and are considered globally rare, have 

been captured in the Detroit River. Assessment data have revealed that madtoms use the constructed reefs 

for habitat, indicating that these reefs are contributing to the recovery plan for this rare and valuable 

native fish. Photograph by Andrew Muir, Great Lakes Fishery Commission.

Early Successes

• Two techniques were developed for sampling 

early life stages of lake sturgeon and other fish 

in the Detroit River, which is a deep, flowing 

Great Lakes connecting channel: (1) buoy-less 

method for sampling fish eggs and spawning 

activity using eggs mats deployed on the river 

bottom and (2) a D-frame drift net system 

to assess larval lake sturgeon for use in the 

deeper Detroit River using an anchor and 

buoy system (http://dx.doi.org/10.1111/j.1439-

0426.2011.01828.x). The techniques are now 

being widely used by USGS in collaboration 

with Federal and State partners to assess habitat 

restoration efforts in the St. Clair and Detroit 

Rivers. 

• USGS scientists identified nine sites for fish 

spawning habitat restoration in the Detroit 

River and in the St. Clair River with deep, 

fast-flowing water suitable for spawning by 

native fish species. These sites were identified by using monitoring data collected for 

this project in conjunction with a geographic, 

hydrodynamic model (http://dx.doi.org/10.1016/j.

jglr.2014.02.002).

• Spawning reefs were constructed in the Detroit 

and St. Clair Rivers. The positive response of 

lake sturgeon to a spawning reef constructed in 

2008 in the Detroit River was documented in a 

2011 journal article (http://dx.doi.org/10.1111/

j.1439-0426.2011.01829.x)

• Since 2010, nine northern madtoms (a freshwater catfish), which are considered endangered in 

Lakes Michigan and Ontario and globally rare, 

have been captured in the Detroit River. Assessment data have revealed that the madtoms use 

the constructed reefs created in the Detroit River 

(http://dx.doi.org/10.1016/j.jglr.2014.01.005).

2013 Successes

• The construction of three additional spawning 

reefs was completed in 2013. These fish 

spawning reefs are used by at least 14 species 

of native fish, including economically important 

walleye, lake sturgeon (threatened in Michigan 

and Ontario), and lake whitefish.

• Four years of intensive field sampling was 

completed in 2013 at sites throughout the HuronErie Corridor and across many habitat types to 

evaluate fish spawning and nursery habitats. This 

work provides new and critical information for 

measuring the success of the restored spawning 

reefs to inform future habitat restoration efforts.

• Physical habitat characterization efforts that 

began in 2012 continued in 2013. The habitat 

data from these efforts are being used to evaluate potential sites for restoration efforts. A total 

of 71 sonar transects were run at 1 site in the 

Detroit River and 4 sites in the St. Clair River. 

These transects totaled more than 106 kilometers 

in length. More than 70 underwater video drift 

transects also were completed.

• An article was published describing the diet, age, 

and growth of larval (age-0) deepwater sculpin 

(a deepwater fish), transport of larvae through 

the St. Clair-Detroit River system, and the 

potential for larvae to drift from Lake Huron 

through the Huron-Erie Corridor and help 

restore populations in the lower Great Lakes 

(http://dx.doi.org/10.1016/j.jglr.2013.07.004). 

Deepwater sculpins are a preferred prey of lake 

trout and burbot (a cod-like fish) that reside in 

the deep offshore waters of the Great Lakes.

• An article describing results of fish habitat 

assessments and fish use of nearshore habitats 

in the Detroit River was published (http://dx.doi.

org/10.1016/j.jglr.2013.10.001). Results of diet, 

age, and growth analyses are presented for native 

fishes as well as for the invasive round goby 

(a small, soft-bodied fish). Rehabilitation and 

maintenance of nearshore embayments in efforts 

to provide adequate resources for larval and juvenile fishes will result in enhanced recruitment of 

larval fishes and add resilience to populations.
Identifying Sources of Toxic Contaminants

The USGS is analyzing water and sediment samples for legacy contaminants and contaminants of emerging 

concern at 59 tributaries to the Great Lakes, including many 

sites in Areas of Concern (places in the Great Lakes with the 

largest legacies of toxic contamination), to locate sources 

of these contaminants and to estimate the amount of these 

contaminants flowing into the Great Lakes. Monitoring at 

tributary sites provides important baseline information that 

can be used to measure progress towards restoration goals 

and assess new threats. This information also provides an 

understanding of how these contaminants reach the Great 

Lakes and where they originate, so that future restoration 

actions can be assessed. This work is coordinated with the 

U.S. Environmental Protection Agency, U.S. Army Corps of 

Engineers, U.S. Fish and Wildlife Service, individual States, 

many local agencies, and other monitoring and modeling 

entities.

Preliminary monitoring information indicates that the 

toxic substances found most frequently in water samples 

include polycyclic aromatic hydrocarbons (PAHs), pesticides, 

fragrances, flame retardants, and chemicals used in the 

manufacture of other substances. The legacy contaminants 

polychlorinated biphenyls (PCBs) in sediment samples from 

several tributaries were found at concentrations likely to affect 

aquatic life. Concentrations of legacy pesticides, such as 

DDT, were present in watersheds with a variety of land cover 

ranging from mostly urban to mostly agricultural. Human 

waste indicators, such as human-specific viruses and bacteria, 

and wastewater-specific trace organic compounds, were 

detected in all tributaries monitored, with the greatest concentrations in urban streams, followed by agricultural streams, 

and, at lower concentrations, in forest streams. Genetic 

markers of one or more pathogenic (disease-causing) bacteria 

were detected in 74 percent of all water samples analyzed for 

these genes. Knowing which contaminants are most problematic and where they are found provides important information 

to decision makers to help prioritize watersheds for restoration, 

develop strategies to reduce contaminants, and measure the 

success of those efforts in meeting restoration goals. 

Monitoring site at the Clinton River at Mount Clemens, Michigan, with 

custom automatic sampling system for monitoring waterborne pathogens, 

human-specific bacteria, mercury, and trace organic chemicals. 

Photograph by Peter Lenaker, USGS.

8 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

(Below left) The USGS is identifying the types and spatial distribution of 

legacy contaminants and contaminants of emerging concern in the water 

and sediments in the Great Lakes at Area of Concern sites. Decision makers 

can use this information to prioritize watersheds for restoration, develop 

strategies to reduce contaminants, and measure the success of those efforts 

in meeting restoration goals.
Identifying Sources of Toxic Contaminants 9

Early Successes

• Initial monitoring effort was completed at 59 major 

tributary sites in fall 2010 to provide critical information 

for restoration efforts.

• Water samples were collected in 2010 and 2011 at 

57 sites and analyzed for 69 legacy contaminants (such as 

mercury) and contaminants of emerging concern (such as 

pharmaceuticals).

• Passive samplers were deployed at 55 sites in the fall of 

2010. These samplers passively accumulated contaminants 

from the water column over a period of 1 month and were 

analyzed for more than 170 legacy contaminants (such 

as PCBs and pesticides) and contaminants of emerging 

concern (such as pharmaceuticals and flame retardants). 

• A total of 165 water samples collected from 22 tributary 

sites during the recreational season in 2011 were analyzed 

for fecal indicator bacteria and pathogenic bacteria 

including Shigella, Campylobacter, and Salmonella.

• Intensive sampling was performed at 17 monitoring sites 

2013 Successes

to characterize variability in the types and concentrations 

of toxic contaminants by season and flow. Water samples 

were collected approximately monthly and during highflow events and analyzed for 69 chemicals including 

pesticides, flame retardants, solvents, PAHs, and fuels. 

This monitoring provides information on which 

contaminants are most problematic and where they are 

found—important information to decision makers to help 

prioritize watersheds for restoration, develop strategies 

to reduce contaminants, and measure the success of those 

efforts in meeting restoration goals.

• Samples from eight of the intensive sampling sites were 

analyzed for mercury and waterborne pathogens (organisms capable of causing disease, such as enteric viruses, 

that may be transmitted through water and acquired 

through ingestion, bathing, or by other means), including 

human viruses, bovine viruses, pathogenic bacteria, 

protozoa, and human-specific bacteria. Analysis of data is 

in progress to provide important baseline information that 

can be used to measure progress towards restoration goals 

and assess new threats.

• At 15 Area of Concern sites, sediment samples were 

collected and analyzed for legacy contaminants (such as 

PCBs and pesticides) to provide a baseline for measuring 

restoration outcomes.

Lake Superior

Lake Erie

Lake Ontario

L

a

k

e

Mi chigan

Lake

Huro

n

Fox

Bad

Ford

Rocky

Rouge

Rifle

Burns

Oswego

Maumee

Raisin

Paw Paw

Oconto

Peshtigo

St. Regis

Black

Grass

Genesee

Grand

Black

HuronVermilion

Sandusky Portage

Huron

Clinton

Black

Saginaw

Au Sable

White

Grand

White

Raquette

Cuyahoga

Manistee

Muskegon

St. Joseph

Escanaba

Sturgeon

Montreal

Tonawanda

Indiana Canal

Manitowoc

Menominee

Ontonagon

Presque Isle

Thunder Bay

Cheboygan

Kalamazoo

Sheboygan

Pigeon

Manistique

Oswegatchie

Cattaraugus

Tahquamenon

Pere Marquette

Milwaukee mouth

St. Louis

Nemadji

Wisconsin

M i c h i g a n

Illinois

Indiana Ohio

Pennsylvania

New York

Minnesota

CANADA

UNITED STATES

Land cover

EXPLANATION

Tributary sampling site

Watershed boundary

State boundary

Open water

Developed, open and low 

intensity

Developed, medium and high 

intensity

Forest, shrubland, herbaceous, 

and barren

Planted/cultivated

Wetland

0 50 100 150 200 Miles 25

(Above map) Water and sediment samples from 59 tributaries to the 

Great Lakes are being analyzed for toxic contaminants.
Studying Mercury Processes

Mercury is a highly toxic substance that is found naturally in the environment but can also be 

released into the air through industrial activity, such 

as from coal-burning power plants. Mercury falls from 

the air and can accumulate in streams, wetlands, and 

oceans, where it can be transformed into methylmercury (the type of mercury that can be most harmful to 

humans) through chemical processes in the environment. Fish absorb the methylmercury as they feed 

in contaminated waters, and it builds up in the fish 

because it is not easily excreted. Humans, especially 

pregnant women and young children, risk ingesting 

dangerous levels of mercury when they eat contaminated fish. As of 2006, mercury was responsible for 

80 percent of the fish consumption advisories posted in 

the United States, and high levels of mercury are still 

found in sport and commercial fish across the Great 

Lakes Basin. Understanding the sources and processes 

that control the formation and movement of methylmercury is critical to reducing fish mercury levels and 

improving the overall health of the Great Lakes and 

its ecosystems. The USGS is working to improve the 

health of the Great Lakes sport and commercial fisheries by studying the processes that result in mercury 

entering the food chain, determining how mercury 

affects the fish, and helping to evaluate the implications for public health. As part of this effort, USGS 

scientists in collaboration with the U.S. Environmental 

Protection Agency are sampling throughout the Great 

Lakes and establishing the relations between the 

Large patches of Cladophora, a genus 

of green algae, line the shore of 

Lake Michigan in Chicago, Illinois. 

Significant methylmercury formation 

occurs in the Great Lakes in the 

nearshore zone when large masses of 

Cladophora wash ashore. Background 

photograph by Ashley Spoljaric, USGS.

(Map, right) Spatial distribution of 

methylmercury concentrations in surface 

water across the Great Lakes. Results show 

differences among the lakes and regions 

within each lake where more or less 

methylmercury is present. Lake Michigan 

has some of the highest concentrations of 

methylmercury whereas Lake Superior has 

some of the lowest. 

EXPLANATION

Methylmercury 

 concentration

0.05 (high)

0.00 (low)

Sampling location

(nanograms per liter)

Source: Esri, DigitalGlobe, GeoEye, i-cubed, USDA, USGS, AEX, Getmapping, Aerogrid, IGN, IGP, swisstopo, and the GIS User Community

Lake Superio r

Lake Huron

Lake Michigan

L a k e E r i e

Lake

Ontario
various chemical forms of mercury and their concentrations in the water column (from the water surface to the 

bottom sediments) and where mercury is found in the 

food web. 

Monitoring for this study has produced new data on 

total mercury and methylmercury in the water column 

of the Great Lakes to help evaluate mercury in sediment, plant, and animal life. In addition, two previously 

unrecognized sources of methylmercury were identified. The first source is the formation of methylmercury 

within the lakes themselves, deep in the lake’s water 

column near the thermocline (the point where warm 

and cold water meet). The thermocline is a location of 

significant importance for biological production and fish 

foraging. The second source identified is in the nearshore zone where large masses of a certain type of algae 

(Cladophora) accumulate and wash ashore every year. 

The comprehensive dataset and the new understanding 

of methylmercury sources for the Great Lakes will help 

inform decision makers and restoration managers on 

effective steps toward reducing mercury contamination 

in fish. 

Studying Mercury Processes 11

(Three photos this page) Sampling is facilitated with a special sampling 

device called a rosette that was purchased through the GLRI effort to 

upgrade capabilities of the U.S. Environmental Protection Agency’s 

Research Vessel Lake Guardian. The device allows 12 samples to be 

collected at different depths for a single cast. 
Early Successes

• Samples of water, sediment, fish, and other aquatic 

organisms were collected during April and August 

2010–2012 during biannual (April and August) 

monitoring cruises of all five Great Lakes and were 

analyzed for mercury and methylmercury.

• A journal article (http://dx.doi.org/10.1007/s00244-

012-9767-2) was published in 2012 that increases 

the understanding of factors controlling methylmercury and inorganic mercury in lake trout from the 

Great Lakes. Results indicate that methylmercury 

elimination rates for fish have been overestimated in 

previous studies; thus, the fish have a much harder 

time ridding themselves of toxic methylmercury 

than previously thought.

2013 Successes

• The seventh and eighth sampling surveys across the 

entire Great Lakes Basin were completed to provide 

important information on the water column, bottom 

sediments, benthic fauna (organisms found on and 

within the bottom of a water body), and zooplankton 

(microscopic animals found in water bodies) at about 

80 sites during each survey. 

• Two previously unrecognized sources of methylmercury were identified: (1) within the lakes themselves, 

deep in the lake’s water column near the thermocline 

and (2) in the nearshore zone where large masses of 

a certain type of algae (Cladophora) accumulate and 

wash ashore every year.

Sample of sediment collected from Lake Michigan during a biannual 

monitoring cruise that was analyzed for mercury and methylmercury. 

Photograph by John Walker, USGS. 

USGS researchers lower a submersible light profiler into the water. 

This instrument measures how fast sunlight dissipates through the 

water column. This monitoring information is important because 

light penetration affects mercury processes and is crucial for algae 

production. 

12 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

USGS researchers collect a sediment sample from Lake Superior. 
Using Birds as Indicators of Toxic Exposure 13

The USGS is quantifying effects of legacy (historical) and newly emerging contaminants on select Great Lakes food 

chains and is evaluating exposure and effects of these contaminants on sentinel indicator species—specifically, selected 

species of birds, such as colonial waterbirds (herons and cormorants) and tree swallows. Results of this study are being used by 

State agencies and the U.S. Environmental Protection Agency 

in their assessments of beneficial use impairments (BUIs; http://

epa.gov/greatlakes/lakeerie/buia/index.html) and remedy effectiveness assessments. Birds are ideal sentinel species (a species 

whose presence, absence, or relative well-being in a given environment is a sign of the overall health of its ecosystem) because 

of their sensitivity to the presence of and changes in chemical 

concentrations in the environment. The monitoring results from 

this study are used to identify important sources and effects 

of legacy contaminants (polychlorinated biphenyls or PCBs, 

mercury, dioxins, and furans) and newly emerging toxic contaminants (such as chemicals that resist sticking or staining and 

flame retardants) to the Great Lakes ecosystem through broad 

surveillance and laboratory and field research of sentinel bird 

species. Because cleaning up contaminated areas is an important component of the GLRI program, the monitoring results 

from this study will not only contribute to assessments of Great 

Lakes ecosystem health and science-based decision-making but 

also provide a baseline for future trend analysis, including a 

determination of the effectiveness of recently remediated Areas 

of Concern and other known hotspots. This study is a close 

collaboration with the U.S. Environmental Protection Agency, 

National Oceanic and Atmospheric Administration, U.S. Fish 

and Wildlife Service, State and Tribal agencies, and others.

Using Birds as Indicators of Toxic Exposure

Reduced hatching or fledging success is one measurement that is being 

quantified at all sites to determine population viability. Photograph by 

Christine Custer, USGS.
Through 2013, detailed monitoring information on 

avian health has been collected at 52 study sites encompassing 25 Areas of Concern across all five Great Lakes. 

This monitoring information can be used to determine 

whether exposures to certain toxic chemicals are at or 

above levels of concern for reproductive problems and 

population viability. Additionally, reproductive effects and 

genetic damage are directly measured as part of this study, 

which has resulted in the most comprehensive set of avian 

data available for the Great Lakes. The monitoring data 

collected for this study are already being used by several 

States in their assessments of and potential removal of 

BUIs, which were the basis for the designation of specific 

locations as Areas of Concern. The two BUIs where these 

data are especially useful are “Bird or Animals Deformities or Reproductive Problems” and “Degradation of Fish 

and Wildlife Populations.” The monitoring data are used 

to indicate increases or decreases in contaminants, and the 

association, if any, with reproductive impairments, which 

can be used by managers to determine whether the two 

BUIs can be removed. The monitoring information also 

can be used by decision makers to prioritize watersheds 

for future restoration and provides important baseline 

information to measure the success of restoration and 

remediation activities that are ongoing or planned.

14 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

(Above) USGS researcher processes field samples. Nest boxes 

were installed in Areas of Concern. At each active nest box at the 

sites, 14 different measures of toxic exposure and effects of legacy 

contaminant and emerging contaminants are being monitored, 

including genetic damage and reproduction effects. Photograph by 

Christine Custer, USGS.

Sheboygan River 

Milwaukee (2) 

Muskegon 

Lake (2)

Lake Calumet 

area

Apostle Islands 

Green Bay 

Portage

Manistique 

Midland & Bay City 

White Lake 

Menominee 

Waukegon 

St. Clair 

River (2) 

Niagara River (2) 

Kalamazoo 

 River 

Black River 

Presque Isle 

Buffalo River 

Rochester 

New sites for 2011 

Established in 2010 

New sites for 2012 

New sites for 2013 

Cape 

Vincent (2) 

St. Marys River (2)

Ottawa Nat’l 

Wildlife Refuge 

Ottawa (3) & Maumee 

Rivers

River Raisin 

River Rouge 

Detroit River 

Clinton River 

Wild Rice Lake & 

St. Louis 

River (3)

Grand Calumet 

Torch Lake

LAKE ERIE

LAKE 

SUPERIOR

LAKE

HURON

LAKE

ERIE 

LAKE ONTARIO

L

A

K

E

M

I

C

H I

G A N

Map showing study sites where detailed monitoring information on avian health has been collected through 2013 in 25 Areas of Concern 

across all five Great Lakes.
(Above) USGS researcher checks a tree swallow nest box. The swallow’s diet consists primarily of aquatic insects that they eat within about 1 kilometer 

of their nest box, so contamination in their tissues is closely tied to sediment contamination and the cleanup of those sediments. Photograph by Christine 

Custer, USGS. (Below) Nest box in the Connor Creek landscape. Photograph by Thomas W. Custer, USGS.

2013 Successes

• Collection of baseline contaminant information 

began at five new Areas of Concern in 2013 and 

Using Birds as Indicators of Toxic Exposure 15

Early Successes

• Baseline contaminant information was collected from 

sites at all five Great Lakes at a total of 20 Areas of 

Concern during 2010 to 2012. Samples were analyzed 

for legacy and emerging contaminants. This information is critical for measuring progress of remediation 

efforts in Areas of Concern and BUI assessment.

• A web site was established to provide information and 

preliminary findings: (http://www.umesc.usgs.gov/

wildlife_toxicology/glri_project80.html).

• Several presentations, posters, handouts, and video 

were presented at meetings for the public and partners. Public meetings are an important venue to reach 

a diverse audience and provide important access to 

preliminary information about this project.

• USGS co-led the Bird or Animal Deformity or Reproductive Problem BUI workshop for the U.S. Areas of 

Concern meeting in Cleveland, Ohio, in 2012.

continued at sites established previously. Samples 

were analyzed for legacy and emerging contaminants.

• At each active tree swallow nest box at the sites, 

14 different measures of toxic exposure and effects 

of legacy contaminant and emerging contaminants 

are being measured, including genetic damage and 

reproduction effects.
Efforts to clean up contaminants from past industrial 

discharges are underway in the 30 U.S. Great Lakes 

Areas of Concern (AOCs) as part of the GLRI. Cleanup 

actions for AOCs are directed toward restoring beneficial 

uses that have been impaired. “Degradation of benthos” 

and “degradation of phytoplankton and zooplankton” are 

2 of 14 beneficial use impairments (BUIs; http://epa.gov/

greatlakes/lakeerie/buia/index.html) identified in many 

Great Lakes AOCs and refer to the negative impairment 

in the structure or function of the communities of benthic 

invertebrates (benthos) in sediments and plankton in water. 

Benthic invertebrates are macroscopic insect larvae and 

crustaceans that live on or in the bottom sediments. Plankton are microscopic plants (phytoplankton) and animals 

(zooplankton). The benthos and plankton communities are 

strongly affected by their environment and can serve as 

biological indicators of the overall condition of the aquatic 

environment. Many benthic invertebrates and plankton also 

are important components of fish diets and constitute an 

important link in the food chain. 

Recent investigations indicated that sediment and 

water-quality conditions may have improved and that 

benthos and plankton communities may have recovered 

substantially in the Rochester Embayment and Massena 

AOCs in New York. The USGS, in cooperation with the 

U.S. Environmental Protection Agency, New York State 

Department of Environmental Conservation, and others, is 

collecting data to characterize the toxicity of sediments 

and the condition or health of the benthos and plankton 

communities in the Rochester Embayment AOC and the 

St. Lawrence River and its tributaries in the Massena AOC. 

The measures will be used by the local Remediation Action 

Planning committees to determine whether water and bed 

sediments meet established criteria for removing the benthos and plankton BUIs in both AOCs. 

Community composition and toxicity results from the 

New York sites generally indicate that water and sediments 

in both AOCs currently are not toxic and should not significantly impair the health of resident benthos and plankton 

communities. The findings from relatively simple, standardized toxicity and community assessments generally show 

that most criteria for removing plankton and benthos BUIs 

can be attained in multiple AOCs across New York. Assessments of community composition and toxicity of water and 

sediments are critical to decisions regarding the potential 

removal of benthos and plankton BUIs in many AOCs.

Supporting Restoration of Beneficial Uses in Areas of Concern by

Using Measures of Plankton and Benthos Conditions
Early Successes

• Water samples from nine St. Lawrence River tributary 

sites inside the Massena AOC and five control sites 

outside the AOC were collected during May, August, 

and October 2011 and used to quantify potential toxicity 

of these whole waters to the green algae Selenastrum 

capricornutum and to the water flea Ceriodaphnia dubia. 

Data from the three water surveys were published in 

a journal article in 2012 (http://dx.doi.org/10.1016/j.

jglr.2012.09.008) that provides important information 

that managers need for BUI removal. 

• Sediment surveys were done at AOC and control sites on 

the St. Lawrence River and its tributaries in the Massena 

AOC in August 2012 to evaluate the composition of benthic invertebrate communities and toxicity of sediments.

2013 Successes

• Bed sediments were collected at seven sites inside the 

Rochester Embayment AOC and at seven control sites 

outside the AOC during summer 2013 to evaluate 

differences in the composition of benthic macroinvertebrate communities and toxicity of bed sediments.

• The toxicity of bed sediments in the Rochester Embayment and Massena AOCs was assessed with standard 

(U.S. Environmental Protection Agency) 10-day 

survival and growth toxicity tests using the midge 

(small two-winged fly) Chironomus dilutus. Percent 

survival and weight of midges after exposures were 

evaluated to determine the significance of differences 

between control and AOC sites.

• Water surveys began in the Rochester Embayment 

AOC at sites inside the AOC and control sites outside 

the AOC during August 2013, and will continue 

through 2014. 

• Acute and chronic toxicity of waters at AOC and 

control sites are being assessed by using the growth 

of the green algae Selenastrum capricornutum and the 

survival and reproductive capacity of the water flea 

Ceriodaphnia dubia in standard U.S. Environmental 

Protection Agency toxicity tests.

• Planning began in 2013 to conduct comparable 

assessments of sediment toxicity and composition of 

benthic communities at AOC and control sites in the 

Eighteenmile Creek AOC and Niagara River AOC 

during 2014‒15.

• The assessments of community composition and 

toxicity of water and sediments listed above are critical 

to decisions regarding the potential removal of benthos 

and plankton BUIs in the AOCs.

(Photos above and far left) Water samples were collected from sites 

inside and outside the Rochester Embayment and Massena Areas of 

Concern. Acute and chronic toxicity of waters from sites inside Areas of 

Concern and from control sites outside Areas of Concern were assessed 

by using the growth of the green algae Selenastrum capricornutum and 

the survival and reproductive capacity of the water flea Ceriodaphnia 

dubia in standard toxicity tests. 

The midge Chironomus dilutus was used as a surrogate to 

determine impacts to survival and growth of resident 

benthic invertebrates when exposed to sediments 

from sites inside Areas of Concern compared 

to exposure to sediments from control sites 

outside the Area of Concern. 

Measures of Plankton and Benthos Conditions 17

Researcher with the New York State Department of Environmental 

Conservation sifting debris from a benthic invertebrate sample in the 

Rochester Embayment Area of Concern in Rochester, New York.
Invasive quagga mussels. Photograph by Dan Schrimsher, California Department of Fish and Game.
Preventing and Controlling Invasive Species 19

Highlights

Preventing and Controlling Invasive Species

Enhanced prevention and control efforts are critical to halting new invasive (non-native) 

aquatic, wetland, and terrestrial species from becoming established in the Great Lakes. 

More than 180 aquatic nuisance species now exist in the Great Lakes. By rapidly 

reproducing and spreading, invasive species can degrade habitat, harm native species, 

and jeopardize food webs. Prevention is the most cost-effective approach to dealing with 

organisms that have not yet arrived and could potentially threaten the Great Lakes. New 

invasive species can be introduced into the Great Lakes region through various pathways, 

including commercial shipping, canals and waterways, trade of live organisms, and 

activities of recreational and resource users. Once invasive species establish a foothold in 

the Great Lakes, they are virtually impossible to eradicate; however, invasive species still 

need to be controlled to maintain the health of the Great Lakes ecosystem. The GLRI is 

supporting efforts to prevent and control invasive species. As part of this effort, the USGS 

is working with others to help prevent and control Phragmites (common reed), Asian carp, 

and dreissenid mussels.
20 Great Lakes Restoration—2013 Success through Science

The common reed (Phragmites australis) is a tall, invasive wetland grass that continues to spread throughout the Great 

Lakes. Phragmites alters the soil, produces copious seeds, forms 

very dense stands, and has unfavorable impacts on coastal 

resources, including critical fish and wildlife habitat and coastal 

views. Current control strategies of manipulating water levels, 

applying herbicides, mowing, and burning are time, labor, and 

resource intensive and require multiple years of follow-up to 

prove success. A recent survey from 2005 to 2009 found that 

managers spend roughly $4.6 million per year on Phragmites

management in the United States with no clear idea of the 

relation between size of the investment and management success 

(http://dx.doi.org/10.1007/s12237-013-9593-4). These findings 

highlight the need for new, innovative tools to control the spread 

of Phragmites. 

USGS scientists are testing strategies to reduce the invasive 

properties of Phragmites and minimize its competitive advantage. 

This effort includes two lines of research, gene silencing and 

microbiome manipulation. Gene silencing is a molecular genetic 

technique whereby specific traits, such as photosynthetic ability 

or flower development, can be minimized by blocking the genetic 

codes for proteins that express the traits. This technology takes 

advantage of a widely-known natural defense mechanism in 

cells known as RNA interference in which cells degrade suspicious-looking code that resembles viral RNA. The USGS Great 

Lakes Science Center has partnered with researchers at Wayne 

State University to develop technology to silence the genes in 

Phragmites that allow it to reproduce and grow. For example, if 

researchers target and silence the genetic code essential for photosynthesis, a plant will not be able to harness the sun’s energy 

and growth will be stunted. Gene silencing is a species-specific 

approach that could provide managers with new treatment options 

for invasive species without having detrimental effects on nontarget plant or animal species.

Researchers at the USGS are also exploring Phragmites control through microbiome manipulation. This research stems from 

the fact that all plants have relationships with microbes. Some of 

these relationships are mutually beneficial and can confer benefits 

(such as increased growth rate and stress tolerance) to the host 

plant. Such benefits may help Phragmites gain a competitive edge 

over other species. Therefore, opportunities exist to identify and 

disrupt these relationships as a form of control. The USGS, with 

partners at Indiana University and Rutgers University, is creating 

Developing Innovative Control Strategies for Phragmites

“Through their leadership in the Great 

Lakes Phragmites Collaborative, the 

USGS has brought both strategic vision 

and scientific rigor to the complexity 

of issues surrounding non-native 

Phragmites research and management. 

The USGS has spearheaded innovative 

research on biological control while 

simultaneously, encouraging a regional 

dialogue on the ecological, economic 

and philosophical implications of 

invasive species management, to 

maximize the collective impact of this 

growing natural resource challenge.” (Left) Stands of Phragmites are invading a Great Lakes coastal wetland near Oak 

Harbor, Ohio. This tall wetland grass was introduced from Europe in the early 19th 

century and aggressively displaces native vegetation, causing plant diversity to 

decline and critical habitat for fish and other wildlife to be altered. Photograph by 

Kurt Kowalski, USGS. 

—Heather Braun, Great Lakes Commission
a microbial inventory around the Phragmites microbiome and 

beginning to identify the roles played by the members of the 

microbial community as part of a strategy to develop management approaches that both decrease the competitive advantage 

of Phragmites and increase the competitive abilities of native 

species in restoration projects. The innovative strategies being 

developed for Phragmites will provide additional tools for 

managers in fighting invasive Phragmites and could have broad 

applications for controlling other invasive species as well. 

To further increase effectiveness of Phragmites management, the USGS formed a critical partnership with the Great 

Lakes Commission to launch the Great Lakes Phragmites

Collaborative (GLPC) in 2012. The GLPC is a regional partnership to improve communication and lead to more coordinated, 

efficient, and strategic approaches to Phragmites management, 

restoration, and research across the Great Lakes Basin. The 

GLPC serves as a communication conduit via an interactive 

Web site (http://greatlakesphragmites.net/), a webinar series, 

and social media outlets to facilitate access to information and 

resources and to encourage technology transfer and network 

building among habitat managers, governmental agencies, and 

private landowners. The GLPC embraces the idea of collective impact as a framework for solving the complex problem of 

Phragmites management. By linking researchers, managers, and 

decision makers in a coordinated way, establishing a common 

agenda, establishing shared metrics, and fostering mutually reinforcing activities, the GLPC is in a position to improve the level 

of success of Phragmites management regionwide.

Early Successes

• A study conducted in 2012 indicated that treatment of 

fungal endophytes (microbes that live in all parts of 

plants) with a general use fungicide can decrease the 

number of new Phragmites stems.

2013 Successes

• In partnership with the Great Lakes Commission, the 

USGS developed the Collaborative for Microbial 

Symbiosis and Phragmites Management composed 

of an international group of microbial ecologists 

focused on identifying the key players in the microbial community surrounding Phragmites. The group 

meets regularly and is preparing a science agenda 

manuscript for publication.

• Researchers at Wayne State University were able to 

sequence and analyze a Phragmites transcriptome 

(a genetic road map) and use results from experiments 

with model plants similar to Phragmites (such as 

maize) to expand laboratory testing of gene silencing 

techniques in Phragmites. 

• The Great Lakes Phragmites Collaborative (GLPC) 

continued to add content to its Web site, share 

information via social media, and host several wellattended (greater than 150 people) webinars on highprofile research and management topics. 

Developing Innovative Control Strategies for Phragmites 21

(Above) A USGS researcher in an invasive Phragmites stand in the Great Lakes 

area. The species is rapidly invading the few remaining marshes in the Great 

Lakes, but USGS scientists and their colleagues are using cutting-edge research 

to try to fight back. Photograph by Kurt Kowalski, USGS. (Right) Fungal microbes 

cultured from Phragmites seeds. Photograph by Zack Shearin, Indiana University.
22 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Developing Control Tools and Strategies for Asian Carp

Asian carp were originally imported from Asia to the  southern United States to control algae and unwanted 

plants in controlled settings such as water treatment lagoons. 

Flooding allowed these fish to escape into the Mississippi 

River system and migrate into the Illinois River, which 

is connected to the Great Lakes (Lake Michigan) by the 

Chicago Sanitary and Ship Canal. Asian carp have harmed the 

ecosystem, economy, property, and boaters in the Mississippi 

River system, and they are now threatening the Great Lakes. 

Four species of Asian carp are considered invasive and a 

threat to the Great Lakes: the bighead, silver, grass, and black 

carp, but the Asian Carp Control Strategy Framework (http://

asiancarp.us/) is primarily focused on silver and bighead carp. 

This Framework was developed by the Asian Carp Regional 

Coordinating Committee (ACRCC), a multiagency team led 

by the White House Council on Environmental Quality with 

the goal to prevent sustainable populations of Asian carp 

from becoming established in the Great Lakes and to reduce 

existing populations in the Mississippi River Basin. As a 

partner in these efforts, the USGS focused on developing 

control tools and technologies, methods for early detection, 

and assessing the risk of successful of Asian carp reproduction 

and survival. The overall strategy is to use an Integrated 

Pest Management approach to detect, aggregate, and remove 

Asian carp. Essential to these efforts is the application of the 

extensive knowledge of Asian carp life history that guides 

design, development, and application strategies. 

Monitoring for the presence of Asian carp by using early 

detection methods is vital in determining where to focus control measures if detected and to determine the effectiveness of 

control methods. Other types of monitoring also are important 

in combating invasive species. As an example, monitoring by 

the USGS is providing critical hourly water-level information 

at an adult Asian carp barrier fence in Eagle Marsh, a high 

risk pathway for Asian carp to migrate from the Wabash 

River to Lake Erie. When flooding raises water levels at the 

fence, alerts are sent to State and local biologists and resource 

staff who respond and inspect the fence line for adult Asian 

carp. Collectively, the lessons learned in efforts to control 

the spread of Asian carp as part of the GLRI and new control 

technologies and methods directly transfer to invasive species 

outside the Great Lakes area.

Asian carp control technologies were demonstrated in August 2013 

near Morris, Illinois, at a backwater pond of the Illinois River. State and 

Federal partners were invited to visit an application of Integrated Pest 

Management to Asian carp control. Water guns, algal feeding attractant, 

acoustic fish tracking, and commercial fishing were implemented 

in a coordinated manner to reduce the Asian carp population of the 

backwater pond. Photograph by Jon Amberg, USGS.

A USGS scientist prepares to collect data to assess how flow and water 

quality affect Asian carp movement, spawning, and recruitment from 

the Illinois River near Seneca, Illinois. Monitoring is providing a greater 

understanding of the preferred habitat of Asian carp with regards to flow 

and water-quality characteristics and insight into how habitat may be 

altered to deter them from spreading into new areas. Photograph by Jon 

Amberg, USGS.
Developing Control Tools and Strategies for Asian Carp 23

Early Successes

• Information on the developmental rate and behavior 

of early life stages of bighead carp and silver carp was 

published in 2011 (http://pubs.usgs.gov/sir/2011/5076/) 

and 2013 (http://dx.doi.org/10.1371/journal.

pone.0073829). 

• Studies of the effects of water hardness on hatching success of Asian carp eggs showed that the soft water 

of the Great Lakes is not likely to inhibit the invasion 

of Asian carp, as had previously been thought 

(http://dx.doi.org/10.1577/T09-004.1 and http://dx.doi.

org/10.1577/M09-067.1).

• Two successful examples of the use of dye tracing 

during the large-scale applications of a piscicide 

(a pesticide designed to kill fish) in the Chicago 

Sanitary and Ship Canal in 2009 and 2010 to combat 

invasive Asian carp were documented in the USGS 

report (http://pubs.usgs.gov/sir/2013/5211/). The use of 

dye allowed real-time monitoring of the piscicide plume 

to support application and deactivation strategies.

• Scientists field tested water guns, which use compressed 

air to fire a sound pressure wave into the water, to 

assess how silver and bighead carp respond to them and 

evaluate the potential use of water guns as a control tool. 

Preliminary results indicate that the carp move away 

from the water guns. Additional field tests are being 

conducted in 2014. 

2013 Successes

• In collaboration with the Illinois Department of 

Natural Resources and Southern Illinois University, 

an Integrated Pest Management approach to Asian 

carp control was used in the field, combining food 

attractants, water guns, hydroacoustics, and commercial fishing to capture and remove large numbers 

of Asian carp from an Illinois River backwater pond 

(see video at http://gallery.usgs.gov/videos/813).

• Preliminary results of field testing of water guns are 

promising for altering Asian carp behavior and can 

be used to contain, repel, or herd carp. Initial field 

testing of this technology was completed in 2013 in 

a backwater pond of the Illinois River. 

• Scientists discovered that Asian carp are strongly 

attracted to certain mixtures of algae and have been 

testing methods for using the attractants as lures to 

facilitate capture and removal. Testing was done in 

the Missouri River and Illinois River.

• Microparticles filled with a registered toxin are being 

designed to specifically target Asian carp. When 

eaten by Asian carp, the toxin is released while 

inside the fish, avoiding harm to native species. 

• A new Tributary Assessment Tool has been 

developed by the USGS in collaboration with the 

University of Illinois to assess risk of successful 

Asian carp spawning in rivers based on river length, 

water velocity, water temperature, and egg and 

larval development (http://dx.doi.org/10.1016/j.

ecolmodel.2013.05.005). The risk assessment is 

focused on egg and larval development, which 

are important knowledge for informing management control efforts. As part of this study, scientists 

discovered that river reaches as short as 16 miles 

in length may allow Asian carp eggs sufficient 

time to develop and hatch (http://pubs.usgs.gov/

sir/2013/5106/). 

• In collaboration with the U.S. Army Corps of 

Engineers and U.S. Fish and Wildlife Service, 

USGS scientists have developed faster methods 

of processing water samples to determine whether 

DNA of Asian carp is present in a water body. Early 

detection of Asian carp is of paramount importance 

in the battle against this invasive species. Scientists 

also have designed more than 20 genetic markers to 

identify silver carp and bighead carp DNA in water 

samples.

• Another early detection method being developed that 

complements the DNA efforts is microbial source 

tracking. Mapping the unique microbes present in 

the digestive systems of Asian carp holds promise 

for monitoring their presence in rivers and other 

water bodies.

These silver and bighead carp were collected from the Illinois River 

to learn more about the anatomy and physiology of Asian carp. This 

information is important to the development of potential biological 

or chemical controls as part of an Integrated Pest Management 

approach for resource managers. Photograph by Jon Amberg, USGS.
Preventing Spread of Dreissenid Mussels

The USGS is working with the U.S. Fish and Wildlife Service and other partners to find effective and safe tools to control 

and prevent the spread of invasive dreissenid mussels (namely 

zebra mussels Dreissena polymorpha and quagga mussels 

D. rostriformis bugensis) in and around the Great Lakes. Both 

the zebra and quagga mussels are small (about the size of a 

pistachio), non-native mussels that were transported to North 

America in the ballast water of transoceanic ships in the late 

1980s. These mussels quickly spread to all five Great Lakes 

causing substantial ecological and environmental impacts 

including clogging of pipes in water systems, disruption of food 

cycles, and alteration of aquatic habitats. No methods currently exist to safely control dreissenid mussels; however, new 

advances in research in identifying “weak” points associated 

with the feeding, reproductive, and other characteristics are 

paving the way for development of tools to prevent the spread 

of these invasive mussels. Research has shown that dreissenid 

mussel spawning is initiated and inhibited by natural chemical 

cues released by algae and that these natural products can be useful for control. The USGS is currently researching one of these 

weak points—natural spawning inhibitors, such as compounds 

released by specific species of algae—which could be used to 

control reproduction of this invasive species. 

Tools that target specific invasive species without harming 

other aquatic organisms, animals, or humans are needed to 

prevent the further spread of invasive species, such as dreissenid mussels, in the Great Lakes area. The invasive zebra 

and quagga mussels are an immediate threat to the survival of 

freshwater unionids, such as pocketbook mussels, in the Great 

Lakes area. One potential tool for limited open-water control 

of dreissenid mussels is the commercially formulated product, 

Zequanox®, which contains killed cells of the common soil bacterium Pseudomonas fluorescens (strain CL145A). Zequanox® is 

produced by Marrone Bio Innovations (Davis, California) and is 

registered by the U.S. Environmental Protection Agency for specific applications. Preliminary tests with Zequanox® indicate that 

this may be a promising new tool that could be used to prevent 

the spread of zebra and quagga mussels but that does not appear 

to be harmful other organisms, including the freshwater unionids. 

Comprehensive research is needed to determine the potential 

of this dreissenid management tool for use in natural aquatic 

habitats. Determining this potential may ultimately allow this 

new technology to be used to support ecosystem restoration and 

rehabilitation efforts in and around the Great Lakes. In addition, 

experiments are ongoing with Microcystis aeruginosa and other 

species of algae to discover natural product spawning inhibitors 

that could be used to control dreissenid mussels.

The preliminary testing of Zequanox® indicates that this may 

be a promising new tool that could be used to prevent the 

spread of zebra and quagga mussels but that does not appear 

to be harmful to other organisms, including the freshwater 

unionids. Photograph by James Luoma, USGS.

24 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

USGS researchers are performing tests to determine the 

mortality and stress of dreissenid mussels in response to 

Microcystis aeruginosa algae. Photograph courtesy of Donna 

Kashian, Wayne State University.
Early Successes

• In 2012, the USGS completed field studies in 

Lake Carlos in Minnesota and Shawano Lake 

in Wisconsin to assess the effectiveness of 

Zequanox® to control dreissenid mussels in a 

controlled field laboratory designed to simulate 

open water exposures. Mortality of zebra 

mussels in these studies exceeded 90 percent.

2013 Successes

• The USGS completed a field study in the 

Black River in Wisconsin to assess the impacts 

of Zequanox® exposure to seven species of 

adult native mussels, including several species 

of concern, in a controlled field laboratory 

designed to simulate open water exposures. 

There were no detrimental impacts to native 

mussels. 

• The USGS completed field studies to assess 

the effectiveness of Zequanox® to control 

dreissenid mussels adhering to native mussels 

in Lake Darling near Alexandria, Minnesota, 

and to bottom/rocky habitats in Lake Minnetonka near Alexandria, Minnesota. In field 

studies, Zequanox® treatment significantly 

reduced zebra mussel colonization of native 

mussels without increasing mortality of the 

native mussels relative to the untreated mussels. 

• Research on natural spawning inhibitors 

showed that dreissenid mussels co-cultured 

with Microcystis aeruginosa algae spawned 

significantly less frequently than those in the 

absence of Microcystis aeruginosa, whereas 

experiments showed that exposure to the 

Chlorella algae enhances the rate at which 

dreissenid mussels spawn. 

• Probes that measure eDNA (environmental 

DNA, such as from feces, mucus, skin, or urine, 

that can be used to detect aquatic organisms) 

have been developed to distinguish between 

dreissenid and native unionids. Once tested, 

these probes can be used to identify bodies of 

water where control measures are warranted.

Preventing Spread of Dreissenid Mussels 25

(Left) USGS researchers are performing tests on natural spawning 

inhibitors for quagga mussels. The male is on the left with 

the water clouded by sperm. The female is on the right, and a 

cluster of clearish-white eggs is visible on the bottom of the vial. 

Photograph courtesy of Donna Kashian, Wayne State University.

(Right) More than 40 species of freshwater mussels, such as this 

pocketbook mussel, are native to the Great Lakes, and most species are 

endangered. Photograph by Alissa Ganser, USGS. (Below) Native 

freshwater mussels are threatened by invasive species such 

as dreissenid mussels. The faster-growing dreissenid 

mussels settle on the shells of the native mussels, 

effectively smothering them. Invasive zebra mussels in 

Detroit, Michigan. Photograph by Jeff Allen, USGS.

Promoting Nearshore Health 27

Highlights

Promoting Nearshore Health 

Nearshore and open waters provide drinking water for municipalities and habitat for 

numerous species of birds, fish, and other aquatic life. This is the area in which most 

residents and visitors experience the Great Lakes through swimming, boating, and other 

forms of recreation. Nearshore water quality has become degraded, as evidenced by 

eutrophication—the process by which a water body is enriched by nutrients such as 

nitrogen and phosphorus, resulting in excessive growth of algae, depletion of the 

dissolved oxygen that aquatic species need to survive, beach closings, and other impacts. 

In the nearshore zones of the Great Lakes, eutrophication has sometimes been manifested 

by harmful algal blooms; by unsightly, odorous rotting mats of the green algae Cladophora 

washed ashore on beaches; and by avian botulism. The environmental stressors causing 

these problems include excessive nutrient loadings (the mass of nutrients carried by water 

into surrounding waterways over a period of time) from both point sources (single, discrete 

places) and nonpoint sources (broad areas, such as runoff from drainage basins); bacteria 

and other pathogens responsible for outbreaks of botulism and beach closures; development 

and shoreline hardening that disrupt habitat and alter nutrient and contaminant runoff; and 

agricultural practices, which may increase nutrient and sediment loadings. Additional 

shoreline stresses can be traced to failing septic systems, gray-water pipes (pipes containing 

nonhazardous household substances like soap), inadequate pump-out stations for 

recreational boats, and even invasive species. The GLRI is supporting efforts to promote 

nearshore health. As part of this effort, the USGS is evaluating best management practices; 

using automated samplers and probes to monitor nutrient and sediment loadings at 30 of 

the Great Lakes National Monitoring Network sites; and providing beach managers with the 

tools necessary to make effective beach closure and advisory decisions.

(Left) Monitoring by USGS provides important information about the processes that affect beach contamination 

and helps to ensure that beaches are safe for public recreational use. Photograph by Meredith Nevers, USGS.
Saginaw River

Michigan

Maumee River

Ohio

Lower Fox River

Wisconsin

East River

Alger Creek

Eagle Creek

Evaluating Best Management Practices in

Targeted Geographic Watersheds

The USGS is collaborating with the U.S. Department of Agriculture’s Natural Resources Conservation Service 

(NRCS) and U.S. Environmental Protection Agency (EPA) 

to assess the effects conservation practices have on waterquality issues as part of the Priority Watershed component of 

the GLRI. The goal of this effort is to improve and protect 

water quality and reduce the sediment and nutrients (nitrogen 

and phosphorus) flowing into the Great Lakes. Monitoring is 

being used to demonstrate the effectiveness of agricultural 

management practices in diverse landscapes in three priority 

watersheds: Fox River, Wisconsin; Maumee River, Ohio; and 

Saginaw River, Michigan. The monitoring work for this study 

ranges from the subwatershed scale to individual agricultural 

fields (edge-of-field scale) and involves the direct participation 

of local conservation groups, agricultural groups, and private 

landowners. Edge-of-field monitoring provides information 

about the amount of runoff, soil, and nutrients (such as nitrogen 

and phosphorus) moving off a given agricultural field into an 

adjacent waterway. Ongoing sampling at edge-of-field monitoring sites, as well as the subwatershed location in each of the 

three Priority Watersheds, is providing baseline information 

prior to the implementation of best management practices 

(BMPs) designed by the NRCS. At this scale of monitoring, the 

water quality, under a full range of weather conditions, can be 

affected immediately by land-use and management changes. 

Thus, the information gathered from this study will allow for 

a rapid assessment of implemented conservation practices. 

This study will be used to develop an understanding of 

the effects of differing agriculture practices on the quantity 

and quality of runoff water from monitored farms, including 

edges of fields and subsurface drains, and the effect of this 

water on streams receiving runoff water. Volumes and losses of 

sediment, nutrients, and other selected constituents are being 

quantified through monitoring. Weather data also are collected 

to help establish cause-and-effect relations between agricultural 

practices and water quantity and quality. The monitoring information collected as part of this study can be incorporated into 

models or used in education on conservation practices.

28 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

(Left upper) Map showing locations of GLRI priority watersheds. 

(Left middle) Surface runoff at an edge-of-field monitoring site on a private 

farm in the Upper East River Basin, Wisconsin.

(Left lower) Ice and snow were removed to prepare for oncoming snowmelt 

at edge-of-field (left) and subsurface tile (right) monitoring sites in the 

Upper East River Basin in Wisconsin. 
“The explosion of harmful algae growth 

from phosphorus runoff is a clear and 

present danger to community, economic 

and ecological health. This work is 

driving us to target the biggest sources 

of phosphorus to make the biggest 

difference for the most people.”

—Cameron Davis, Senior Advisor to the Administrator, 

U.S. Environmental Protection Agency, 

USGS staff finishing the installation of an edge-of-field 

(above) and subsurface-tile (below) monitoring site on a 

private farm in the Saginaw River watershed in Michigan. 

Evaluating BMPs in Targeted Geographic Watersheds 29
Early Successes

• Selection and establishment of monitoring locations 

was completed, including the coordinated effort 

between the USGS, NRCS, EPA, and private 

landowners.

• Construction of four edge-of-field stations, two subsurface drains, and three streamgages was completed 

in water year 2012 to collect baseline data prior to 

BMP implementation. (A water year is the 12-month 

period, October 1 through September 30, and is 

designated by the calendar year in which it ends.) 

• Data collection at the monitoring sites began in water 

year 2012.

2013 Successes

• Data collection at the monitoring sites continued. 

Measurement devices monitor the amount of runoff from 

the agricultural field on a continuous basis in intervals 

of every 1 to 5 minutes during rainfall events and every 

15 to 60 minutes at all other times. The water-quality 

sampler is triggered automatically by runoff or activated 

remotely from the USGS office. 

• Collected samples are analyzed for nutrients and other 

constituents at the Water and Environmental Analysis 

Lab in Stevens Point, Wisconsin.

• Annual updates were provided to EPA and NRCS 

partners as well as to the local conservation staff and 

participating landowners on monitoring results and uses.

“We know many conservation practices can improve water quality, and we are 

always looking for ways to enhance that effectiveness. Edge-of-field monitoring 

stations allow us to measure the benefits of conservation for improving water 

quality right at the edge of farm fields, rather than assume conservation effects 

from in-stream measurements that are subject to influences outside of the 

farmer’s control. Such influences include legacy nutrient and sediment inputs, 

as well as other land uses within a watershed.”

—Dr. Wayne Honeycutt, Deputy Chief for Science and Technology, 

U.S. Department of Agriculture 

Natural Resources Conservation Service

USGS staff finishing installation of the wingwall at an edge-of-field 

monitoring site in the Blanchard River Basin in Ohio. 

30 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Finalized subsurface-tile monitoring site using solar power located 

on a private farm in the Blanchard River Basin in Ohio.
Estimating Real-Time and Forecasted Nutrient and Sediment Loads 31

Estimating Real-Time and Forecasted 

Nutrient and Sediment Loads

Nitrogen and phosphorus are essential nutrients for plant and animal growth, but overabundance of these nutrients leads to one of the most 

widespread, costly, and challenging contamination 

problems in water in the United States. Sediment 

is the loose sand, clay, silt and other soil particles 

that settle at the bottom of a body of water, and 

sediment generally originates as soil erosion from 

locations such as agricultural and construction 

sites. Sediment is the most common contaminant 

in rivers, streams, lakes, and reservoirs, according 

to the U.S. Environmental Protection Agency. 

Excessive nutrients and sediment can hamper 

water supplies and recreation, and can cause harm 

to ecosystems. USGS scientists are collecting 

nutrient, sediment, streamflow, and other data 

from 30 monitoring sites on streams that flow into 

the Great Lakes (“tributaries”). These data will 

provide baseline information on the amount of 

nutrients and sediment that are being transported 

to the lakes, enable managers to determine whether 

restoration and remediation projects are having 

the desired effect on improving water quality, and 

provide real-time reporting of water quality by the 

use of sensors. In the future, the data can be used 

in computer models to forecast changes in the 

amount of sediments and nutrients being transported to the Great Lakes. 

A key component of the GLRI tributary 

monitoring program is the use of real-time sensors 

to estimate nutrient and sediment concentrations. 

Scientists are working to predict nutrient and 

sediment concentrations by the use of statistical 

models that are based on water-quality data 

transmitted from sensors. These models will 

enable real-time prediction of nutrient and sediment concentrations, and computer models will 

eventually allow predictions from unmonitored 

streams. 

(Above) Sediment and algae color the Great Lakes in this image captured by the 

Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua satellite 

on October 9, 2011. The blue in Lake Michigan and Lake Huron is sediment 

brought to the surface when strong winds churned the lakes. The green in 

Lake Erie and in Lake Huron’s Saginaw Bay is toxic algae, Microcystis 

aeruginosa, that forms readily in nutrient-rich water. Image courtesy of NASA. 

(Right) About 2,000 samples have been collected and analyzed for 

nutrients and suspended sediment through August 2013 for this project. 

Photograph by Austin Baldwin, USGS.
Early Successes

• A USGS report published in 2011 contains a list of existing 

watershed models that had been created for tributaries within 

the United States that drain to the Great Lakes (http://pubs.

usgs.gov/of/2011/1202/).

• Thirty monitoring sites were equipped with automated 

samplers and real-time water-quality monitoring sensors 

starting in March 2011. At each site, monthly samples have 

been collected, and as many as six samples per year have 

been collected during large rainfalls.

2013 Successes

• Monitoring data were collected at the sites for the third 

year in 2013. About 2,000 samples (about 75 samples 

per monitoring site) had been collected and analyzed for 

nutrients and suspended sediment as of August 2013 to help 

predict nutrient concentrations.

• Real-time sensors measured dissolved oxygen, turbidity 

(the cloudiness of water), specific conductance (a measure of 

water’s ability to conduct electricity, and therefore a measure 

of the amount of dissolved solids such as salt in the water), 

pH, and water temperature every 15 minutes for the third 

year in 2013, enabling scientists to compare data over time 

and look for changes. All real-time water-quality data are 

available at http://waterwatch.usgs.gov/wqwatch/ for use by 

resource managers and other partners.

• Progress was made toward developing models for the 

Kalamazoo River in Michigan and Tonawanda Creek in 

New York. These watershed models will be used to simulate 

hydrology, water temperature, and phosphorus and sediment 

concentrations and loads.

USGS scientists are collecting nutrient and sediment samples from 

30 monitoring sites on tributaries flowing into the Great Lakes. 

Photograph by Mark Godfrey, The Nature Conservancy.

32 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

The Bad River in northern Wisconsin is one of 30 monitoring sites 

where nutrient and sediment samples are being collected. Monitoring 

is crucial to documenting real-time changes in nutrient and sediment 

loads to the Great Lakes. Photograph by Eric Dantoin, USGS.

Fox

Bad St. Louis

Ford

Rouge

Rifle

Burns

Oswego

Maumee

Raisin

St. Regis

Genesee

Black Vermilion

Portage

Huron

Clinton

Saginaw

Au Sable

Grand

Cuyahoga

Muskegon

St. Joseph

Indiana Canal

Manitowoc

Menominee

Ontonagon

Kalamazoo Milwaukee Cattaraugus

0 50 100 150 200 Miles 25

Wisconsin M i c h i g a n

Illinois

Indiana

Ohio

Pennsylvania

New York

Minnesota

CANADA

UNITED STATES

Land cover

EXPLANATION

Tributary sampling site

Watershed boundary

State boundary

Open water

Developed, open and 

low intensity

Developed, medium and 

high intensity

Forest, shrubland, 

herbaceous, and barren

Planted/cultivated

La

Wetland ke Superior

Lake Erie

Lake Ontario

Lake Michigan

Lake

Huron

Map showing locations of tributaries 

monitored for real-time and forecasted 

nutrient and sediment loading. 
Enhancing Water-Quality Decision-Making at Great Lakes Beaches 33

Enhancing Water-Quality Decision-Making 

at Great Lakes Beaches

Water recreation and associated tourism provide numerous economic opportunities and societal benefits 

to the Great Lakes region with its more than 500 beaches and 

nearly 11,000 miles of coastline. Unfortunately, coastal areas 

can become contaminated with disease-causing microorganisms of fecal origin that threaten the health of people who 

swim in coastal waters. Some beaches have become fouled 

with excess quantities of the algae Cladophora, which may 

harbor human and animal pathogens and produce offensive 

odors that discourage use of beaches by the public. Beach 

advisories and closures are intended to protect swimmers from 

illness caused by fecal contamination. However, several problems face beach managers who issue advisories or closures or 

try to solve contamination problems: (1) traditional laboratory 

analyses for beach water quality take too long, (2) sources of 

fecal contamination in recreational water are often unknown, 

(3) recreational waters are seldom monitored for actual pathogens (disease-causing bacteria, viruses, and protozoa), and 

(4) monitoring strategies and storage of monitoring data are 

sometimes inconsistent between beaches. 

The USGS has been a leader in the science of beach 

health with an overall mission to provide science-based 

information and methods that allow beach managers to 

more accurately make beach closure and advisory decisions, 

understand the sources and physical processes affecting beach 

contaminants, and mitigate and restore beaches and protect 

the public. The USGS is working in collaboration with many 

Federal, State, and local agencies and universities to improve 

beach health and enhance decision-making through realtime assessments of recreational water quality; research on 

the types pathogens present at beaches and use of microbial 

source tracking to determine potential contamination sources; 

and development of tools to aid in data discovery, aggregation, 

and processing to supplement current research needs.

The USGS has been a leader in the science of beach health, with an overall 

mission to provide science-based information and methods that will allow 

beach managers to more accurately make beach closure and advisory 

decisions, understand the sources and physical processes affecting beach 

contaminants, and mitigate and restore beaches and protect the public. 

Photograph, left, by Richard Whitman, USGS.
Water quality can change rapidly at beaches in 

response to varying weather conditions and other factors 

such as currents and waves, sewer overflows, and even 

the number of birds and visitors at the beach. Predictive 

modeling of real-time water-quality conditions (nowcasting) using environmental and water-quality data is an 

important tool for quickly making management decisions on beach advisories or closures. A nowcast system 

(for example, see http://www.ohionowcast.info/index.

asp) estimates current water-quality conditions, and the 

results are posted at the beach and online to inform the 

public. Research efforts on pathogens and microbial 

source tracking for Great Lakes beaches are providing 

information about the types of pathogens present at Great 

Lakes beaches, their relations to fecal indicator bacteria, 

and their sources (such as humans, mammals, and birds). 

Coastal research by USGS scientists is providing important information about the processes that affect beach 

contamination. These findings help establish factors that 

affect fluctuations in microorganism concentrations and 

highlight potential approaches for beach restoration. The 

Great Lakes Beach Health Database currently holds more 

than 7,000 records from sanitary surveys from Great 

Lakes beaches in Wisconsin, New York, Michigan, and 

Ohio. (For more information on the database, see http://

pubs.usgs.gov/fs/2013/3068/.) Data used in the study of 

recreational waters are sometimes inconsistent because 

data are compiled by numerous agencies in a variety of 

formats, making data discovery, compilation, and data 

analysis difficult. Data analyses are being aided through 

the use of the database and associated Web applications 

for standardizing output formats and data visualization.

(Above) USGS dive team members carry an Acoustic Doppler Current 

Profiler (ADCP) into Lake Michigan near Portage, Indiana, to measure 

currents throughout the summer season in order to improve predictive 

modeling at recreational beaches and better predict bacteria 

concentrations in the water, thereby improving the safety of swimmers. 

Photograph by Kasia Kelly, USGS. (Photo immediately right) USGS 

scientists tested different filtration methods for concentrating microbial 

indicators and pathogens in lake water samples at Point Beach, 

Wisconsin. Photograph by Jeff Steuer, USGS.

Beaches like this one (above) on Lake Michigan in Illinois can become 

contaminated with disease-causing bacteria that threaten public health, 

disrupt water recreation, and affect the Great Lakes economies that 

depend on summer tourism. Photograph by Richard Whitman, USGS. 

Similar to weather forecasts, the nowcast systems use near-realtime information to estimate water-quality conditions and bacteria 

concentrations at specific beaches in the Great Lakes region, such 

as at Edgewater Beach in Ohio. Nowcast systems use mathematical 

models that are developed from several years of measurements made 

at particular sites. The USGS is committed to helping beach managers 

develop and implement nowcast programs. Photograph by Donna 

Francy, USGS.

34 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013
Enhancing Water-Quality Decision-Making at Great Lakes Beaches 35

Early Successes

• USGS fact sheets on understanding beach health 

throughout the Great Lakes were published in 2010 

and 2012 (http://pubs.usgs.gov/fs/2010/3093/ and 

http://pubs.usgs.gov/fs/2012/3113/).

• USGS scientists have performed research to identify 

sources of contamination and the environmental 

factors that may create a situation where unhealthy 

bacteria or viruses can live and pose a threat to public 

health. Various processes investigated include sediment transport, wave heights and resuspension of contaminants from beach sands; diurnal pattern of fecal 

indicator bacteria (decrease through daylight hours and 

rebound after dark); changes in lake and groundwater 

levels; and tributary inputs. 

• More than 300 samples were collected in 2010 from 

12 Great Lakes beaches (Lake Michigan, Huron, and 

Erie) and analyzed for waterborne pathogens. Analyses 

indicate that pathogens were not uniformly distributed 

among the 12 beaches (http://dx.doi.org/10.1021/

es402299a). This research helps to increase the understanding of the factors that influence fecal indicator 

bacteria, pathogen occurrence, and microbial sources 

at Great Lakes beaches.

• Real-time assessments of recreational water-quality 

conditions (called nowcasts) were expanded 

throughout the Great Lakes. During 2010–12, the 

USGS worked with 23 local and State agencies to 

improve existing operational beach nowcast systems 

at 4 beaches and expand the use of predictive models 

in nowcasts at an additional 45 beaches throughout the 

Great Lakes in Illinois, Indiana, Michigan, New York, 

Ohio, Pennsylvania, and Wisconsin. During validation of 42 beach models in 2012, the models overall 

performed better than the current method to assess recreational water quality (using the previous day’s E. coli

concentration) (http://pubs.usgs.gov/sir/2013/5166/).

• The USGS created a Great Lakes Beach Health 

Database that uses a Web tool for easy access to beach 

health data from numerous agencies collecting data 

across the Great Lakes region (http://cida.usgs.gov/

enddat/). 

2013 Successes

• Four USGS fact sheets were published in 2013 highlighting USGS research on Great Lake beaches:

• Real-time assessments of water quality (nowcasts) 

(http://pubs.usgs.gov/fs/2013/3069/)

• Pathogens (http://pubs.usgs.gov/fs/2013/3071/)

• Coastal processes (http://pubs.usgs.gov/

fs/2013/3070/)

• Tools for beach health data management 

(http://pubs.usgs.gov/fs/2013/3068/)

• A USGS report on potential sources and transport 

processes of fecal indicator bacteria to beach water at 

Murphy Park Beach on Green Bay in Wisconsin was 

published (http://pubs.usgs.gov/sir/2012/5190/). This 

research helps to increase understanding on transport 

processes affecting fecal indicator bacteria at beaches.

• A journal article comparing filtration methods for 

concentrating microbial indicators and pathogens 

in lake water samples was published (http://dx.doi.

org/10.1128/AEM.03117-12). Different filtration 

methods worked best for individual microorganisms; 

however, the ultrafiltration method resulted in the 

highest recovery while maintaining low variability for 

the nine microorganisms tested (bacteria, viruses, and 

protozoa).

• A journal article was published that examines the new 

recreational water-quality criteria and how differences 

in available methods that are used to classify beach 

water as exceeding a “beach action value” can result in 

variations in how often a beach is posted with an advisory or closing (http://dx.doi.org/10.1021/es304408y).

• The USGS tested two rapid analytical methods to 

detect fecal-indicator bacteria and pathogenic organisms in beach water—quantitative polymerase chain 

reaction (qPCR) and immunomagnetic separation 

with adenosine triphosphate detection (IMS/ATP). 

These rapid analytical methods can provide results in 

2 to 3 hours—a substantial improvement compared to 

traditional methods that take 18 to 24 hours. Because 

substantial water-quality change can occur quickly, the 

safety of the water can be more accurately assessed by 

using the rapid analytical methods, thus providing an 

improved tool to beach managers. 

• The USGS continued to work with local agencies 

to improve real-time predictions and implement 

more nowcast systems (see http://www.ohionowcast.

info/ and http://www.wibeaches.us/apex/

f?p=BEACH:HOME). 
36 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013
Protecting and Restoring Habitat and Wildlife 37

Highlights

Protecting and Restoring Habitat and Wildlife 

The health of Great Lakes habitats and wildlife depends upon the protection and restoration 

of ecosystems. Fully resilient ecosystems buffer the impacts of potential problems such as 

climate change. A multitude of threats—among which is competition from invasive 

species—affect the health of Great Lakes habitats and wildlife and have led to an altered 

food web, loss of biodiversity, and, in places, poorly functioning ecosystems. Scientists are 

researching particular human effects on the ecosystems and are applying lessons learned 

from past and ongoing restoration projects and programs to advance protection and 

restoration of habitat and wildlife. As part of the GRLI, the USGS is working with others to 

support the protection and restoration of critical elements of the Great Lakes ecosystem by 

providing the science to restore native fishes in Lake Ontario, restore coastal wetlands in 

the Ottawa National Wildlife Refuge and adjacent Lake Erie, develop breakthroughs in the 

prediction and prevention of botulism outbreaks that affect fish and fish-eating birds, and 

survey food-web interactions within all five Great Lakes. 

Lake herring (left) along with Atlantic salmon smolts (page 39) are being raised at the USGS Tunison Laboratory of Aquatic Science for release into Lake 

Ontario and tributaries. This laboratory’s state-of-the-art capabilities for holding wild-captured eggs and raising fish for release and would not have been 

possible without GLRI funding. Photo credits: Marisa Lubeck, USGS, and Emily Waldt, Tunison Laboratory of Aquatic Science.
38 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Supporting Restoration of Native Fish in Lake Ontario

The USGS is taking an innovative approach to supporting restoration by simultaneously helping to restore native 

predator fish and their native food sources (prey fish) in 

Lake Ontario. These species are Atlantic salmon and two 

whitefishes. Restoring them at the same time increases the 

prized predator’s chance of survival. Historically, the Lake 

Ontario population of Atlantic salmon represented the largest 

freshwater population of salmon in the world, but overfishing 

and loss of spawning habitat led to their local extinction in 

Lake Ontario in the late 1800s. Two whitefishes—deepwater 

cisco (also known as bloater) and a shallower water species, 

lake herring—are either extirpated (bloater) or have declined 

dramatically (lake herring) in Lake Ontario because of 

invasive species, such as alewife and rainbow smelt. Bloater 

and lake herring were once very abundant in Lake Ontario, 

serving as important prey for native salmon and lake trout, 

and supporting commercial fisheries. Although populations 

of deepwater cisco and lake herring have persisted in Lakes 

Superior, Michigan, and Huron, the deepwater cisco disappeared from Lake Ontario by the 1970s, and lake herring 

population declined dramatically by the mid-1900s. 

The USGS focus on providing the science to restore 

Atlantic salmon, deepwater cisco, and lake herring in Lake 

Ontario and its tributaries, marks a first-of-its-kind effort in 

the region. A state-of-the-art experimental fish culture facility 

has been established with funds from the GLRI at the USGS 

Great Lakes Science Center, Tunison Laboratory of Aquatic 

Science in Cortland, New York, where USGS scientists are 

working to support restoration of these native fishes in Lake 

Ontario and the St. Lawrence River by raising and stocking 

them, and evaluating the success of these efforts. Working 

closely with the State of New York, the St. Regis Mohawk 

Tribe, and Ontario governments, the USGS is ensuring that 

scientifically based techniques and strategies are used to maximize rehabilitation success and avoid potential fish diseases. 

All stocked fish are marked with a dye that allows researchers 

to monitor fish survival.

Reintroduction of Atlantic salmon is expected to provide 

greater fishing opportunities in Lake Ontario and restore the 

natural balance of the Lake Ontario food web by adding more 

predator fish to the system. Reintroduction of deepwater cisco 

and lake herring is essential for increasing food choices and 

enhancing the natural recruitment potential of predator fish, 

such as Atlantic salmon and lake trout. Restoration of native 

fish is also expected to mitigate previous effects of invasive 

species, such as alewife and rainbow smelt, and reduce 

opportunities for new invasive species to colonize the lake 

by increasing food web resistance to invasion. Restoring a 

resilient native fish community in Lake Ontario is a critical first 

step not only to strengthen the local fish ecosystem, but also to 

guide native species restoration throughout the Great Lakes. 

(Right) Stocking of Atlantic salmon will increase fishing opportunities in 

Lake Ontario and restore the natural balance of the food web through providing 

additional top predators. Thousands of young Atlantic salmon were reared at 

the USGS Tunison Laboratory and released into the St. Regis River system 

(a tributary of the St. Lawrence River) by USGS scientists and members of the 

Mohawk Tribe. Photograph by Tony David, St. Regis Mohawk Tribe.

An Atlantic salmon is marked with a dye that will allow researchers to 

evaluate poststocking success. Photograph by Emily Waldt, Tunison 

Laboratory of Aquatic Science.

Deepwater cisco are being raised at the USGS Tunison Laboratory of Aquatic 

Science for release into Lake Ontario and tributaries. Photograph courtesy of 

Tunison Laboratory of Aquatic Science.
Supporting Restoration of Native Fishes in Lake Ontario 39

Early Successes

• The state-or-the art culture facility at Tunison Laboratory 

of Aquatic Science became operational in 2011 to enable 

restoration of Atlantic salmon in Lake Ontario and the 

St. Lawrence River through development of new and 

innovative restoration techniques.

• Atlantic salmon were raised at the Tunison Laboratory of 

Aquatic Science and multiple salmon strains were evaluated 

to determine their suitability for restoration. The salmon 

were released in Lake Ontario tributaries during 2011 and 

2012 in collaboration with the St. Regis Mohawk Tribe and 

the New York State Department of Environmental Conservation (NYDEC). 

• Deepwater cisco and lake herring also were raised at the 

Tunison Laboratory of Aquatic Science and were first 

released in 2012 in partnership with the NYDEC. 

2013 Successes

• The following native fishes were released in 2013:

• 17,000 yearling Atlantic salmon smolts in Lake Ontario 

tributaries in April,

• 65,000 fall fingerling Atlantic salmon in Lake Ontario 

tributaries in September,

• 9,000 fall fingerling lake herring into Irondequoit Bay 

in Lake Ontario in November, and

• 7,200 fall fingerling deepwater cisco in Lake Ontario 

near Oswego, New York in November.

• In July 2013, scientists captured the first returning adult 

Atlantic salmon that had been released as part of the GRLI. 

Two wild Atlantic salmon fry 

were captured in the 

Salmon River in July of 2013,

which represented documented 

evidence of natural reproduction 

in the Salmon River. 

These successes highlight 

the importance of monitoring 

fish survival in evaluating 

restoration progress.

“Lake Ontario’s sport fisheries are 

a significant economic driver in 

New York State, and were valued at 

more than $113 million in 2007. 

Re-establishing bloaters in 

Lake Ontario will diversify the fish 

community, adding stability to the 

lake’s ecosystem and sport fisheries.”

—Joe Martens, New York State Department 

of Environmental Conservation Commissioner
40 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Supporting Restoration of Coastal Wetlands in the

Ottawa National Wildlife Refuge and Adjacent Lake Erie

The western shore of Lake Erie has lost more than 95 percent of its wetland habitat since the 1860s. Most of the coastal wetlands 

were isolated from Lake Erie by an extensive network of earthen 

dikes that were constructed to protect habitat from wave attack. The 

diked wetlands historically provided critical migratory waterbird 

habitat, but their isolation from Lake Erie limits certain wetland 

functions such as providing fish habitat and improving water quality. 

The few remnant coastal wetlands (that is, the wetlands still 

connected to Lake Erie) have been severely degraded by altered 

hydrology, nutrient and sediment loading, and invasive species. 

This collective loss of suitable coastal wetland habitat has negatively 

affected the habitats for about 43 species of important Great Lakes 

fish that depend on productive wetland habitats to feed (such as longnose gar, channel catfish, and bowfin), to spawn (such as northern 

pike and yellow perch), or to provide protection for juveniles (such 

as gizzard shad, emerald shiner, and largemouth bass). 

USGS scientists are focused on supporting the restoration of 

natural water flow and ecological processes between diked coastal 

wetlands and major adjacent water bodies (Lake Erie) to improve 

fish and wildlife habitat. Flow reconnection and habitat restoration 

strategies were tested initially at the U.S. Fish and Wildlife Service 

(USFWS) Ottawa National Wildlife Refuge as part of the GLRI 

and through partnerships with the USFWS, Ducks Unlimited, and 

many others. A water-control structure (opened in March 2011) 

restored hydrologic connection for the first time in nearly 40 years 

between a 99-acre diked coastal wetland and Crane Creek, a tributary to Lake Erie. This control structure allows exchange of water, 

fish, mussels, and other wildlife and provides a unique opportunity 

to quantify the response of reconnected wetlands through field 

sampling of fish, birds, invertebrates, plants, water quality, and 

water levels.

Intense data collection by the USGS and close interaction with 

refuge managers and other partners have led to an unprecedented 

look at the wetland ecosystem response to a large restoration action, 

implementation of adaptive management practices, and recognition 

of water-quality improvements associated with habitat restoration 

(Left upper) Constructed water-control structure connecting a managed 

pool to Crane Creek wetland (Lake Erie). This water-control structure 

allows critical fish passage between Lake Erie and the previously diked 

wetland. Photograph by Kurt Kowalski, USGS.

(Left middle) Sampling for this study indicates water-quality improvements 

since the wetland was reconnected to Lake Erie. Photograph by Kurt 

Kowalski, USGS. 

(Left lower) Northern pike depend on productive wetland habitats for 

spawning, and are an example of a fish species positively affected by the 

reconnection of a diked wetland to Lake Erie. 
in the Maumee River Area of Concern. The reconnection has 

improved habitat for commercially and recreationally important fish while maintaining high quality habitat for migratory 

waterbirds. Water-quality improvements (such as reduced 

phosphorous load to Lake Erie) associated with this type of 

wetland restoration were observed and provided baseline data 

used to support similar restoration efforts in the Maumee Area of 

Concern, Saginaw Bay/River Area of Concern, and other Great 

Lakes coastal areas. This project has developed a foundation 

of sustainable approaches that can be used as a model in other 

regions of the Great Lakes basin to restore coastal wetland 

function and increase ecosystem resilience.

Early Successes

• Fish diversity and abundance in the restored wetland 

has increased dramatically since reconnection. Sixteen 

new fish species were found to be using the restored 

wetland.

• The availability of wetland habitat was crucial in 2012 

when low water levels stranded some coastal wetlands 

and drought contributed to dry conditions in many 

diked wetlands in the area. However, the reconnected 

wetland held water throughout the summer and was 

used extensively by migrating waterfowl in the 

autumn.

2013 Successes

• Waterfowl and piscivorous (fish-eating) bird usage 

of the wetland increased after the reconnection to 

Lake Erie. 

• The wetland has been serving as a nursery and breeding grounds for many species including northern 

pike, largemouth bass, white and black crappies, and 

numerous species of sunfish. High resolution sonar 

data have shown that fish access the wetland at all 

times of the day from late winter to late autumn. 

• Fish species richness and abundance in the restored 

wetland increased substantially (more than 10 times in 

some cases) since wetland habitats were reconnected.

• Invasive common carp were effectively excluded 

from the restored wetland habitat through the use of 

specially designed gates in the water-control structure 

that allow northern pike and other native fish to pass 

into the wetlands but exclude mature breeding size 

carp.

• The reconnected wetland continues to be a sink for 

phosphorus, nitrogen, and sediment from Crane 

Creek. High levels of sediment and nutrient retention 

(approximately 50 percent) have been observed during 

the passage of storm or flood events that move large 

quantities of water into the wetland.

Supporting Restoration of Coastal Wetlands in the Ottawa National Wildlife Refuge and Adjacent Lake Erie 41

Sampling for wetland fish provides important information on the success of habitat restoration efforts. Photograph by Kurt Kowalski, USGS. 
42 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Developing Breakthroughs in the Prediction and

Prevention of Botulism Outbreaks

Botulism outbreaks are causing extensive mortality of fish and fish-eating birds in the Great Lakes. Botulism 

is a form of “food poisoning” that results from ingestion of 

neurotoxins produced by the naturally occurring bacterium 

Clostridium botulinum, which leads to paralysis and death 

of intoxicated animals. The toxin is thought to accumulate in 

some species of fish, which are then eaten by birds. Periodic 

outbreaks of type E botulism have occurred in the Great Lakes 

since at least the 1960s, but outbreaks have become more 

common and widespread since 1999, particularly in Lakes 

Michigan, Erie, and Ontario. Concurrent with outbreak resurgence, non-native zebra and quagga mussels and round gobies 

invaded the Great Lakes, but the role these invasive species 

play in the outbreaks has not been fully identified. Botulism 

has been responsible for the deaths of more than 100,000 birds 

and countless fish in the Great Lakes since 1999 including the 

federally endangered piping plover, common loons, and lake 

sturgeon.

The USGS is bringing together scientists with diverse 

areas of expertise to address botulism outbreaks in the 

Great Lakes through the GLRI. This team of experts, which 

includes the USGS, National Park Service, U.S. Fish and 

Wildlife Service, state wildlife agencies in Michigan and 

Wisconsin, and other organizations, is taking a comprehensive approach to understanding what factors need to link 

together to trigger a botulism outbreak, and how future 

outbreaks can be predicted and prevented in the Great Lakes. 

To accomplish this goal, scientists are developing methods 

to detect the presence of botulinum toxin in the environment and determining how the botulinum toxin reaches bird 

populations through Great Lakes food webs.

The development of a new method to test for the botulinum toxin is a major step forward in the study of botulism 

outbreaks in the Great Lakes and can be applied to other 

locations. Understanding how the botulinum toxin moves 

up the food chain from the lake sediments to birds is a key 

component to understanding how botulism outbreaks occur. 

Monitoring information collected for this study indicates 

that Clostridium botulinum may occur in high abundance 

in decomposing Cladophora algae. The toxin likely moves 

from bacteria in lakebed sediments into small invertebrates, 

which are then consumed by fish, which in turn, are eaten 

by waterbirds. Through monitoring, scientists have already 

demonstrated that fish communities in the area are now 

dominated by highly abundant and invasive round gobies. 

Preliminary results indicate that all of the loons that tested 

positive for botulism had eaten round gobies prior to death, 

suggesting that gobies may be a source of botulinum toxin. 

Another key component to understanding how birds come 

into contact with botulinum toxin is to better define the distribution and abundance of waterbirds during fall migration 

along with foraging patterns to determine where waterbirds 

are likely to be harmed or killed by botulism. Through monitoring efforts for this study, scientists obtained the first ever 

dive profiles for loons and have learned that loons dive as 

deep as 150 feet to feed in Lake Michigan, which indicates 

that botulism intoxication could be taking place at least that 

deep in the lake. The comprehensive approach to addressing 

botulism outbreaks as part of the GLRI provides important 

steps forward in predicting and preventing future botulism 

outbreaks in the Great Lakes.

The USGS coordinator for AMBLE (Avian Monitoring for Botulism Lakeshore 

Events) inspects a ring-billed gull submitted for avian botulism type E testing. 

Some sick and dead gulls found on Lake Michigan beaches had avian 

botulism. Photograph by Stephanie Steinfeldt, USGS.
Early Successes

• The collection of lake bottom sediment began in 

2010‒12 near Sleeping Bear Dunes National Lakeshore on Lake Michigan. A total of 435 samples 

were analyzed for the presence of the botulinum 

toxin gene. Results from this analysis have been 

used to understand the ways through which birds 

come into contact with botulinum toxin.

• A new method to detect botulinum toxin was 

developed that performs as well as the traditional 

method. This new method is faster and cheaper than 

the traditional method, and is a major step forward 

in the study of botulism (http://dx.doi.org/10.1128/

AEM.06165-11). 

• Scientists have learned that avian botulism is the 

main cause of bird mortality in northern Lake Michigan. More than 950 sick or dead birds have been collected through this project. Seventy-six birds have 

been tested for botulinum toxin, of which 42 were 

positive (55% positive).

• A citizen science program (Lake Michigan Volunteer 

AMBLE: Avian Monitoring for Botulism Lakeshore 

Events) was established to collect data on bird carcasses that wash ashore near Sleeping Bear Dunes 

and the Upper Peninsula of Michigan, and across 

the lake in Door County, Wisconsin (http://www.

nwhc.usgs.gov/mortality_events/amble/). This team 

effort has considerably increased our knowledge of 

the timing, numbers, and species affected by avian 

botulism.

• Links between type-E botulism outbreaks, lake levels, and surface-water temperatures in Lake Michigan indicated that avian botulism outbreaks occurred 

most frequently in years with low water levels and 

that surface-water temperature in Lake Michigan 

was higher in outbreak years than in other years 

(http://dx.doi.org/10.1016/j.jglr.2010.10.003).

(Above) Round goby. Photograph by S. Yavno. (Immediately right) Scientists 

sample fish in Lake Michigan near Sleeping Bear Dunes National Lakeshore 

to determine if Clostridium botulinum is commonly present in any particular 

species or locations. Photograph by Bryan Maitland, contractor to the USGS.

(Right) Common loons were 

marked with a satellite 

transmitter and geolocator 

tag to study the distribution, 

migration movements, and 

foraging patterns to identify 

where fish-eating waterbirds 

are likely to be exposed 

to the botulinum toxin. 

Photographs by Luke Fara 

and Kevin Kenow, USGS.

Developing Breakthroughs in the Prediction and Prevention of Botulism Outbreaks 43
44 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Botulism has been responsible for the deaths of more than 100,000 birds and fish in the Great Lakes since 1999 including the federally endangered piping plover shown 

in inset. The piping plover is a small migratory shorebird listed as endangered in Canada and the U.S. Great Lakes and threatened throughout the remainder of its U.S. 

breeding and winter range. Recent surveys indicate that only about 8,000 adult piping plovers exist. Inset photograph by Susan Haig, USGS. Background photograph by 

John Tracey, USGS.

2013 Successes

• The distribution and relative abundance of more 

than 30 waterbird species were determined through 

aerial surveys of Lake Michigan. Movements of 

more than 70 common loons while on the Great 

Lakes were determined through the use of satellite 

transmitters and archival geolocator tags during 

the summers of 2009‒13 to reveal where loons are 

likely to be exposed to prey fish carrying botulinum toxin. Geolocator tags also were used to 

capture feeding behavior. Movements of loons can 

be tracked by visiting the USGS loon migration 

Web site at http://www.umesc.usgs.gov/terrestrial/

migratory_birds/loons/migrations.html.

• Sediment samples continued to be collected at 

Sleeping Bear Dunes National Lakeshore in 2013 

and analyzed for the botulinum toxin gene. 

• Researchers have collected fish and invertebrates, 

and testing is underway to determine whether 

Clostridium botulinum is commonly present in any 

particular species or locations. Hundreds of round 

goby stomachs have been analyzed to determine 

which invertebrates are common food items.

• Avian mortality was assessed by using data collected 

for this study. Large mortality events (greater than 

1,000 carcasses) occurred in 2010 and 2012 (2,399 carcasses) and smaller events (fewer than 500 carcasses) 

occurred in 2011 and 2013.

• Scientists assessed peak carcass detection for the study 

years. Peak carcass detection for all study years except 

2011 was in October, with mostly migratory fish-eating 

and diving birds reported during these peaks: 2010 

(long-tailed ducks), 2012 (common loons), and 2013 

(red-breasted mergansers). Peak carcass detection 

in 2011 occurred in August and involved primarily 

summer residents such as gulls and double-crested 

cormorants.

• Scientists are also developing carcass drift models to 

aid in pinpointing potential sites of botulinum toxin 

exposure. During 2013, current, wave, and wind 

force measures were determined in the laboratory to 

compute drag coefficients operating on portions of carcasses in air and under water. This information is being 

incorporated into a hydrodynamic probabilistic source 

tracking model to estimate the trajectory and origin of 

bird carcasses deposited at a given beach location.
 45

Surveying Food Web Interactions 

within All Five Great Lakes The Great Lakes have been under persistent pressure from 

numerous environmental threats for more than two centuries. 

More than 180 invasive species now make their homes in the 

Great Lakes, many of which thrive at the expense of native spe-

cies. Additionally, excessive nutrients (nitrogen and phosphorus) 

can cause harm to ecosystems. The USGS is leading the way 

to understand how multiple environmental threats affect Great 

Lakes restoration by surveying the health of food web interactions 

(“who-eats-what”) in all five Great Lakes. With GLRI funding, 

scientists are sampling species throughout the food web, from top 

predator fishes to bottom-dwelling invertebrates, to microscopic 

animals (zooplankton) and plants (phytoplankton). In each year of 

this study, a different Great Lake is intensively sampled following 

the schedule of the U.S. Environmental Protection Agency’s and 

Environment Canada’s Coordinated Science and Monitoring Initia-

tive: Lake Michigan (2010), Lake Superior (2011), Lake Huron 

(2012), Lake Ontario (2013), and Lake Erie (2014). This monitor-

ing marks the largest effort ever to characterize Great Lakes food 

webs at broad geographic and seasonal scales, providing valuable 

information to restore native fish and foster the health of existing 

fisheries.

Knowledge generated through this project is critical to deci-

phering how environmental threats, such as invasive species and 

changes in nutrient input, ripple through food webs to ultimately 

affect native fish production and restoration. Scientists are creating 

a food web “roadmap” for each Great Lake that details the feeding 

linkages between species. These maps are decision support tools 

that allow scientists to explore how impacts of environmental 

threats spread through each lake’s ecosystem by way of connec-

tions between species. For example, USGS scientists are using 

food web maps to understand how spiny water fleas—an invasive 

zooplankton found in all the Great Lakes—and other invasive 

species affect native fish. Scientists are currently using the Lake 

Michigan map to study how native predators such as lake trout 

and prey fishes such as bloater are affected by invasions of species 

lower in the food web, such as zebra mussels, quagga mussels, 

spiny water fleas, and round gobies. Through use of this tool, 

managers are able to make informed decisions that ultimately 

benefit Great Lakes restoration. In addition, this project is 

generating a geographically and seasonally extensive database of 

Great Lakes species and feeding relationships for all of the lakes. 

This information allows scientists to assess the current health of the 

Great Lakes, and it also serves as a valuable baseline from which 

future ecosystem changes can be monitored. Together, these studies 

are providing numerous insights into the structure and function of 

Great Lakes food webs that should substantially enhance our 

ability to understand how purposeful and unexpected changes 

affect restoration in these valuable ecosystems.

USGS researcher deploys 

a zooplankton net in Lake 

Ontario in April 2013. 
46 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

(Above) USGS researchers filtering chlorophyll from various depths. (Below) 

USGS researchers pull gill nets from Lake Ontario for inshore fish diet study. 
Surveying Food Web Interactions within All Five Great Lakes 47

(Left) A trawl was used to collect mussels from a depth 

of 175 meters in Lake Ontario by USGS researchers 

studying food web interactions. (Below) Invasive spiny 

water flea (Bythotrephes) collected from Lake Huron. 

This invasive zooplankton is found in all the Great 

Lakes. USGS scientisits are using food web maps to 

understand how spiny water fleas and other invasive 

species affect native fish. Spiny water flea photograph 

by Kevin Keeler and Lynn Lesko, USGS.

Early Successes

• Extensive sampling for three of the Great Lakes was 

completed: Lake Michigan, Lake Superior, and Lake 

Huron. This work has allowed scientists to gain in-depth 

knowledge of the diets of top predators, such as salmon 

and lake trout, and a stronger understanding of the geographic and seasonal dynamics of numerous other Great 

Lakes prey fish and invertebrate species.

• A decision-support tool that can explore different scenarios 

(for example, increased stocking of lake trout, control of 

invasive mussels, or reductions in phosphorus inputs) was 

developed for Lake Michigan. Simulation results can be 

used to support management decisions to restore native fish. 

• Scientists studying Lake Michigan learned that a greater 

proportion of the Chinook salmon diet now consists of 

alewife (an invasive prey fish) than the diet of Chinook 

salmon surveyed in the 1990s, a finding that is important 

for determining salmon stocking targets in the changing 

Lake Michigan ecosystem (http://dx.doi.org/10.1080/00028

487.2012.739981).

• Scientists studying Lake Superior have determined that the 

food web and water quality are currently in good condition. 

Scientists documented a diverse fish community living 

throughout the lake, even in many of the deepest areas.

• In Lake Huron, scientists observed abundant lake trout, 

consistent with recovery of this keystone native predator 

being well underway. Scientists also discovered that the 

spiny water flea occupies greater depths in Lake Huron 

than was formerly known, which demonstrated a previously 

unrecognized potential for this invasive species to interact 

with native deepwater fish and zooplankton.

2013 Successes

• Extensive sampling of Lake Ontario was completed. 

Specimens were taken to the laboratory where they 

were identified and counted, gut contents were examined, and chemical analyses were completed.

• An article that explores the key ecological drivers of 

Great Lakes food webs was published (http://dx.doi.

org/10.1093/biosci/bit001). Water clarity increased 

and phytoplankton, native invertebrates, and prey fish 

decreased since 1998 in at least three of the five lakes. 

The article concluded that food was limiting several 

different food web levels (the position an organism 

occupies in a food chain) in Lake Michigan and Lake 

Huron, highlighting the long-term effects of varying 

nutrient inputs and shorter-term consequences of quagga 

mussel’s altering of energy availability.

• A new method for analyzing data from acoustic 

sampling of the fish community was developed on the 

basis of the 2011 sampling in Lake Superior (http://

dx.doi.org/10.1016/j.fishres.2012.12.012). The results 

for Lake Superior revealed non-native rainbow smelt 

(Osmerus mordax) to be the most common species at 

depths less than 330 feet with a lakewide estimated 

population of 755 million fish. Native kiyi (Coregonus 

kiyi) were the most abundant species at depths greater 

than 330 feet with a population of 384 million. Native 

cisco (Coregonus artedi) were widely distributed over 

all depths with their population estimated at 

182 million.
USGS researchers collect water samples from a stream in northeastern Minnesota. 

The Lakewide Action and Management Plan for Lake Superior places emphasis on 

collecting baseline environmental data in areas with potential for mine development. 
Tracking Progress and Working With Partners 49

Highlights

Tracking Progress and Working With Partners

The success of the GLRI program requires accountability, education, monitoring, evaluations, 

communication, and partnerships to succeed. The information obtained from GLRI efforts 

needs to be based on the best available science and assembled and communicated 

consistently to decision makers to allow them to assess ecosystem conditions and to track 

restoration progress. Outreach and education are also crucial in the effort to restore the 

Great Lakes. Because the Great Lakes span many different government jurisdictions, it is 

critical that partnerships continue and are further strengthened to address the complex 

issues faced by the Great Lakes. As part of the GRLI, the USGS is tracking progress and 

working strategically with partners to support Lakewide Management Plans, to characterize 

rivermouth ecosystems, and to provide forecasting tools for stream ecosystem management. 
Supporting Lakewide Action and Management Plans

The USGS is providing expertise, capacity, and support for the implementation of Lakewide Action and Management Plans (LAMPs; formerly Lakewide Management 

Plans, or LaMPs) and the associated goals, objectives, and 

targets for each of the Great Lakes. The LAMPs are critical binational collaborations that plan and integrate Great 

Lakes restoration actions. USGS work involves participation in binational Cooperative Science and Monitoring Initiative (CSMI) planning and field sampling. Each year, U.S. 

and Canadian organizations assess one of the Great Lakes 

as part of the CSMI, which is tied to the needs of LAMP 

committees. Information collected during CSMI assessments supports Great Lakes management programs. The 

USGS participates in LAMP processes, programs, workshops and projects; serves on work groups and technical 

committees; participates in interagency actions that implement LAMP programs and priorities; and incorporates 

LAMP goals and objectives into USGS planning efforts. 

USGS scientists work closely with partners to coordinate 

activities to ensure that projects and results are applicable, useful, and supportive of LAMP goals and projects that focus on 

the restoration and protection of the Great Lakes. Substantial 

progress has been made in compiling USGS monitoring and 

research information into a Great Lakes Web mapper called 

the Science in the Great Lakes (SiGL; pronounced “seagull”) 

Mapper. The SiGL Mapper will be able to be used in the 

assessment of areas where data are being collected, missing, 

or sparse, and also of areas where ecosystems are vulnerable. 

The SiGL Mapper will be a great asset for decision makers in 

the protection and restoration of Great Lakes ecosystems. In 

addition, development of a nearshore-coastal framework will 

be able to be used in conjunction with the SiGL Mapper to 

develop a strategy for coordinated research and monitoring. 

Early Successes

• Efforts for Lake Michigan included compilation of 

historical data and information needed to inform partners 

about monitoring and data available in nearshore 

ecosystems. For example, USGS maps of manmade 

fill distributions were provided to assist environmental 

restoration and redevelopment efforts in economically 

distressed areas of southern Lake Michigan watersheds 

in an Area of Concern.

• For Lake Erie, emphasis was placed on coordinating 

activities with partners. 

• For Lake Huron, emphasis focused on issues affecting 

fisheries and nutrient inputs.

• For Lake Superior, emphasis was placed on support of 

data activities in areas with potential for mining 

development.

• Lake Ontario efforts focused around attending LAMP 

meetings and providing science expertise for collecting 

data on benthos (bottom-dwelling organisms) to provide 

information needed for management decisions for Areas 

of Concern. A journal article on the 2008 Lake Ontario 

CSMI was published in 2012 (http://dx.doi.org/10.1016/j.

jglr.2012.07.005).
(Photograph far left) USGS researcher deploys a passive sampler at Scanlon, 

Minnesota, as part of the GLRI program to monitor Great Lakes tributary 

streams. The Lakewide Action and Management Plan for Lake Superior places 

emphasis on understanding contaminant loading to the lake. 

2013 Successes

• Substantial progress was made in compiling monitoring information, including information collected as 

part of the CSMI, into the SiGL Mapper and in support of summary publications describing the status of 

monitoring data for each of the Great Lakes. These 

efforts included coordination with Tribal and State 

partners, the U.S. Environmental Protection Agency, 

and LAMPs to ensure that products and results are 

applicable and useful.

• A new version of the SiGL Mapper was released and 

can be accessed at http://wimcloud.usgs.gov/SIGL/.

• The nearshore-coastal framework was completed and 

is being used in conjunction with the SiGL Mapper 

to develop a strategy for coordinated research and 

monitoring (http://pubs.usgs.gov/of/2013/1138/).

• The USGS continues to participate in LAMP steering 

committees that represent each of the Great Lakes. 

Individual USGS Science Centers continue to coordinate with partners for each of the Great Lakes and to 

support sampling and monitoring activities.

Supporting Lakewide Action and Management Plans 51

“The USGS empowers our stakeholders by 

providing shared data and scientific tools 

that overcome jurisdictional boundaries 

and helps form collaborations that promote 

beach health and water quality improvements 

of Lake Michigan and its tributaries. 

USGS participation in Lake Michigan 

groups such as the Urban Waters Federal 

Partnership has helped to develop and 

strengthen relationships among 

communities and local, State and Federal 

partners. Their assistance contributes to 

the development of meaningful stakeholder 

projects that enhance ecosystems and 

improve public uses of Lake Michigan, and 

its nearshore waters and tributaries.”

—Natalie Johnson, Coordinator,

Northwest Indiana Urban Waters Partnership

(http://urbanwaters.gov/nwi)

The waterfalls at Niagara Falls straddle the international border between 

Canada and the United States. Binational collaborations comprise the 

Lakewide Action and Management Plans that are critical to planning and 

integrating Great Lakes restoration actions. Photograph by Jim Nicholas, 

USGS. 
52 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

Characterizing Rivermouth Ecosystems

Rivermouths are at the heart of most large cities on the Great Lakes because they provide ideal hubs 

for shipping and allow easier access to the lakes 

themselves. Rivermouths are thus the center of where 

people interact with the Great Lakes. Rivermouths 

are highly valued as urban, industrial, and shipping 

centers, but historically were also places that supported 

extensive fish and wildlife production. As the connection between the river and lake, rivermouths are also of 

great importance ecologically because they are the last 

step connecting land use to the coastal waters. Today, 

interest is great in restoring these mixing zones of 

river and lake waters that result in unique, diverse, and 

productive ecosystems, which are important to both 

nearshore and deepwater fisheries in the Great Lakes. 

Despite the importance of rivermouths, little is known 

about how rivermouth ecosystems function or how 

human changes have altered those processes. This lack 

of understanding severely limits the ability to manage 

or restore these ecosystems effectively and efficiently. 

To improve our understanding, USGS scientists are 

working to identify and understand the role that Great 

Lakes rivermouths play in the quality of nearshore and 

deepwater habitats, and how the mixing dynamics of 

river and lake waters is related to biological production. 

A scientific framework has been developed to support 

restoration and management in these important rivermouth areas. This framework will be especially useful 

to managers seeking remediation and delisting of Areas 

of Concern, which are predominantly rivermouths.

The intensive monitoring information on rivermouth characteristics is being used to develop a 

classification system to guide synthesis of research 

on rivermouths and help define “reference conditions” (historical benchmarks necessary to develop and 

establish ecosystems under undisturbed conditions) 

in support of rivermouth restoration across the Great 

Lakes. Decision makers can use this framework to 

match habitat restoration targets for Areas of Concern 

to previously identified stream and rivermouth impacts 

on the lakes. This framework serves as a guide to a 

variety of restoration activities including identifying 

critical habitat needs, ensuring alignment with fundamental ecosystem processes, and planning for effects 

of land use and climate change.

Early Successes

• Intensive rivermouth sampling on the Ford, Pere 

Marquette, and Manitowoc Rivers (Lake Michigan) 

was completed in 2011 and on the Thunder Bay River 

(Lake Huron) was completed in 2012. Intensive 

sampling includes characterization of water chemistry, 

food web structure, mixing between riverine and lake 

inputs, and habitat use by aquatic organisms including 

fish and benthic invertebrates.

• A journal article (http://dx.doi.org/10.1016/j.

jglr.2012.09.016) was published in 2012 that describes 

the importance of rivermouths in the processing and 

delivery of nitrogen and carbon to the nearshore zone.

A USGS sampling team travelling between sampling locations on the 

Manitowoc River. As many as five laptops were used to collect data from 

multiple deployed instruments. 
2013 Successes

• A database of rivermouth characteristics was created. 

Information such as streamflow, water temperature, 

habitats, food-web structure (how plants and animals are 

interconnected), and watershed properties are stored in the 

database for more than 2,300 Great Lakes 

rivermouths. 

• Intensive monitoring of the distribution of ecosystem 

processes in the Maumee River and extending into 

Lake Erie was initiated and will be used to assess goals 

and progress for restoration efforts in coastal wetlands 

near Toledo, Ohio. The information also can be used to 

assess how harmful algal species and blooms affect 

the growth of aquatic species in the Maumee River 

and Lake Erie.

• The “Great Lakes Rivermouths: A Primer for Managers” 

by the Great Lakes Rivermouth Collaboratory was 

published (http://glc.org/files/main/RivermouthPrimerFINAL-2013.pdf). This primer synthesizes existing 

information in a new way that aims to support 

management of rivermouths as distinct and important 

ecosystems.

• A journal article (http://dx.doi.org/10.1371/journal.

pone.0070666) was published describing how habitats and 

watershed land use affects fatty acid composition of algae 

at the base of aquatic food webs at rivermouths.

• A journal article (http://dx.doi.org/10.1371/journal.

pone.0069313) was published describing how rivermouths 

alter the effect of agricultural land use on the stable 

nitrogen ratios in tissues of rivermouth consumers.

• A synthesis of current knowledge about ecosystem 

structure and function in Great Lakes rivermouths was 

published (http://dx.doi.org/10.1016/j.jglr.2013.06.002). 

The synthesis was based on studies of rivermouths, coastal 

wetlands, and marine estuarine systems and helps identify 

the critical gaps in understanding rivermouth ecology.

1600s 1800s 2000s

Wildlifeproduction

Fish production

Floraproduction

Harbor

Cultural services

Suppoting services

Waste assimilation

Water supply

Erosion andsedimentation

Waterquality

PRE-SETTLEMENT INDUSTRIAL ERA MODERN-DAY

SOCIETAL VALUE

RELATIVE SCALE

Hypothetical example 

of how the values of 

communities around the 

Great Lakes and particular 

rivermouth ecosystem 

services have changed 

considerably over the last 

several hundred years.

High flows are common in early spring on the Manitowoc River (above) 

and Ford River (below). USGS researchers completed intensive rivermouth 

sampling on both of these rivers in 2011.

Characterizing Rivermouth Ecosystems 53

The confluence of the Ford River with Lake Michigan near Escanaba, 

Michigan. The natural delta shown in the photograph is one of the few 

undisturbed river deltas in the Great Lakes. USGS scientists are intensively 

sampling Great Lakes rivermouths to provide a scientific framework for 

restoration and management in these important areas. 
Watershed Modeling for Stream Ecosystem Management

This project is determining fish distributions in Great Lakes tributaries and how changes 

in streamflow may affect them. This information will help guide restoration efforts to 

achieve maximum effectiveness and success.
USGS scientists are providing forecasting tools for 

managers to determine how water withdrawals, landscape 

changes, or other changes in watersheds may affect ecological 

flows in the Great Lakes. Ecological flows can be defined as 

the flow of water in a stream, river, or lake that sustains healthy 

ecosystems and maintains appropriate ecosystem functions 

such as fish productions and access to spawning habitat. Flows 

vary in magnitude, especially during flood and drought events, 

and flows also are affected by artificial alterations such as 

damming, diversions, and channelization. These changes have 

many effects of the survival of aquatic organisms and the functioning of aquatic ecosystems. Efforts to determine appropriate ecological flows seek to preserve or restore enough of the 

“natural” flow magnitude and variability to protect the ecological functions essential for supporting diverse aquatic communities. Effective management decisions must recognize the 

natural diversity of stream ecosystems. At the same time, trying 

to manage every stream as a unique system would be extraordinarily challenging. To address these needs, USGS scientists 

and regional partners are creating a regionally consistent data 

framework to support modeling of landscape and hydrologic 

variables to relate changes in environmental conditions such as 

water withdrawals or climate change to ecological changes in 

aquatic ecosystems. The forecasting tools being developed will 

help assess the health of aquatic ecosystems and identify areas 

in need of protection, conservation, enhancement, and restoration. The information will help guide stream ecosystem efforts 

to achieve maximum effectiveness and success.

This project provides unified information across the 

Great Lakes Basin for ecosystem restoration, assessment, and 

management by incorporating models that relate changes in 

landscape and hydrologic variables and stresses to changes in 

ecosystem function. The information can be used by managers 

to assess stream ecosystem health, by natural resources professionals to identify and prioritize locations to focus stream restoration efforts and to assess stream ecosystems across jurisdictional boundaries, by managers for planning and management 

of game and non-game species, and by policy makers to make 

informed decisions on topics that relate to stream ecosystem 

health. The approach for classifying streams achieves a balance 

by incorporating natural stream diversity while minimizing 

challenges that management of individual streams would present. Additionally, classifying streams allows scientists, managers, and stakeholders to identify restoration and management 

actions that can be effective for different parts of the system. 

The models of ungaged streamflow, stream temperature, and 

fish abundance can be used to develop additional models 

describing how fish communities may change in response to 

streamflow changes and identify stream ecosystems that are 

most sensitive to landscape and climate changes.

Early Successes

• Modeling techniques were developed to estimate 

streamflow at ungaged stream sites. These techniques 

are important because stream ecosystem management 

relies on understanding the relationship between 

streamflow and stream ecology.

2013 Successes

• Project researchers worked with the USGS Center 

for Integrated Data Analytics (CIDA) to develop 

an online mapper that will deliver the ungaged flow 

estimates produced by the modeling techniques to 

ecologists, managers, and the public. 

• Preliminary information describing fish species 

response to altered streamflow were developed.

• A general set of stream characteristics that are 

critically important to fish and other aquifer organisms (such as stream size, stream temperature, and 

streamflow) were used to classify streams and create 

predictive models of stream temperature and fish 

abundance. 

Watershed Modeling for Stream Ecosystem Management 55

The USGS is creating forecasting tools for managers to determine how water 

withdrawals or other hydrologic or land use changes in watersheds may 

affect Great Lakes ecosystems.
56 Great Lakes Restoration Success through Science—USGS accomplishments 2010 through 2013

TheFuture

of Communicating Science for GLRI

The USGS has developed a new tool for communicating science for the USGS GLRI 

to provide resource managers, scientists, and the public with the information and 

decision-making tools needed to help with Great Lakes restoration efforts. This new tool is 

called “The Great Lakes Restoration Initiative Science Explorer.” The GLRI Science Explorer 

is a Web-based interface that allows users to search and discover the valuable research 

USGS scientists are conducting in the Great Lakes region.

This search tool can be used to find information about current and past science projects. 

Each project record provides descriptive information about a study (such as start date, 

description, principal investigator, and location) along with links to associated information 

products and datasets that resulted from the GLRI projects including the projects described 

in this document.

Discover USGS science by visiting http://cida.usgs.gov/glri/glri-catalog/.

Publishing support provided by the Columbus Publishing Service Center

Graphics and layout by Marta Anderson

Graphics assistance by Rosemary Stenback

Report preparation by Janet Carter and Sandra Morrison

For more information concerning this publication, contact:

Norman Granneman, USGS Great Lakes Coordinator

6520 Mercantile Way, Suite 5

Lansing, MI 48911

(517) 887-8936

Or visit the USGS Great Lakes Restoration Web site at:

http://cida.usgs.gov/glri/

(Photo, inside front cover) This astronaut photograph of the Great Lakes in sunlight 

was acquired on June 14, 2012, from the vantage point of the International Space 

Station. Lake Ontario is in the foreground, Lake Erie is on the left in the background, 

and Lake Huron is to the right in the background. (Photo, inside back cover) Threads 

of light at night surrounding the Great Lakes as viewed from the International Space 

Station. Photographs courtesy of National Aeronautics and Space Administration.
We thank the Great Lakes Restoration Initiative for the funding support that 

enabled us to conduct science in support of Great Lakes restoration, and thank 

our many Federal, Tribal, State, Provincial, local, nongovernmental organizations, 

university, industry and other partners and the public who have worked with 

USGS on these science accomplishments. Our collective commitment to and 

support of Great Lakes restoration is truly making a difference now and for future 

generations!
U.S. Geological Survey—Great Lakes Restoration Success——U.S. Geological Survey Accomplishments 2010 through 2013—Circular 1404

ISSN 1067-084X (print)

ISSN 2330-5703 (online)

http://dx.doi.org/10.3133/cir1404