Habitats and Ecosystems
Coastal areas provide essential habitat for numerous species of fish, waterfowl, migratory birds and mammals. But the continuing development of our coastlines has destroyed much of our wetlands, degraded water quality and severely stressed ecosystems. Understanding the complex dynamics between terrestrial and aquatic environments is critical to resource quality, sustainability and management in the Great Lakes region.

State of the Bay 2013 Report

The State of the Bay 2013 Report
“State of the Bay: The Condition of the Bay of Green Bay/Lake Michigan 2013” is the first comprehensive look at the ecological health of the region in 20 years. It offers details on the bay’s “dead zone,” the effect of aquatic invasive species, the good news about walleye and more. Read more...

Cat Island Chain Restoration

Cat Island Chain Information
A plan is underway to restore a chain of islands in southern Green Bay that were washed away in the 1970s. Read more...

The beginning
On June 1, 2012, crews began work to restore the Cat Island chain. Read more...

Potential Climate Change Impacts on the Bay of Green Bay - An Assessment Report

Climate change poses new threats to Green Bay and its resources because it may alter the impacts of already existing stresses on the ecosystem. As part of the Wisconsin Initiative on Climate Change Impacts, a Green Bay Ecosystem Working Group was formed and held several workshops during 2008-10. The Working Group assessment report identifies existing stresses and vulnerabilities of the Green Bay ecosystem, suggests how climate change may affect key ecosystem components, and proposes adaptation strategies for mitigating impacts. Read more...

Lake Superior National Estuarine Research Reserve (LSNERR)

The River Talks

A free, informal speaker series about the St. Louis River Estuary in Duluth-Superior and a cooperative project between the Wisconsin and Minnesota Sea Grant programs and the Lake Superior National Estuarine Research Reserve.

Grab a mug of coffee or maybe a glass of beer and learn about the St. Louis River at the same time. Scientists, businesses, and agency staff who work and depend on the St. Louis River Estuary will share their thoughts and information about river projects each month during the academic year. But the evening presentations won’t be a one-way street. You’ll get to ask questions and share your thoughts, too.


Lake Superior National Estuarine Research Reserve (LSNERR)
A 16,697-acre area of freshwater marshes, uplands and river on the shores of Lake Superior in Wisconsin has become the 28th member of the NOAA's National Estuarine Research Reserve System in a designation ceremony at Superior in October, 2010.  The Lake Superior National Estuarine Research Reserve is located in Douglas County, in the northwestern corner of Wisconsin where the St. Louis River flows into Lake Superior. Read more...

South Bay Marina Habitat Enhancement

Completed in 2003, South Bay marina in Green Bay is not just a marina, but features a variety of habitat enhancements. Read more...


Julia Noordyk: Helping Coastal Communities
Julia Noordyk, Wisconsin Sea Grant's Green Bay-based coastal storms outreach specialist, has been with the organizaiton two years. But she's just begun to get her feet wet. Read more...

Revitalizing Local Waterfront Economies
This video outlines the Great Lakes Legacy Act and highlights benefits it brings to communities. Read more...

Sheboygan River: A Little Patience, A Big Payback
In the summer of 2012, the cleanup of the Sheboygan River got underway. The benefits to the community will be enormous--but through 2012, some patience will be required. Crews will be working around the clock to dredge the river, clean up contaminated sediment and restore wildlife habitat. Read more...

What Will Round Gobies Do to Great Lakes Streams?
Researchers investigated just what kind of impact the round gobies might be having in streams flowing into the Great Lakes. Using nets and a portable electro-fishing system, they sampled and analyzed goby populations at 150 different stream locations along Wiscosins' Lake Michigan coast. Read more...

Are Flame Retardants Harming Frogs?
In Dr. William Karasov's lab, the frog is front and center in a series of research experiments, funded in part by the UW Sea Grant Institute, designed to explore how environmental toxins may be affecting the frog's immune system, growth and development. Read more...

How Many Sport Fish Can Lake Michigan Support?
A research project is finding out how invasive species may be changing the food web in Lake Michigan. Read more...

Beyond the Usual Suspects
E. coli bacteria sometimes contaminates the waters of Bradford Beach in Milwaukee. Where does it come from? How can it be reduced? Dr. Sandra MacLellan cracks the case. Read more...

Part 1: All Washed Up, Lake Michigan's Algae Challenge
See what effect excessive algae is having on beaches, homeowners, and industry. Read more...

See More Videos on Habitats and Ecosystems


Extreme Events, Watershed Loadings and Climate Change: Implications for the Management and Long Term Health of the Green Bay, Lake Michigan, Ecosystem

Michael Zorn, UW-Green Bay, (920) 465-5758, zornm@uwgb.edu

Green Bay, Lake Michigan, is severely affected by excessive nutrient inputs from its upstream watershed, which increases the risk of harmful algal blooms (HABs) and other problems. The percentage of blue-green algae in phytoplankton in the Lower Fox River and Green Bay is expected to decrease if TMDL goals for total phosphorus are met. However, current management plans acknowledge that the relationship between phosphorus levels and blue-green algae are not well defined for this system and that other factors may be important. Additionally, nutrient and suspended solids inputs are extremely dependent on large precipitation events (which cause pulse loading), and climate change projections predict an increase in these events by ~50%. The researchers plan to understand the dynamics of the pulse delivery of nutrients to Green Bay and their influence on structuring the algal community by deploying high frequency, in-situ nutrient and pigment sensors at strategic locations in Lake Winnebago, the Lower Fox River, and Green Bay. (R/HCE-25)

The Basis for Microbially Mediated Mercury Methylation in Oxygen-Depleted Zones of the Great Lakes

Katherine McMahon, UW-Madison, (608) 263-3137, tmcmahon@engr.wisc.edu

Elevated levels of the potent neurotoxin methylmercury (MeHg) are present in fish throughout the Great Lakes. An inability to balance sources and sinks of MeHg in aquatic ecosystems suggests that we are missing significant processes and/or locations of MeHg production. In this project, we will test hypotheses about the organisms and their genes expected to be responsible for Hg methylation in the Great Lakes. We will use molecular techniques to relate microbial community composition to MeHg and total Hg levels at depth-resolve intervals within the water column of all five Great Lakes, at stations known to have significant MeHg concentrations. We will also target recently identified genes known to be involved in methylation in pure cultures of anaerobic bacteria. Finally, we will evaluate the effect of thiols on methylation in lake microbial communities. This work will advance our understanding of the freshwater Hg cycle, providing evidence for the mechanisms at play in microbial communities mediating methylation.  R/HCE-22

An Ancient but Unrecognized Mechanism for Harvesting Light Energy in Great Lakes Bacterioplankton

Katherine McMahon, UW-Madison, (608) 263-3137, tmcmahon@engr.wisc.edu

Aquatic microorganisms play a critical role in the Great Lakes. They mediate nearly all biogeochemical cycling of carbon and nutrients. Recent findings suggest a previously unrecognized mode of light harvesting to support microbial biomass, with broad implications for our understanding of the microbial loop and the underpinnings of Great Lakes food webs. Some very abundant and prevalent freshwater bacteria carry genes that seem to encode protonpumping rhodopsins, which allow  for  energy  generation  independent from conventional phytopigments, such as chlorophyll in algae and phycocyanin in cyanobacteria. Similar genes have been found in marine bacteria, and a recent study identified genes encoding novel rhodopsin-like proteins in Actinobacteria, by targeting single cells recovered from inland lakes. We know almost nothing about how and when these enzymes work, but we now have preliminary data that allow us to tackle this knowledge gap. Our overarching research goal is to functionally characterize these freshwater actinorhodopsin proteins. R/HCE-14

Quantifying Coastal Wetland – Nearshore Linkages in Lake Michigan for Sustaining Sport Fishes

Patrick Forsythe, UW-Green Bay, (920) 465-2525, forsythp@uwgb.edu

Coastal wetlands support rich and diverse faunal communities, providing habitat for 90% of Great Lake fish species. Estimates of the linkages between coastal wetlands and other lake habitats will fill a major data gap concerning how wetland degradation and restoration of previously degraded wetlands affect the Lake Michigan nearshore food web. Otolith microchemistry analysis will provide an estimate of fish use of wetland-nearshore habitats. Isotope mixing models will be used to construct cross-habitat food webs and provide estimates of wetland and nearshore energy sources for piscivorous fish. These results will determine both how and when nearshore sport fish use wetland habitats and accumulate wetland energy. By understanding wetland-nearshore linkages, we can incorporate coastal wetlands into long-term management of Great Lakes food webs and the Lake Michigan fishery, and set appropriate protection and restoration priorities for the Lake Michigan coastal zone.  R/SFA-09

A New Tool for Studying Food Web Changes

Jake Vander Zanden, UW-Madison, (608) 262-9464, mjvanderzand@wisc.edu

Great Lakes ecosystems have undergone dramatic changes due to a suite of interacting anthropogenic stressors. For example, Dreissenid mussels have shunted productivity to the nearshore benthos and caused severe oligotrophication in the offshore zone. What are the underlying  food web changes that both drive and respond to these remarkable ecological shifts? Amino acid-specific nitrogen isotope analysis (AA-NIA) is a novel approach for measuring food web change in freshwater systems. We will develop the basis for long-term retrospective food web analysis from preserved museum specimens and calcified tissues (fish scales and otoliths). Using this approach, we will test hypotheses about historical trophic niche partitioning among deepwater coregonids in the upper Great Lakes. In addition, we will test hypotheses about food web responses to Dreissenid-driven changes in nearshore and offshore habitats. This innovative approach has exciting potential to serve as an integrative ecological indicator of Great Lakes ecosystem health. (R/HCE-24)

Investigate the Proliferation of Antimicrobial Resistance in Lake Michigan Coastal Waters

Krassimira Hristova, Marquette University, (414) 288-5120, krassimira.hristova@mu.edu

The focus of this project is to investigate a novel role of the invasive Dreissenid mussels, zebra and quagga, on the dissemination of antibiotic resistance genes (ARGs) in the Great Lakes coastal ecosystem through horizontal gene transfer (HGT). We hypothesize that the primary source of ARG proliferation in Great Lakes coastal ecosystems is the gastrointestinal microbiome of humans and animals consuming antibiotics and invasive Dreissenid mussels that concentrate bacteria in their gut. The project goal is to characterize the surface water resistome in Lake Michigan and an inland Wisconsin lake by characterizing ARG diversity, HGT rates and the impact of zebra and quagga mussels on the dissemination of ARGs. This project will provide novel information of how the interactions of many ecosystem factors including treated wastewater, invasive species, and the microbiome of coastal waters interact to lead to potential reservoirs of antibiotic resistant bacteria. R/HCE-20

Modeling the Chequamegon Bay Ecosystem to Facilitate Climate Adaptation

Randy Lehr, Northland College, (715) 682-1261, rlehr@northland.edu

To manage the Lake Superior ecosystem effectively in the presence of changing climatic conditions, it is necessary to understand the relationship between increases in water temperature, changes in tributary runoff —particularly nutrient, sediment and organic matter loads—and nearshore water quality conditions. Water temperatures and stream hydrology are anticipated to continue to shift in the coming decades. Given that water temperature and tributary runoff are both key drivers of the nearshore environment in Lake Superior, it is likely that water quality in these ecosystems will also shift in response. However, it is unclear what the resulting water quality conditions will be under future climatic scenarios. This project will estimate the potential impacts of climate change on water quality conditions in the Chequamegon Bay, and results from this work will describe an integrated framework for assessing the individual and combined effects of climate stressors, providing valuable information to communities making decisions related to climate adaptation. R/HCE-19

Integrating Prior Vegetation Surveys to Test Spatial and Temporal Patterns of Wetland Floristic Quality in the St. Louis River Estuary

Nicholas Danz, UW-Superior, (715) 394-8161, ndanz@uwsuper.edu

The St. Louis River widens into a 12,000-acre freshwater estuary near its entry into Lake Superior. The estuary has serious pollution issues resulting from a history of heavy industrial use, but high-quality wetlands are widely distributed throughout this system. These wetlands play many critical ecological roles, but there is very little available scientific information regarding plant composition and floristic quality throughout the estuary. This information would allow us to address several research questions of current management interest, including creating target species lists for restoration, identifying drivers of floristic quality and developing a vegetation baseline for judging future changes. Our goal in this project is to use existing data from a multitude of plant studies in the estuary over the past few decades to create an emergent synthesis of wetland vegetation in the St. Louis River estuary that will address these management questions.  R/HCE-18

Constructing a Lake Michigan Nearshore Ecosystem Model

Harvey Bootsma, UW-Milwaukee, (414) 382-1717, hbootsma@uwm.edu

As a result of fundamental changes in the functioning of Lake Michigan and the other Great Lakes in the past two decades, nearshore biogeochemical processes have become somewhat distinct from offshore processes. While pelagic waters have become oligotrophic to the point of negatively affecting fish populations, the nearshore zone, which in many parts is dominated by Dreissenid mussels, experiences excessive levels of nuisance algal growth on the lake bottom. In recognition of these changes, the revised Great Lakes Water Quality Agreement has stressed the need to update phosphorus targets for nearshore water. New targets require science-based models that can predict the response of nearshore biota and water quality to phosphorus loads and concentrations. We propose to address this need by integrating research findings and models of specific nearshore processes that we have developed over the past seven years into a linked physical-biogeochemical nearshore ecosystem model. The model will be calibrated with existing data and validated with new data collected during this study.  R/HCE-17

Role of Invasive Quagga Mussels in Regulating Organic Carbon Dynamics in Lake Michigan

Laodong Guo, UW-Milwaukee, (414) 382-1742, guol@uwm.edu

The Great Lakes have experienced significant ecological changes due to increasing anthropogenic influences and the introduction of invasive species, resulting in the decline of fish biomass and changes in ecosystem function, food web structure and carbon/nutrient dynamics. However, the pathways/mechanisms and changes in nutrient/carbon dynamics remain elusive. Quantitative linkages between quagga mussels and changes in carbon/nutrient dynamics in Lake Michigan remain poorly known. Understanding the uptake pathways and interactions of quagga mussels with dissolved, colloidal and particulate organic matter in the water column is likely at the heart of this issue. Our working hypothesis is that ultra-fine colloidal or nanoparticulate organic matter is either retained or taken up by quagga mussels, consequently competing for food sources with zooplankton and altering carbon/energy flow in the water column. Our results from controlled laboratory experiments should provide new insights into biogeochemical consequences of invasive species in Lake Michigan. (R/HCE-16)

Algal Bioremediation of Wastewater Inputs to Great Lakes Ecosystems

Erica Young, UW-Milwaukee, (414) 229-3257, ebyoung@uwm.edu

Future sustainability of coastal communities demands a reduction of nutrients in effluents from wastewater treatment plants, and population growth is increasing pressure on communities’ infrastructure to manage and treat waste water. Algal species like Cladophora can tolerate and take up high concentrations of nutrients, and this can be exploited for nutrient remediation of wastewater. The researchers have already shown in laboratory tests that Cladophora can deplete sewerage effluent of soluble reactive phosphorus to <5 ug/L and also provide a good biomass feedstock for biofuels production, offering combined sustainability benefits for use in remediation of wastewater. This project aims to develop algal nutrient remediation of wastewater that will provide cost savings to coastal communities and offer more sustainable options to improve lake ecosystem health. (R/SCD-06)

Changing Benthic Metabolism in the Great Lakes

J. Val Klump, UW-Milwaukee, (414) 382-1700, vklump@uwm.edu

The Great Lakes have experienced arguably the largest short-term ecological shift in their history within the last decade and face a long-term climate shift in the decades to come. The invasion of Dreissenid mussels, the disappearance of Diporeia, and the predicted increasing temperatures and lengthening stratification have altered and will alter the role of benthic metabolism. The nearshore habitat is a complex of newly colonized cobble, gravel, hard clay and silty sands. Deepwater bottoms have been overrun with mussels. Production and respiration of oxygen are notoriously difficult to measure in such environments since many of the common methods—oxygen and pore water gradients, sediment or chamber incubations—all have limitations. The researchers propose to employ new, nondisruptive eddy correlation techniques to study oxygen exchange at the benthic boundary in a range of Great Lakes environments that have undergone or will undergo significant change. (R/HCE-12)

Climate Change Impacts on Anuran Ecotoxicology in Great Lakes Ecosystems

William Karasov, UW-Madison,(608) 263-9319, wkarasov@wisc.edu

Generally, most contaminants become more toxic as temperature increases. However, the exact mechanism(s) underlying this relationship are not well understood. The focus of this project is temperature-dependent effects of chronic exposure to persistent organic pollutants (POPs)-polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). The researchers hypothesize that increased temperature (as predicted with climate change in Great Lakes ecosystems) will increase food and hence toxicant intake rate, but may also increase the biotransformation and elimination rates that influence overall bioaccumulation; contaminant toxicity will also increase. The researchers seek to determine the temperature dependence of exposure kinetics (uptake, elimination and bioaccumulation) for POPs at environmentally relevant concentrations in northern leopard frogs and determine the temperature dependence of toxicity for POPs. (R/HCE-14)


Climate Change and Green Bay Hypoxia Decision Support Tool
This project, on which Sea Grant provides supportive outreach activities for two partner campuses, will create a decision-support tool for use within the Lower Fox River watershed to support ecosystem-based management using alternative sediment and phosphorous loading and climate trend scenarios. Funding source: University of Michigan Water Center.

Total Maximum Daily Load and Area of Concern
Through the work of the Total Maximum Daily Load (TMDL) Outreach Committee, which consists of multiple partners, Sea Grant will support implementation efforts of the Lower Fox River TMDL plan. The efforts will focus on the three primary stakeholder groups impacted by the TMDL targets: (1) MS4 stormwater permit holders, (2) agricultural producers and farmers and (3) point source dischargers. The committee will work with NEW Water, the Green Bay sewerage district, to foster collaboration throughout the watershed using an adaptive management strategy. Related work is chairing the Area of Concern-Citizen Advisory Committee Outreach and Education Subcommittee that will identify and coordinate outreach and education activities to improve water quality in the watershed.

Related Publications

State of the Bay 2013
For the most recent information about water quality, fish and wildlife populations, aquatic invasive species, beach conditions and the status of contaminants in Green Bay, Wisconsin, see this free downloadable publication. Read more...

Related Websites

Great Lakes Restoration Initiative (GLRI)

Wisconsin is the beneficiary of funding made available under the Great Lakes Restoration Initiative, a $475 million program to restore fish and wildlife habitat, clean up toxic pollution, reduce nonpoint source pollution, and control and prevent the spread of aquatic invasive species in the Great Lakes.  Wisconsin Sea Grant will be involved in several projects that are regional in nature and will be implemented with multiple partners.  They are: 

  • developing a beach information communication system
  • developing a regional public outreach campaign on aquatic invasive species
  • developing a regional green marina education and outreach project
  • expanding our understanding of the Lake Michigan food web
  •

    Migratory Birds of the Great Lakes
    Learn about field identification, habitats, migration, conservation status, nests and eggs, songs, and issues challenging 20 species of Great Lakes migratory birds. Read more...

    Visit this website to learn facts about frogs, field identification, and take quizzes about frogs, plus this website includes various activities for kids and teachers. Read more...

    Coastal Wetlands of Wisconsin's Great Lakes: A Data Compilation and Assessment
    This Wisconsin DNR website provides information on wetland sites throughout the coastal regions of Wisconsin. Read more...

    Wisconsin Breeding Bird Atlas
    Visit the Wisconsin Society for Ornithology's website to access information (maps, data, images) about bird species breeding in the state. Read more...

    Great Lakes Birding and Nature Trails
    Wisconsin DNR's website allows you to download birding trail guides for different regions in the state including Lake Michigan and Lake Superior. Read more...

    State of the Lakes Ecosystem Conference (SOLEC)
    The State of the Lakes Ecosystem Conferences (SOLEC) and State of the Great Lakes reports are produced jointly by the U. S. EPA and Environment Canada. They provide independent, science-based reporting on the state of the health of the Great Lakes basin ecosystem.  For information on the conference and to access the reports, Read more...

    Wisconsin's Water Library
    Established in 1964 by the UW Water Resources Institute, Wisconsin's Water Library (formerly known as the Water Resources Library) is unique among UW-Madison's many libraries for its collection of almost 30,000 volumes of water-related information about the Great Lakes and the waters of Wisconsin. The library includes a curriculum collection, dozens of educational videos, a children's collection, and more than 20 journals and 100 newsletters. Read more...