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U.S. Geological Survey - Great Lakes Science Center

Habitat Remediation

Over the past two centuries, Great Lakes ecosystems have endured significant changes, many of which drastically altered life in the region. To successfully remediate the Great Lakes ecosystem, researchers must provide sound data that allow resource managers to make informed decisions. The USGS-GLSC is working toward Great Lakes remediation by examining results following the restoration of natural water-flow between a previously diked wetland and Lake Erie, exploring ways to promote oak savanna dune restoration along the coast of Lake Michigan, predicting animal community change with Great Lakes terrestrial ecosystem restoration, and restoring fish spawning habitats in the Huron-Erie Corridor’s degraded environment. Additionally, as a result of the skill-set and resources of USGS-GLSC researchers, a large-scale, collaborative study is currently underway that involves assessing long-term ecological changes in lakes of the Former Soviet Republics (FSR). Many of these lakes have experienced severe environmental degradation and resources in the respective countries are inadequate to tackle the problem. The USGS-GLSC is leading this project and working with other international partners to help scientists in the FSR find solutions for these major environmental problems.


Problem Statement
The hydrologic isolation of most remaining coastal wetlands, especially in and around the Maumee River Area of Concern, limits ecosystem functions and services. As a result, intensive wetland management strategies can limit both access to fish habitat and the retention of phosphorus and other nutrients.


  1. Characterize 5 years of ecosystem response to reconnection of diked wetlands and their parent water body
  2. Develop sustainable strategies for consistent sampling among study sites and contributing to the delisting of BUIs
  3. Provide design and monitoring guidance for other wetland reconnection projects throughout the Great Lakes and support widespread integration of adaptive management principles

Background & Justification
Over 95% of the original wetland habitats along the U.S. shoreline of western Lake Erie have been lost since the 1860s. Most of the remaining coastal wetlands have been isolated by earthen dikes to protect them from wave attack and promote management as migratory waterfowl habitat. Although these diked wetlands are adjacent to the Lake Erie shoreline, they no longer provide many of the functions and services of coastal wetlands (e.g., fish habitat, water quality improvement) because they are separated from the lake hydrologically. Fish, mussels, and organisms with limited mobility are especially impacted because they are not able to use the diked wetland habitats as they would hydrologically connected wetland habitats (e.g., for seasonal movement). Unfortunately, most of the few remaining undiked wetlands are severely degraded and contribute to the beneficial use impairments identified in the Maumee River Area of Concern. They remain connected to the lake hydrologically, but the wetland vegetation that provides vital fish habitat is sufficiently degraded to negatively impact the approximately 43 species of Great Lakes fish that use wetland habitats as spawning and nursery locations. Many commercially and recreationally important fish depend on these productive habitats to feed (e.g., longnose gar, channel catfish, bowfin), spawn (e.g., northern pike, yellow perch), or provide protection to young-of-the year fish (e.g., gizzard shad, emerald shiner, largemouth bass). Therefore, restoring the connection between coastal wetlands and diked wetland habitats will increase the amount of habitat available to fish, mollusks, and other biota and promote the sustainable reestablishment of lake-driven hydrology as the ecological driver of the system. Restoring the flow of water into and out of isolated wetlands will affect the transport of nutrients, nutrient cycling, water quality, flood storage, and many other abiotic conditions associated with beneficial use impairments.

Hydrologic and landscape alteration resulting in wetland degradation is not unique to western Lake Erie. Michigan’s Shiawassee flats, over 16,100 ha (40,000 ac) of floodplain forest, fields, and wetlands formed as the Shiawassee, Flint, Tittawabassee, Bad, and Cass Rivers come together to form the Saginaw River, is influenced by both agricultural watersheds, shoreline hardening, and stressors associated with the areas within the Saginaw River/Bay Area of Concern. Water availability (amount and timing) is highly variable as water flowing off the altered landscape is influenced by higher Lake Huron water levels that back water up the Saginaw River.

Principal Investigator: Kurt Kowalski

Problem Statement
There is no comprehensive assessment of current and potential wetland habitats that provides sufficient specificity to guide restoration action or evaluate the regional effects of action in the coastal zone of western Lake Erie. Similarly, a structured and collaborative approach to regional coastal wetland research, management, and restoration is not available to guide the decision-making process.


  1. Develop the ability to identify, prioritize, pursue, and track ongoing and future coastal restoration and management opportunities that can contribute to beneficial use impairment delisting and improvements in ecosystem health
  2. Create a framework for research and monitoring that will create a greater understanding of restoration potential across the Western Lake Erie landscape
  3. Use the structured decision making (SDM) process to set the framework for coordinated coastal wetland habitat management and restoration in the coastal Great Lakes

Background & Justification
Coastal wetland management activities and restoration efforts in Western Lake Erie have historically been done on a parcel by parcel basis. Owners of multiple parcels (e.g., USFWS, ODNR, hunting clubs) often coordinate their management efforts within their own holdings, but the scope of decision-making often is limited by the geographic extent of the areas that they are familiar with and responsible for. A full accounting of active coastal, diked, and other potentially restorable wetlands in western Lake Erie does not exist, so landscape coordination of their management and restoration is very difficult. Similarly, potential restoration efforts often are limited to the areas that are already under management as wetlands (e.g., diked wetlands) or are known locations of former wetlands (e.g., wet agricultural fields). The suite of sites that have high restoration potential (e.g., those that are geographically close to Lake Erie or a tributary, are at lower elevations, contain hydric soils, rich wetland seed bank) is not well documented regionally, so selecting priority areas for restoration is difficult both on a landscape level and within ownership or agency constraints.

Structured decision making (SDM) is an organized analysis of problems that seeks to identify and evaluate creative solutions focused clearly on achieving fundamental objectives. The USFWS has been implementing this approach for several years, and new opportunities exist to partner with USGS and apply the SDM process to regional strategies and science exploration of Great Lakes coastal wetland restoration and management. Staff from the USFWS Shiawassee NWR, Ottawa NWR, and Midwest Regional Office (Refuges), and USGS will collaborate to analyze research needs, monitoring protocols, management strategies, and habitat rehabilitation techniques within a regional context. The group will seek to increase the landscape-level understanding of coastal wetland ecosystem function, outcomes of specific management strategies, and long-term effects of coastal wetland restoration efforts.

Principal Investigator: Kurt Kowalski

Problem Statement
The presence of water is of course necessary to support aquatic organisms. The quantity, quality, and dynamic conditions of water in lotic systems also influence populations and communities of aquatic organisms. Human exploitation of water resources can greatly affect flow of water through lotic systems, but the specific responses of fish and other aquatic organisms to altered flow regimes is poorly understood. This study investigates effects of water throughput in a lotic system and its variability on the biodiversity, community structure, and abundance of fish populations and communities.


  • Apply newly generated model-estimated stream flows (AFINCH) with GLGap model-predicted fish occurrence and abundance in lotic systems of the Great Lakes Region to evaluate the response of fish assemblages and selected species to changes in stream flow regime.
  • Use the above predicted community responses to map areas of Great Lakes watersheds that are sensitive to flow alteration.
  • Provide support to those responsible for implementation of the Great Lakes Water Compact.

Hypotheses to Test

  • Lotic fish assemblages do not vary with flow regime.
  • There is no differential spatial response of lotic fish assemblages to flow alteration.

Background & Description
This study is a component of the multidisciplinary Great lakes Restoration Initiative, “Watershed modeling for stream ecosystem management” study (Task #81) -- Point of contact: Howard W. Reeves, Michigan Water Science Center; 517-887-8914.

Assessment, management, and any restoration of Great Lakes Basin aquatic ecosystems require an understanding of the relations between landscape characteristics and ecological structure and function, including effects of water withdrawals and returns, and streamflow. This project is designed to provide predictive models of the responses of aquatic communities to changes in stream flow developed in the larger study (Reeves, Task #81). The results of this research will be used in combination with other components of the larger study to support implementation of the Great Lakes-St. Lawrence River Basin Water Resources Compact (GRBWRC) (Council of Great Lakes Governors, 2005).

The GRBWRC was signed into law in 2008 (U.S. Congress, 2008). This compact and agreement builds upon the Great Lakes Charter Annex of 2001 (Council of Great Lakes Governors, 2001) and seeks to “protect, conserve, restore, improve and effectively manage the waters and water dependent natural resources of the Great Lakes basin.” Implementation legislation in the State of Michigan has led to the development of a water-withdrawal assessment process and on-line water-withdrawal assessment screening tool (Michigan State Legislature, 2008; The assessment process and screening tool is built upon a consistent hydrologic data framework based on the National Hydrography Dataset Plus (NHDPlus). This research project will integrate the results of the USGS Great Lakes Regional Aquatic Gap Analysis Project (GLGap) (for example, Morrison et al. 2003; Brenden et al. 2006, McKenna and Castiglione 2010) and other regional efforts to create a regionally consistent data framework that will support modeling of landscape and hydrologic variables to relate changes in environmental conditions such as large-scale water withdrawals or climate change to ecological change.

The GLGap project has cooperated with state and federal natural resource agencies, Universities, and NGOs to map and classify aquatic habitats, define fish distributions, and identify gaps in the distribution and conservation of fish species and their habitats for lotic systems of the US Great Lakes watershed using the 1:100,000 scale NHD. The GLGap results consist of regionally consistent spatial data components that may form the basis of the proposed framework and include landscape characterization of inter-confluence stream reaches and associated watersheds with more than 300 habitat attributes, empirical models to predict fish species abundance for more than 130 fish species, empirical models to predict summer stream temperature, a hierarchical aquatic habitat classification framework, a fish-based lotic habitat classification, and a central relational database to store results (Morrison et al. 2003; Brenden et al. 2006; Brenden et al. 2008; Lyons et al. 2009; McKenna et al. 2006; Steen et al. 2010; Steen et al., 2006; Steen et al., 2008; Stewart et al., 2006, McKenna et al. 2010, McKenna and Castiglione 2010, McKenna and Johnson 2011). These results have been achieved for all lotic habitats within the U.S. Great Lakes-St. Lawrence River Basin and for a limited number of nearshore Great Lake areas (McKenna and Castiglione 2010). Many of these results have already been adopted by state natural resource agencies for use by natural resource managers and policy makers to better understand, manage, and conserve our aquatic natural resources. These tools and data substantially extend our ability to assist managers with planning and identification of priorities for conservation goals.
Effective implementation of the Great Lakes Water Compact and maintenance of high quality aquatic living resources in the Great Lakes Basin depend on effective management of water flow in Great Lakes tributaries, such that natural ecological processes and aquatic communities are maintained. However, the dependence of ecological functions and aquatic communities on particular levels of flow (relative to natural conditions for a given stream reach) are poorly known in the Great Lakes Basin – even base flows are not well known. This study will quantify the relationships between landscape variables and aquatic community structure and develop a means of assessing the potential effects of altered stream flow conditions. The investigations will address a number of important aquatic resource questions, including, what classes of flow are appropriate for management? Where are the breaks where significant changes in assemblage structure or diversity occur? What are significant ecological changes?

Principal Investigator: James E. McKenna, Jr.

The Huron-Erie Corridor (HEC) is the connecting channel between lake  Huron and Erie, including the St. Clair River, Lake St. Clair, Detroit River, and western Lake Erie. The HEC contains the largest freshwater delta in the Great Lakes, supports over 65 species of fish, 16 of which are classified as threatened or endangered, and is one of the busiest navigation centers in the United States. Historically, the HEC supported a highly productive fishery, providing spawning and nursery habitat for 80 species, including lake trout, lake sturgeon, lake whitefish, lake herring, walleye, and yellow perch. Unfortunately, over the last century, fish productivity in the HEC has been dramatically reduced due to construction of shipping channels, which severely altered fish spawning grounds and nursery habitats. The main objective of this project is to identify locations within the St. Clair and Detroit Rivers that provide the best opportunities for remediation of fish spawning and nursery habitats, with the ultimate goal of enhancing native fish populations. The goal of this GLRI project is to enhance native fish populations through restoration of fish spawning and nursery habitats in the HEC and St. Clair and Detroit Rivers Areas of Concern (AOCs). The USGS is providing vital information to define restoration targets in AOCs, and is measuring restoration success through pre- and post- habitat construction assessments. This work is being completed as part of the greater Huron-Erie Corridor Initiative (, a highly collaborative initiative started in 2004 by the USGS Great Lakes Science Center and over 20 partners to restore habitats and native fish and wildlife species in the corridor, ultimately providing societal, economic, and environmental benefits to the Great Lakes region.

Principal Investigator: Ed Roseman

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