Great Lakes Habitat Restoration: Partnering to Promote Fish Production

A new Regional Habitat Partnership between the Great Lakes Fishery Commission and National Oceanic and Atmospheric Administration will support fish habitat restoration priorities in the Great Lakes.

Authors: Andrea Miehls, GLFC, Jeff Tyson, GLFC, Jill Wingfield, GLFC, and Julie Simmons, NOAA

Degradation of coastal, nearshore, and riverine habitats has adversely affected fish communities and fisheries in the Great Lakes for more than a century. Now a partnership between the National Oceanic and Atmospheric Administration (NOAA) and the Great Lakes Fishery Commission (Commission) is advancing restoration goals for important habitat for Great Lakes fish. Working with NOAA Fisheries through a Regional Habitat Partnership funded at $4.8 million by NOAA, the Commission, along with local partners, is leading implementation of high priority projects as identified by Lake Committees across the Great Lakes basin.

The Lake Committees, which include representation by senior officials from state, provincial, and U.S. intertribal fishery agencies, conducted an extensive process to identify habitat constraints on native fish production and to prioritize restoration efforts during the next decade in each of the Great Lakes. High-quality connected habitats are important for sustained fish production—by protecting and improving habitat, fish communities and their associated fisheries can directly benefit. Fish habitat improvement techniques range from regional-scale actions that impact water quality and sediment erosion, to local actions that improve connectivity (e.g., dam removal) or restore open-lake physical habitat (e.g., reef construction). Selecting appropriate strategies and locations for habitat protection and improvement is critical. Consequently, the development of priorities is an important step for progress toward protecting and improving fish habitat.

Prioritization Process

The prioritization process conducted by the Lake Committees yielded a set of priority projects in each Great Lake. A subset of six of the priority projects—ranging from shovel-ready to conceptual—was included as part of the regional partnership. All six projects will directly contribute to fish production in areas identified by the Lake Committees as priorities. The six projects span the breadth of the Great Lakes with at least one project in each Great Lake, and will benefit a variety of fish species such as state-listed species (lake sturgeon) and targeted species in formal restoration plans (walleye, brook trout, Atlantic salmon, cisco, lake trout). Impairments addressed in these projects include degraded reef substrates, hydrologic barriers in tributaries, excessive in-stream bank erosion, and lack of productive capacity. The projects include four projects being addressed in the first wave of activity (detailed below) and two additional projects which will move forward in a second wave.

A map of the Great Lakes with five locations noted: Nebagamon Creek, Northern Lake Michigan, Inner Saginaw Bay, Flat Rock & Huroc Dam, and the Salmon River.

Map of the six project sites selected during the prioritization process, with at least one site on each Great Lake. Note that the Salmon River site includes two projects. Credit: Andrea Miehls, GLFC.

Project Spotlight

Lake Superior: Nebagamon Creek Railroad Embankment and Culvert Removal Project

Location: Nebagamon Creek, Douglas County, Wisconsin.

Partners: GLFC, NOAA, Wisconsin Department of Natural Resources, Wisconsin Department of Agriculture, Trade and Consumer Protection, Douglas County, and the Town of Brule.

Timeline: Construction began in summer 2023 and will complete by fall 2023, followed by post-restoration monitoring in 2023-2025.

Overview: Nebagamon Creek is a tributary to the Bois Brule River. The Nebagamon Creek restoration site is a collapsing culvert and abandoned railroad grade that impedes fish passage for all life stages of brook trout and other Lake Superior and resident salmonids in the Bois Brule River watershed. In its current condition, the site also poses a high-risk sediment threat to downstream spawning and rearing areas in Nebagamon Creek and the Bois Brule River. The project will remove the collapsed culvert and railroad embankment and will restore natural hydrologic conditions for fish passage and sediment transport in the project area.

More information:

A photo of a deteriorating culvert overgrown with plants and with a creek blocked by debris.

The Nebagamon Creek Railroad Embankment and Culvert Removal Project site. The collapsed culvert, which impedes nearly all fish passage, is visible in the center-right of the photo. Credit: Jeff Tyson, GLFC.

Project Spotlight

Lake Ontario: Salmon River Trestle Pool Project

Location: Salmon River, Oswego County, New York.

Partners: GLFC, NOAA, New York State Department of Environmental Conservation, US Fish & Wildlife Service-New York Field Office, and the Finger Lakes Lake Ontario Watershed Protection Association.

Timeline: Construction began in summer 2023 and is anticipated to be completed by fall 2024, followed by post-restoration monitoring in 2024 and 2025.

Overview: The Salmon River is a key tributary to Lake Ontario for Atlantic salmon restoration. The trestle pool restoration site, which consists of an abandoned railroad trestle with associated abutments, backs up water during high flow events, inhibits sediment transport, increases upstream sedimentation, and induces streambank erosion in the downstream reaches. The area contains degraded riparian and stream conditions which contribute to unsuitable habitats for Atlantic salmon spawning and rearing. This project will remove the abandoned railroad central pier and left abutment to provide hydrologic reconnection to the floodplain and restore habitat heterogeneity, while reducing in-stream and bank erosion through installation of in-stream structures and toe-wood bank stabilization structures. This work is being guided under the Lower Salmon River Restoration and Recreation Enhancement Plan.

More information:

A photo of a river with concrete structures on both banks and in the center of the river.

The Salmon River Trestle Pool Project site. The abandoned railroad central pier and left abutment slated for removal are visible in the center-left of the photo. Credit: Jeff Tyson, GLFC.

Project Spotlight

Lake Erie: Flat Rock/Huroc Dam Fish Passage Project

Location: Huron River, Wayne County, Michigan.

Partners: GLFC, NOAA, Huron-Clinton Metroparks, Michigan Department of Natural Resources, Huron River Watershed Council, and the City of Flat Rock.

Timeline: The feasibility study is being conducted from spring 2023 to spring 2024.

Overview: The Flat Rock and Huroc dams are located on the Huron River, Michigan and are the first significant fish passage barriers upstream from Lake Erie. The two barriers restrict fish passage and limit production for multiple species of common concern including lake sturgeon, walleye, and white bass, and have downstream impacts to hydraulic connectivity and habitat. Additionally, multiple species of concern, including native mussels such as snuffbox, elktoe, purple wartyback, and the wavy-rayed lampmussel, as well as their host-fish species, logperch, smallmouth bass, eastern sand darter, and spotted sucker, are documented in this river system. This project is focused on developing a feasibility study that considers alternatives for the Flat Rock and Huroc dams that will benefit the community and surrounding natural habitats and enhance fish passage at the site. Goals include improved fish passage and reconnecting important tributary habitat to Great Lakes species while also minimizing the risk of invasive sea lamprey infestation.

More information:

: Photos of two dams that cross large rivers, with transportation structures over the top of each dam. : Photos of two dams that cross large rivers, with transportation structures over the top of each dam.

The Flat Rock (left) and Huroc (right) dams in the Huron River, Michigan. Credit: Jeff Tyson, GLFC.

Project Spotlight

Lake Huron: Inner Saginaw Bay Reef Restoration Project

Location: Saginaw Bay, Bay County, Michigan, with restoration sites in the vicinity of the Kawkawlin River outlet and/or near Spoils Island.

Partners: GLFC, NOAA, Michigan Department of Natural Resources, Michigan Department of Environment, Great Lakes, and Energy, and Michigan Sea Grant.

Timeline: Stakeholder workshop scoping, feasibility work, and completion of design plans is expected in late 2023 or 2024, with construction planned in 2024-2025 after identification of the preferred restoration site and completion of final design plans.

Overview: Reef habitats in Saginaw Bay have been degraded by impacts from physical destruction, degradation from shoreline development, sedimentation, chemical contamination, and aquatic invasive species. This project will establish needed spawning habitat in inner Saginaw Bay for multiple species of common concern, including lake trout, lake whitefish, walleye, and cisco. Natural materials and established techniques will be used in the construction of the reef, and the reef will be located in proximity to appropriate thermal conditions for spawning and rearing of these species. In addition to enhancing production for important fish species that support fisheries, this project has the potential to be conducted in concert with other shoreline infrastructure work to reduce coastal flooding and erosion, reduce the frequency of navigational dredging, increase recreational access, and increase coastal resilience to climate change.

More information:

: A map of an island within a large lake. : A map of a river outlet into a large lake.

Inner Saginaw Bay Reef Restoration Project potential locations at Spoils Island (left) and the Kawkawlin River outlet (right). Source: Saginaw Bay Reef Feasibility Study, February 2022, ECT No.200654.

Additional Priority Projects Soon to be Addressed

In addition to the four ongoing projects highlighted above, two additional projects are planned for the future. The first is reef restoration in northern Lake Michigan (near Charlevoix, Michigan – exact location to be determined). This project will identify restoration locations and guide restoration actions for reef rehabilitation in northern Lake Michigan, improving habitat for lake whitefish, lake trout, and cisco. The second is additional in-stream habitat restoration in the Salmon River, Lake Ontario (Oswego County, New York). This project will focus on restoration of natural erosion and sedimentation processes, and reconnection to the floodplain, in two reaches directly downstream of the Trestle Pool site to improve habitats for Atlantic salmon and other native species.

Strengthening Great Lakes Fisheries, Ecosystems, and Communities

The Great Lakes and St. Lawrence River basin include more than 10,000 miles of coastline that are home to more than 3,500 plant and animal species, some of which are found nowhere else on Earth. Yet, extensive human activity for more than a century has led to the loss of habitat for fish, negatively impacting fish production and fisheries in addition to other negative impacts on the region's rich and diverse ecosystems.

The new Regional Habitat Partnership between NOAA and the Commission is working to address critical habitat needs in priority areas of the Great Lakes, thereby contributing to healthy Great Lakes ecosystems and fisheries.

"NOAA is proud to partner with the Great Lakes Fishery Commission on these important efforts to restore habitat and bring benefits to Great Lakes fisheries and communities," said Carrie Selberg Robinson, director of the NOAA Fisheries Office of Habitat Conservation.

"Habitat restoration efforts enacted through the partnership will further the Strategic Vision of the Commission and missions of project partners by restoring healthy Great Lakes ecosystems and sustainable fisheries and through the development of strategic alliances and partnerships," said James McKane, the Commission's chair.

McKane added, "Working together through the Regional Habitat Partnership, the Commission, NOAA, and other project partners endeavor to sustain the many benefits the Great Lakes provide to our environment and communities."

A photo of a fisherman holding a large fish while gripping his fishing pole in his mouth . A photo of a smaller fish held in a fisherperson's hand.

Anglers hold an Atlantic salmon (left) and brook trout (right), two species which will benefit from habitat restoration activities through the Regional Habitat Partnership between NOAA and the Commission. Credits: USGS (left) and Zac Wickert (right).

Read more Pulse on Science: Project Spotlights