WDFW moving forward with estuary restoration projects in North Puget Sound

Restoration of intertidal marsh habitats on WDFW-managed lands in Skagit, Stillaguamish and Snohomish estuaries benefits salmon and other species.

Restored intertidal marsh and estuary habitat at the Leque Island Unit of Skagit Wildlife Area near Stanwood.

Puget Sound’s estuaries are teeming with life; from salmon smolts to dabbling ducks, seals to shorebirds, bull trout to bivalves. Estuaries are vitally important for many species of fish and wildlife. During the last century, widespread reduction or alteration of estuaries through conversion to support agriculture and land development has contributed significantly to species declines.

This loss of naturally functioning estuary habitat has been particularly harmful for juvenile Chinook salmon, who use intertidal marshes and sloughs to feed and grow before venturing further into Puget Sound and on to the open Pacific Ocean. To recover this iconic species, we need to restore more of our region’s estuaries.

Along with Native American tribes, state and federal agencies, and many other partners, the Washington Department of Fish and Wildlife (WDFW) is working to restore estuary habitat on lands we manage on behalf of Washingtonians and our state’s fish and wildlife.

Much of this work is supported by the Estuary and Salmon Restoration Program (ESRP) as well as the Puget Sound Acquisition and Restoration Fund (PSAR) and Salmon Recovery Funding Board (SRFB), among other funding sources.

In the North Puget Sound Region, a focus area for this work has been the Skagit, Stillaguamish, and Snohomish river deltas, which together makeup the Whidbey Basin

As of early 2023, WDFW has restored hundreds of acres back to estuary across multiple State Wildlife Areas and other lands. Sites that have been restored such as Leque Island, Wiley Slough (at our Skagit Headquarters Unit), and Fir Island Farm are now providing habitat for Chinook salmon and more than 20 other species of fish, as well as numerous waterfowl, shorebirds, Dungeness crab and other wildlife.

Work is also moving forward on other sites such as Milltown and Island Unit in the South Fork Skagit River estuary, and Spencer Island in the Snohomish River estuary.

Estuaries form where freshwater and saltwater mix, and provide a wealth of environmental services that make them valuable habitats to conserve and restore. They serve as nursery habitats for a variety of marine life, filter nutrients from run-off, support a host of wildlife species, and can shield coastal areas from storm surge, flooding, and erosion.

Importance of estuarine habitat for salmon in Whidbey Basin

Every year adult salmon return to spawn in Puget Sound rivers, producing young that will begin making their way toward saltwater within days or up to a year after hatching from an egg and emerging from the gravel. Along the way to Puget Sound Chinook salmon in particular use rearing habitats in river floodplains and estuaries, typically spending a few weeks to months in the estuary between February and August.

Estuaries provide important habitat for juvenile Chinook in several major ways. Estuary habitats range from tidal freshwater forests and shrubby areas to saltier marshes, sloughs, and unvegetated mud- or sand-flats. Collectively these extremely productive habitats provide abundant marine invertebrates and other food that support juvenile Chinook growth and development, a salinity mixing zone where they transition from fresh to salt water, and refuge from predation.

These rich feeding and rearing grounds allow fish to grow bigger, so they have a better chance of survival in Puget Sound and beyond.

A Chinook salmon parr. Soon after this stage young Chinook will “smoltify” and head out to the estuary, where they will feed and grow before migrating further into Puget Sound and on to the ocean.

Estuaries also support a host of other fish and wildlife, from smelt and sea run coastal cutthroat trout to shorebirds, herons, and raptors.

Declines in Puget Sound Chinook tied to estuary loss

Loss of estuaries has led to the decline in Chinook and other salmon. In Puget Sound, 70–80% of estuary habitat has been lost as it was diked and drained to make land suitable for agriculture and development.

Puget Sound Chinook were listed as Threatened under the federal Endangered Species Act in 1999 and a recovery plan was completed in 2007. Estuary restoration is an important action to recover Chinook in the Whidbey Basin (see map below) and across the North Puget Sound Region.

A map of Whidbey Basin, including Skagit and Port Susan bays and other waterbodies in Island, Skagit and Snohomish counties. Map: Erica Sloniker/The Nature Conservancy in Washington.

WDFW and others have completed a number of estuary restoration projects in Whidbey Basin over the last 20 years. Restoration involves removing or setting back dikes and levees, excavating channels, and establishing native vegetation. Infrastructure such as dikes, levees, tidegates and pumps are often incorporated into projects to maintain drainage and flood protection on neighboring lands.

These projects have been extremely successful for Chinook and other fish. Monitoring has shown that when new areas are restored, they are occupied as soon as juveniles come down the river.

Hundreds of thousands of juvenile Chinook are using restored sites each year and are growing bigger. Scientists also found up to 22 other species of fish using restored estuary including juvenile chum, pink, and coho salmon, steelhead and coastal cutthroat trout, native char, three-spine stickleback, starry flounder, prickly sculpin, and peamouth chub.

Estuary Restoration in the Skagit Basin

WDFW has been engaged in estuary restoration on agency-owned lands in the Skagit Delta for more than 20 years. Completed projects are heavily used by Chinook and other fish, and are good places for people too. Many folks use these sites for hunting, walking, birdwatching and photography.

Birders and photographers enjoy the trails at Fir Island in the Skagit River Estuary.

Wiley Slough

The Wiley Slough Estuary Restoration Project, which is located on WDFW’s Skagit Wildlife Area Headquarters Unit at the mouth of Freshwater Slough in the lower South Fork Skagit River, was completed in 2009.

Prior to restoration the site was used to grow enhanced waterfowl forage, and a variety of recreational users enjoyed hunting, walking, birding and taking photographs. The project restored 156 acres of estuary by removing over one mile of existing levee, building a setback levee and installing new tidegates.

Post-project monitoring shows the restored estuary is used by hundreds of thousands of juvenile Chinook each year. The site continues to be heavily used by a range of recreational user groups.

Although the habitat has been successfully restored, there are ongoing flood and drainage concerns. The setback dike has overtopped six times since 2016 causing damage to the dike, wildlife area access road and other features on site. It also resulted in flooding of neighboring land. More severe or prolonged overtopping could breach the dike and cause large-scale flooding and damages.

The dike will be raised to a height that will decrease risk of overtopping. Raising the dike requires additional widening on the landward side, which will result in some changes to parking, road alignment and vegetation.

WDFW hired a consultant to design the dike repairs and each phase of design was reviewed by WDFW staff and the local flood control district. Final design and permitting for the dike repair is completed and WDFW hired a construction contractor to build the project. The site will be closed to the public during spring, summer and fall of 2023 for construction.

Estuary restoration work at the Fir Island Farm Unit in 2016.

Fir Island Farm

The Fir Island Farm Estuary Restoration Project, which is located on Fir Island approximately 3 ¼ miles west of Conway, was completed in 2016. The project restored 131 acres of estuary by building a setback dike, excavating tidal channels, and removing a bay-front dike. To ensure equal or better drainage and provide climate resilience into the future, we also constructed new tidegates, a drainage storage pond and a pump station.

Learn more about restoration at Fir Island Farm in this blog post from 2020.

The design was completed by a consultant with review by WDFW staff, a technical team comprised of local engineering and restoration experts, and District 22, which manages diking, drainage and irrigation on Fir Island.

Post-project monitoring shows that the project is good for fish and good for neighbors. Fish monitoring data shows the restored estuary is used by tens of thousands of juvenile Chinook each year. Post-construction monitoring of flood and drainage performance shows the project is functioning as designed. District 22 took over operations of the flood and drainage infrastructure in 2020.

Aerial view of Fir Island Farm Reserve Unit after estuary restoration work.

Milltown Island

The Milltown Island Estuary Restoration Project is located on a mid‐channel island in the South Fork Skagit River and is accessible only by boat. The site was historically diked and drained, and early homesteaders lived and farmed on the island. Since flood‐caused dike breaches and loss of a bridge to Milltown Island decades ago, the site has been left fallow. Between 1999 and 2014, additional breaches and channels were constructed for the benefit of salmon and other fish and wildlife that rely on estuaries.

Because much of the dike system is still in place, the site remains largely cut off from full tidal exchange and river floods. To provide the maximum benefit possible, additional channels are needed. Current conditions also support non‐native weeds such as cattail and reed canarygrass. Restoration will include removing additional sections of dike, excavating new channels. and constructing low‐angle boat landings. The spoils from dike removals and channels will be used to create low mounds. Lastly, we will manage weeds and establish native marsh plants.

WDFW hired a consultant to design the restoration project. Design elements were reviewed by a technical advisory committee, WDFW staff, a small group of waterfowlers and Ducks Unlimited. The design is completed and permit applications are being developed. Construction timing will depend on obtaining full construction funding and when permit authorizations are obtained. The likely timeframe for construction is summer 2024.

An aerial view of the Island Unit near the town of Conway.

Island Unit

Similar to Milltown Island, the Island Unit Estuary Restoration Project is located on two mid-channel islands in the South Fork Skagit River and is accessible only by boat. The site was diked and drained in the 1800s, and early homesteaders lived and farmed on the island. A bridge washed out decades ago making access difficult.

Since the 1950’s WDFW has provided enhanced and managed waterfowl forage, and the site is popular with waterfowl hunters. However, aging infrastructure and changing habitat needs led WDFW to consider other management options. WDFW considered four alternatives from no restoration to full restoration of the 270-acre site. In early 2021 after a comprehensive assessment with input from an advisory group and the public, WDFW selected full restoration.

In 2021, one of two tidegates on the site failed and a dike on the east island breached. WDFW decided not to repair either of these structures due to complex permitting, mitigation requirements, uncertainty about the longevity of other infrastructure, and lack of funding, among other things. While the east island is now inundated regularly with tides and river flows, additional work here and on the west island is needed to fully restore functional estuary and realize the biggest benefit to Chinook and other fish and wildlife.

In 2022, WDFW hired a consultant to complete a preliminary design. The design will include removing dikes, levees and tidegates, and excavating channels. Additional features will be determined as design work progresses. WDFW will continue to seek input from a range of interests, including waterfowl hunters, on the project design. Additional funding for final design, permitting and construction is being sought now. Construction is not likely to happen for several years.

More information on Island Unit Restoration is also available in this FAQ.

Estuary Restoration in the Stillaguamish Basin

WDFW and partners recently completed one of the largest estuary restoration projects in Puget Sound in the Stillaguamish delta at Leque Island. We’ve also launched an initiative to build momentum for recovery of Stillaguamish Chinook salmon and their habitat.

Leque Island

Leque Island is located at the mouth of an old Stillaguamish River channel between Stanwood and Camano Island. Historically it was an intertidal marsh that connected Port Susan Bay and Skagit Bay. Settlers built more than 3 miles of dike around 276 acres of the marsh to drain it and convert the area to farmland and homesteads. WDFW began acquiring properties on Leque Island beginning in the 1970’s and eventually owned the entirety of the island in 2011.

After years of planning and securing grant funding from state and federal programs, WDFW and project partner Ducks Unlimited removed the dike and reintroduced the tides to 250 acres in 2019. This past Fall in 2022, WDFW removed additional dike to restore the entirety of 276-acre project footprint.

WDFW and partners are now monitoring the results of the project. Biologists at Skagit River System Cooperative have found 15 different fish species in the newly restored habitat, including juvenile Chinook, chum, coho, and pink salmon. Scientists are also finding a wider diversity and higher abundance of birds on the site after restoration.

In addition to ecological benefits, the project provides flood protection for the City of Stanwood and is well used by outdoor recreationists. A wave protection berm serves as a breakwater for a vulnerable section of the city and a walking trail sits atop it. Throughout the year the trail is used by birders, waterfowl hunters, and people just getting outside for some fresh air and exercise.

Learn more about the Stillaguamish River in our recent short film.

Estuary Restoration in the Snohomish Basin

The Snohomish estuary has been a focal point for restoration since the mid-1990’s. Although surrounded by a growing urban environment, the Snohomish delta is the focus of a large restoration effort and substantial habitat restoration project have been completed by the state, Snohomish County, The Tulalip Tribes, and others. WDFW, and partners are continuing to restore this river delta that provides critical habitat for ESA-listed Chinook salmon as well as other fish and wildlife.

In 2020 WDFW convened a group of partners, land owners, and municipalities to participate in a planning process that would identify and push forward the next estuary restoration project in the Snohomish Basin. Three properties in public ownership that had been slated for restoration for one or more decades were on the table — Spencer Island, Chinook Marsh, and North Ebey Island.

While the initial goal was to choose only one project to push forward, it was unanimously decided that all three projects should be accelerated. Collectively, group members identified barriers to restoration that had so far delayed each project as well as the methods necessary to overcome those barriers. From this planning process, Chinook Marsh and Spencer Island currently have funding and are on the path to restoration.

Estuary restoration projects led by the county, state, and tribes in Snohomish County. Spencer Island is the middle area of yellow, Ebey Island is in blue. Map: Snohomish County

Spencer Island

Spencer Island is located in the Snohomish River estuary east of the City of Everett. The island is a flat, tidal wetland complex ringed with an old dike with several openings and bridges that serve as a trail. Steamboat Slough borders the property to the east and Union Slough borders the property to the west.

In the early 1900s, the site was diked and developed for grazing and agriculture, resulting in the loss of tidally influenced forested wetlands and channels. WDFW and Snohomish County purchased the property in 1989, with WDFW owning 174 acres on the north end, and Snohomish County owning 240 acres on the south end of the island.

In 1994, Snohomish County completed a restoration project that involved removing sections of dike that allowed tidal water and fish into the southern portion of the property. In 2005, the dike failed on the northern WDFW portion of the site that allowed tides and fish into the entirety of the site. Although the entire site is now tidally inundated, remnant dikes and ditches still occur on the island that reduce habitat benefits for salmon and other species that rely on tidal wetlands.

WDFW is in the early planning stages for a project that will more fully restore habitat on Spencer Island. WDFW is partnering with the United States Army Corps of Engineers on the project, in collaboration with Snohomish County and others. The project is jointly funded by WDFW and the Army Corps, with the Federal government funding the majority of the project.

Properly restoring this property will more fully restore tidal processes that will encourage tidal channel formation and maintenance, channel migration, erosion, accretion of sediments, and better connectivity for aquatic species. The primary habitat to be restored is tidally influenced estuary habitat that will support all species of salmon, primarily ESA listed Chinook salmon. In addition to restoration goals, WDFW intends to retain accessibility to the site for outdoor recreation activities.

WDFW and the Army Corps are currently gathering data that will be used in developing a preliminary design for the project and anticipate providing an update to stakeholders and asking for feedback in mid-2023. Because the project is early in the planning stages, construction is not anticipated for several years.

May 2023 update: More information on restoration planning for Ebey Island Wildlife Area Unit near Everett is now available: https://wdfw.wa.gov/newsroom/news-release/wdfw-seeks-public-input-draft-ebey-island-management-plan

Learn more about our work for estuaries and Puget Sound recovery on this webpage.

Mount Baker above estuary habitat and dabbling ducks at Spencer Island near Everett.



The Washington Department of Fish and Wildlife

The Washington Department of Fish and Wildlife is dedicated to preserving, protecting and perpetuating the state’s fish and wildlife resources.