WSG-funded researchers investigate estuary restoration through the eyes of juvenile salmon

November 10, 2025

By Mel Lemke, WSG Science Communications Fellow

Hatching from their eggs into the waters of the Stillaguamish River, Chinook salmon begin their lives as tiny freshwater fry. No more than a few millimeters long at hatching, these tiny babies spend their early weeks of life nourished by their yolk sacs before they begin feasting on small freshwater invertebrates like bugs, snails and larvae. Carried by the river’s flow, they navigate miles of floodplains, small channels, and man-made levees on their journey to the sea. By the time they are the size of your thumb, many juvenile Chinook reach their critical estuary habitat – where the river meets the sea – and begin to feed on a smorgasbord of terrestrial insects and estuarine invertebrates. In estuarine marshlands like those of the Stillaguamish River delta, Chinook forage and grow before migrating to the nearshore marine waters as young smolts, and eventually the open ocean, where they mature into adults.

Estuaries are an important intermediate habitat for young salmon. There, salmon find critical feeding grounds, safety from large predators, and adapt to different temperatures and salinities as they prepare for life in the ocean. However, their location along coastlines means that estuaries have long been desirable for human occupation and development as well.

Like many estuaries along the West Coast, most of the Stillaguamish delta’s historic tidal marshes were developed into farmland by the late 19th century. Large walls were erected along the bayfront to protect agricultural lands from salty tides, and extensive river levees were built to protect the land against floodwaters. These barriers, however, severed the ecological links between land, river and sea. Ecologically diverse marshland was transformed into a simplified, sediment-starved, and food-limited delta that deprived fish like salmon of both critical habitat and the variety of invertebrates they like to eat.

The decline of salmon in the Stillaguamish and other rivers draining to the Salish Sea is a major ecological concern. As salmon live and grow at sea, they accumulate large amounts of organic material and nutrients. These nutrients are then transferred upstream to freshwater riparian habitats when salmon re-enter freshwater systems to spawn at the end of their lives. Returning adult salmon feed not only people and bears fattening up for the winter, but also seals, orca, shrews, deer, birds, insects, and even trees. Without this keystone species, whole ecosystems are at risk of collapse.

Salmon are also woven into the fabric of Indigenous cultures, livelihoods, and subsistence food systems. Unfortunately, the dramatic decline in the once robust Stillaguamish River Chinook salmon populations is so severe that the Stillaguamish Tribe hasn’t had a commercial or subsistence Chinook fishery since the 1980s. Helping these salmon recover through restoring their critical habitats is a major goal for meeting ecological and human needs.

The Nature Conservancy (TNC), the Stillaguamish Tribe, and the Washington Department of Fish and Wildlife have each led restoration projects in the delta, pouring an immense amount of work into reviving the estuary habitats that salmon need to thrive. Together, these projects will restore more than 1,000 acres of historical tidal marshes and channels to the delta, hopefully allowing the delta to once again support growing salmon while also preparing it for a more resilient future.

An important aspect of the restoration work is evaluating the impacts of the restoration over time, especially to see if the ecological changes implemented create a more productive Chinook salmon habitat. TNC first restored a 150-acre portion of the delta in 2012. After years of monitoring, the team decided a revision to the original restoration would benefit the still-imperiled Chinook population. Guided by advancements in restoration science, the team launched a new phase of restoration in 2023, increasing the number of connection points between the marsh and the surrounding landscape to improve overall connectivity throughout the delta. The new channels were also intended to serve as a gradient of habitat options for salmon, in theory better supporting Chinook recovery and marsh resilience overall.

A team of Washington Sea Grant-funded researchers, including collaborators from University of Washington, The Nature Conservancy, and Skagit River System Cooperative stepped in to assess the ecological success of these efforts. The intent was to study the contribution of estuarine habitat to the diets of Chinook salmon at their critical juvenile life stage. Juvenile salmon can grow very quickly if feeding conditions are right, which greatly increases their chances for survival in the ocean. “One thing that the restoration is doing is restoring those estuary rearing habitats so that salmon can linger longer and hopefully eat a lot, grow a lot, and escape that gauntlet of predators [to] have a higher chance of survival at sea,” explains Dr. Anne Beaudreau, associate professor at University of Washington’s School of Marine and Environmental Affairs (SMEA) and a principal investigator on the project. Therefore, a major part of the restoration assessment was to survey potential salmon food sources, especially which invertebrates were present, how many, and whether they were being eaten by juvenile salmon.

Overall, the study aimed to capture differences in insect and aquatic invertebrate communities among areas of the delta at different stages of restoration, while simultaneously evaluating the feeding environment available for juvenile salmon. The team sampled insect and aquatic invertebrate prey communities from nearshore habitat in the Stillaguamish delta, targeting areas where salmon find food. Because salmon eat critters in the water and the muddy sediment, as well as those that fall onto the water’s surface, the team used sediment samples to extract invertebrates from the tidal channels within the estuary. They also used fallout traps, collection bins for flying insects that fall from overhanging vegetation and land on the water’s surface. Finally, to determine with certainty which invertebrates the salmon were eating, the team collected a small number of juvenile salmon’s stomach contents for prey identification.

Excitingly, almost every invertebrate sampled from the estuary and nearshore environment also showed up in the stomachs of juvenile Chinook salmon. This indicates that Chinook salmon are opportunistic eaters, consuming a larger diversity of prey items than the research team expected. The researchers also found differences in invertebrate communities across spring and summer months and between different areas of the delta. “In fact, sometimes the abundance and diversity of invertebrates was actually comparable or higher in our restoration areas [compared to the reference sites],” notes Molly Bidwell, a recent SMEA graduate and collaborator on the project. This suggests invertebrate communities are responding positively to restoration.

The invertebrates indicated other positive changes in the ecosystem as well. The team was excited to document the presence of nereid (marine polychaete) worms alongside invertebrates more closely associated with fresh or brackish water, such as chironomid fly larvae. As a whole, the sampled invertebrate communities demonstrate re-established connectivity between fresh and salt water for salmon, providing the fish with a gradient of habitat types to occupy and prey types to consume as they prepare themselves for the ocean.

Now equipped with a snapshot of the invertebrate prey diversity and diets of juvenile Chinook within the Stillaguamish estuary, the team is optimistic about the continued recovery of the broader estuarine community. Prior to TNC’s 2023 adaptive management restoration, water movement in the site was not conducive to creating the deep channels that support salmon and other marsh processes. The slow, sloshy water movement within estuaries means it can take decades for these sensitive sites to form channels on their own. However, the positive results Dr. Emily Howe and her colleagues at TNC are seeing provide good feedback for continued restorative adaptive management practices. “It’s validating that these changes are happening on the landscape after restoration actions,” Bidwell says. “We have the salmon as our flagship species, but when we’re supporting them, we’re supporting the whole ecosystem as well. We were out there at sunrise. You could hear all the birds and how beautiful it was there, or you’d see the coyotes running around. There’s so many other critters that depend on these spaces and it’s that whole community that benefits.”

One future avenue for the project includes integrating the findings into a comprehensive bioenergetics model, which will help scientists predict and assess salmon habitat potential. This work will complement the exciting restoration efforts still to come, as the Stillaguamish Tribe plans to restore an additional 240 acres of land next to the existing site. Combined with another 500 acres the Tribe has recently purchased, the marsh restoration project will extend across the entire Stillaguamish delta, yielding extensive connectivity throughout.

As the river is allowed once again to sweep across the landscape, it will regenerate marsh habitats with each pass. With channels rebuilt and reconnected within the Stillaguamish estuary, habitat changes will follow, giving Chinook salmon a better chance to forage, grow, and survive into adulthood. Restoration is rarely a quick and simple process, but with continued work from dedicated teams, we may yet see the return of Chinook to their river.

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Washington Sea Grant, based at the University of Washington, helps people and marine life thrive through research, technical expertise and education supporting the responsible use and conservation of coastal ecosystems. Washington Sea Grant is one of 34 Sea Grant programs supported by the National Oceanic and Atmospheric Administration in coastal and Great Lakes states that encourage the wise stewardship of our marine resources through research, education, outreach and technology transfer.

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