Keywords: Fishes, Estuarine habitat, Floodplains, Salmonids, Tribes, Salish Sea Currents magazine, Land cover conversion

How can Puget Sound generate more salmon? That question has been at the center of ecosystem recovery efforts for decades. But even as scientists and conservationists make progress on many fronts — from breaching dams to cleaning up the water — they have faced one especially complicated and frustrating limitation: Salmon need more estuaries. We look at how local tribes are working to restore this critical habitat.

One afternoon in mid-September, Swinomish tribal member Tino Villaluz stands in a small, open boat on the Skagit River just below the town of Mount Vernon. Family members in other boats nudge by him, setting gillnets to harvest coho salmon in a 24-hour tribal fishery. Villaluz explains why the Swinomish and other tribes around Puget Sound have been working to restore estuary habitats in the lower reaches of the Skagit and other rivers.

“The more life you can return to the river, the better,” says Villaluz, who is also the Hunting & Gathering Program Manager for the Swinomish Indian Tribal Community. “That plays right into our lifeways, and even our sovereignty and what we attempted to protect during treaty time.”

Prior to European settlement, the 16 large rivers that feed into Puget Sound were associated with up to 74,000 acres of estuary – coastal wetlands where freshwater from rivers and saltwater from the sea mix. Beginning around 1850, diking, draining, and other modifications cut off these lands from the sea and reduced the extent of tidal wetlands by an estimated 53% to 80% overall, depending on the study methodology and scope. For individual rivers, the current estuary area has been calculated at 1% to 55% of their historical extent, depending on the river. 

Two maps of the Skagit River Delta comparing a larger area of estuary habitat in the 1860s to a smaller area in 1991.

Historic (1860s) and current (1991) estuarine  habitat  zones  within  Skagit  Delta. Maps: Skagit River System Cooperative, Skagit Chinook Recovery Plan Appendix D

These changes to the landscape cut tribal citizens off from the rivers they depend on for physical, spiritual, and cultural sustenance, Villaluz says. They also contributed to the decline of a centerpiece of tribal culture: salmon.

Salmon are born in freshwater but mature in the ocean, making estuaries important for juvenile fish. The dependence on estuaries as rearing habitat varies both between and within species. Some types of salmon pass through relatively quickly, the estuary’s gradient of salinity helping them make the physiological transition between freshwater and salt. Others take up residence in the estuary for longer periods, finding refuge from predators and abundant food to grow larger before heading out to the open ocean.

Estuaries are especially important for certain life history types of Chinook salmon – a key species for the Puget Sound ecosystem, southern resident orcas, and local tribal cultures alike. “The fish are directly tied to our identity,” Villaluz says. “That commitment to restoring the estuary and its importance is paramount to saving our lifeways as much as anything. It's not just a fish to us, it's who we are.”

Most of the Chinook in Puget Sound are what are known as ocean-type fish, explains Charles Simenstad, an estuarine ecologist and professor emeritus at the University of Washington in Seattle. [Simenstad is on the editorial board of the Encyclopedia of Puget Sound.] These fish “don't spend very much time as juveniles in freshwater, but move down to occupy estuaries for sometimes months, before finally migrating out to Puget Sound and the ocean. And that's the dominant type of Chinook, so that means that although certainly spawning habitat is critical in terms of rearing juvenile Chinook salmon, estuaries are much more important.”

Over the past two decades or so, increasing appreciation of the importance of estuaries for salmon, biodiversity in general, and other ecosystem services such as carbon sequestration and protection from floods and storm surges has touched off a movement to restore the tidal connections of estuary habitats throughout Puget Sound.

Progress has been slow and incremental, not just because such projects can be complex from an ecological and engineering point of view but because they often involve delicate negotiations among different stakeholders and land uses. The Puget Sound Partnership set a goal of restoring 7,380 acres of Puget Sound estuary by 2020 – about one-fifth of the total restoration area judged to be needed to restore ecosystem services including space for salmon rearing. Yet since 2006 only about 3,430 acres of estuary, or about 46% of the target, have been restored to tidal influence.

These restoration projects can involve as many as dozens of funding sources and diverse partners at all levels of government. Still, Tribal governments have often been leaders in coordinating and driving estuary restoration forward, especially the largest projects. “The tribes are working at a scale that is really impressive,” says Patrick Christie, a professor at the University of Washington in Seattle who studies the social and ecological dimensions of marine conservation. [Christie is on the editorial board of the Encyclopedia of Puget Sound.]

The Skagit River

The Skagit River is the third-largest river on the West Coast and produces about 50% of all wild Chinook salmon in Puget Sound. Despite loss of 80% or more of estuary habitat in the system, an average of about three million juvenile salmon migrate through the Skagit delta to Puget Sound every year.

Skagit Chinook stocks are particularly important for southern resident orcas, says Simenstad. “What orcas have historically responded to is Chinook passing to both the Skagit and the Fraser systems, which of course commingle quite a bit in northern Puget Sound,” he says. That makes Skagit estuary restoration particularly important to ensuring the survival of this endangered population of killer whales.

A single juvenile salmon swimming with gravel in the background.

Restoring Skagit estuary habitat is important for juvenile Chinook salmon and southern resident killer whales which depend on the fish for survival. Photo: Roger Tabor/USFWS (CC BY-NC 2.0)

Research in the Skagit River system also provides the best available quantitative evidence that recovering salmon populations requires restoring estuaries. Since the mid-1990s, researchers have tracked the number of juvenile fish entering and leaving the estuary, calculating what scientists call a stock recruitment curve.

If space and resources in the estuary were sufficient, “you would see a linear relationship: the number of fish leaving the river is a prediction of the number of fish in the estuary,” explains Eric Beamer, research director for the Skagit River System Cooperative, which provides natural resources management services for the Sauk-Suiattle and Swinomish Tribes. “What we found though was that there was a cap,” suggesting that estuary habitat limits survival of juvenile Chinook.

Much of the public conversation about salmon recovery today focuses on breaching dams in the upper reaches of salmon-bearing watersheds. But these results suggest that breaching dikes, though less visually dramatic, may be just as important to sustaining healthy salmon populations in the future.

In order to achieve the benchmarks for adult salmon abundance in the Skagit Chinook Recovery Plan, the Skagit estuary needs space for 1.35 million more smolts juveniles each year, Beamer and his team calculated.

At least eight estuary restoration projects completed in the Skagit delta since 2000 are chipping away at that goal. “We're seeing that the projects built really work for the fish as long as the natural processes aren't muted,” Beamer says. “So if you get natural hydrology, you're going to get the fish using it.” Altogether the restoration projects to date have increased the estuary’s carrying capacity for juvenile salmon by an estimated 475,000 fish.

The less welcome news, says Beamer: “If we keep going this same pace, it's going to take us about 90 years to get to the goal” – both because projects are complex and time consuming to plan and carry out, and because erosion and sea level rise are erasing estuary habitat even as restoration projects add it. The Sauk-Suiattle and Swinomish Tribes are advocating for efforts to meet the recovery plan goal in 25 years – a high bar, Beamer acknowledges.


The Skagit and two other neighboring rivers that drain into central Puget Sound, the Snohomish and the Stillaguamish, historically were associated with about 60% of Puget Sound’s estuary habitat. These rivers still have some of the greatest estuary restoration potential because their deltas are not yet industrialized and urbanized like those of the Duwamish and Puyallup Rivers farther south.

On the Snohomish delta, at the outlet of Puget Sound’s second-largest river basin, the Tulalip Tribes have led a 375-acre estuary restoration project about three miles upstream from the river mouth in the city of Marysville. The project’s name, Qwuloolt, is a Lushootseed term that means “marsh.”

An image on the left show bulldozers breaching a levee of Qwuloolt estuary and on the right, the same area one year later with water in the foreground with marshland in the midground.

Restoration of the Qwuloolt (a Lushootseed word for “marsh”) estuary near Marysville, WA involved breaching a century old levee in 2015 (left). The same area is shown one year later in 2016 (right). Photos courtesy: Tulalip Tribes

The project, which took 20 years and $20.5 million to come to fruition, grew out of remediation for wetland damage from a Superfund site elsewhere on the Snohomish estuary. It was designed to restore both the tidal connection between the river and sea, and public and tribal connections to the marsh.

Since the levee along the northern edge of Ebey Slough was breached in August 2015 to inundate the area with saltwater, “we're moving in the right direction in terms of numbers” of fish, including juvenile Chinook salmon, reports Kurt Nelson, Environmental Department Manager for the Tulalip Tribes.

Still, estuary restoration is rarely straightforward. “I think a lot of people think that once a site is breached, the restoration is completed,” Nelson says. “That's really not the case. Because the site has to evolve with the changing functions and processes that are now working on it.”

At the Qwuloolt site, for example, die-off of the invasive reed canary grass that previously formed a near-monoculture in the area happened slowly, perhaps because the salinity levels of the newly inundated marsh weren’t as high as the project planners expected. The site is greening up now, but water temperatures still are higher than at nearby reference sites, Nelson says.

During the 100 years that the site was cut off from tidal influence, the area inside the dikes subsided and the soil became compacted, which is now slowing the development of new marsh. It’s a phenomenon that affects many estuary restoration projects on former agricultural and pasture lands around Puget Sound, restorationists report.


Much of the recent tribal engagement and success with estuary restoration traces back to the 1974 Boldt decision that reaffirmed Native treaty rights. Tribes were coming into their own as comanagers of natural resources as broader concern was increasing about loss of estuary habitat and dwindling salmon stocks. This backdrop empowered the Nisqually Indian Tribe, whose ancestral lands are in southern Puget Sound, to “start to identify habitats that were key for salmon recovery and the persistence of salmon, because now the tribes actually had that voice, to manage the resources,” says Chris Ellings, Salmon Recovery Program Manager for the Nisqually.

The tribe knew that estuary habitat was key not just for Chinook salmon but also for Nisqually winter chum, a genetically unique salmon stock that had traditionally been the basis of the Nisqually winter diet and the foundation for complex and far-flung trading relationships. They worked with managers of the Billy Frank Jr. Nisqually National Wildlife Refuge (named for the Nisqually tribal member and treaty-rights activist) on a series of projects that have now restored nearly 1,000 acres of estuary in the Nisqually delta, representing a 50% increase in potential salt marsh habitat in southern Puget Sound.

It’s work with broader significance. By tracking tiny wire tags that are placed in the noses of some hatchery salmon, Ellings and his team have determined that more than a quarter of the juvenile Chinook in the estuary were born outside the Nisqually watershed and had made their way there from degraded habitats in the Puyallup, White, and Green River basins. “These large deltas are truly regionally significant for salmon, it's not just salmon within the basin that use them and that's something we've shown over and over again,” says Ellings.

Two images show aerial views of the Nisqually River delta before restoration with blocked tidal channels and after with unblocked channels.

Aerial views of the Nisqually River estuary looking east across the delta from McAllister Creek show tidal channels that are blocked in 2005 (left) and unblocked in 2011 after restoration efforts (right). Photos: Jean Takekawa/USFWS

The Nisqually restoration, along with other projects around Puget Sound, also shows that breaching dams versus breaching dikes isn’t an either-or when it comes to salmon recovery. “These types of systems are truly linked from the mountains to the Sound,” says Ellings. Researchers have found that much of the sediment that’s needed to rebuild the Nisqually delta is being trapped by dams upstream. So, in some large areas of the refuge restoration, the elevation is still too low for salt marsh to form, and the delta is accreting slowly – perhaps too slowly to keep pace with sea level rise.

Even so, the efforts have made a difference, Ellings says. “We can sit here today because of that work and say with a straight face that the Nisqually basin is actually in a much better condition than it was 40 years ago,” he says. “And that's pretty remarkable, given the pace of population change and everything else that's occurred around us – and that's all a direct result of the reaffirmation of the Tribe's sovereignty and treaty rights.”

Other estuary restoration efforts elsewhere in Puget Sound show that projects need not be large in area to have a big ecological and cultural impact. On the northwestern Olympic Peninsula, the Jamestown S’Klallam Tribe led restoration efforts at the mouth of Jimmycomelately Creek, which feeds into the southern end of Sequim Bay.

In the early 2000s, the tribe and its partners renatured the lower half-mile of the stream, decommissioned a log dump and log yard and removed an RV park that had been constructed on the former estuary, constructed a new bridge for state highway 101, and restored almost 20 acres of salt marsh.

The creek had historically been an important hunting, fishing, shellfishing, and gathering area for the tribe. It was traditionally reserved for the tribal chief’s harvest of salmon and hosted several salmonid species including an especially impressive run of summer chum.

On the Olympic Peninsula, summer and fall chum are highly dependent on estuary habitat for rearing. “When they emerge from the gravel, they will likely be down in the estuary within a day or two,” says Randy Johnson, Habitat Program Manager with the Jamestown S’Klallam Tribe. “They find a veritable banquet table down in the estuarine marsh.”

In 1999, the same year Hood Canal summer chum (a population that includes on the northwestern Olympic Peninsula) were listed as threatened under the federal Endangered Species Act, just nine of the fish returned to spawn in Jimmycomelately Creek. But thanks to the estuary restoration as well as a stock rebuilding program that has since sunset, “In recent years we generally see returns of somewhere between approximately 1,000 and 4,000 naturally produced summer chum,” says Johnson. “The project to restore Jimmycomelately summer chum has been wildly successful.”


Work by yet other tribes illustrates how strategically placed projects can add up to estuary restoration that is more than the sum of its parts. On Hood Canal, the Skokomish Tribe has provided leadership for a three-phase plan to restore the estuary at the mouth of the Skokomish River near the tribe’s reservation.

The Skokomish River has been heavily impacted by human activities throughout its length. A hydroelectric dam that provides power to the city of Tacoma sits in the upper reaches of the river’s North Fork, while the South Fork and Vance Creek tributary have seen intensive timber harvesting and road building. In the main stem, lower reaches of the river had nearly a century of agricultural development with associated channel straightening diking and draining of tidelands.

“Our strategy and our approach is that all of these things are connected,” says Joseph Pavel, Natural Resources Director for the Skokomish Indian Tribe and former Tribal Chair. So the tribe has done work in both the estuary and the upper watershed.

In the estuary, the Skokomish worked with Mason Conservation District and other partners to remove dikes surrounding 108 acres of former agricultural land in 2007. They conducted similar work in 2011 on 211 acres of an island of tideland between the two main river channels in the delta. Then, in the mid-2010s the tribe reconnected tidal channels and creeks to link the restored areas to remnants of upland marsh and forested wetland.

“The active construction footprint of these is in the neighborhood of around 300 acres, but when you add in all the connectivity and restored function throughout these connections, we're talking about close to 1,000 acres of the estuary environment that's considered to have been restored,” Pavel says.

As for whether that makes the Skokomish the largest estuary restoration project in Puget Sound, “We have a friendly rivalry with our friends over at Nisqually,” Pavel laughs. But natural resources staff at both tribes agree, he adds: “Whoever is ahead, the real winners are the salmon.”

About the author: Sarah DeWeerdt is a Seattle-based freelance science writer specializing in biology, medicine, and the environment. Her work has appeared in publications including Nature, Conservation, and Nautilus.