Estuaries and large river deltas in the Pacific Northwest

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Essential habitat for wild salmon and other wildlife borders river deltas and estuaries in the Pacific Northwest. These estuaries also support industry, agriculture, and a large human population that’s expected to double by the year 2060, but each could suffer from more severe river floods, higher sea level, and storm surges caused by climate change.

Aerial photograph of a wetland area, with waterways, islands, peninsulas, and a town visible.

Typical wetland in Puget Sound that now faces “squeeze” as rising sea level meets human infrastructure.

Water supply and flood control can be controversial issues in large river systems like the Skagit River delta in the Puget Sound area of Washington State. The challenge can be getting all of the separate interests to the table—farmers, ecosystem restoration practitioners, tribal communities, and dozens of land-use managers. During town hall-style meetings where communities voiced their concerns, USGS geologist Eric Grossman informed them about the science of climate change and its impacts in the region. He’s watched a room of apprehensive residents, regional managers, and other stakeholders grow to a full house in a few years. Some now eagerly share their knowledge and data as they seek solutions for problems like abating coastal hazards and improving conditions for salmon and shellfish, which can benefit several groups. Bringing together diverse interests in this Pacific Northwest landscape has spotlighted opportunities to collaborate, and has fostered a more integrated understanding of the scientific and societal issues and what the USGS is doing to address them. 

Aerial photograph alternates between two views, one showing extent of wetlands

Aerial photograph of the Skagit River delta, in the Puget Sound area of Washington, superimposed with geographic information system (GIS) data that illustrate changes between 1850 and 2010. In 1850 the delta included extensive wetlands providing important habitat for salmon spawning (orange color). By 2010 most of the delta had been “reclaimed” for development by a system of dikes and levees (red lines), greatly reducing the habitat available to salmon.

The Issues

Human development of the Pacific Northwest since the 1800s has significantly changed stream and tidal flow in deltas and estuaries. Making land surfaces impervious to water and rerouting river channels through dikes and levees have caused extensive and ongoing disturbance to ecosystems important for the salmon life cycle. Although the construction of levees and dikes in river deltas protects lives and infrastructure—allowing cities and livelihoods to develop—it’s been at the expense of an iconic ecosystem that also provides valuable benefits to people.

Climate change adds a new dimension, and the story becomes largely about sediment and its journey to the coastal zone.

Illustration shows how sediment comes from erosion from slopes (source), is transported, and is deposited in river deltas (sink)

Sediment is the sand, mud, and pebbles that were once solid rock. Sediment flows in tributary streams and river channels of the Skagit, from the Cascade Mountains to Skagit Bay and Puget Sound. Source: Erosion from slopes and migrating river channels generate a lot of sediment. Transport: Rivers move sediment downstream. Sink: Sediment is deposited across natural river deltas and floodplains. Diagram courtesy of Skagit Climate Science Consortium.

Shallow water in a tidal flat where a pulse of muddy water is mixing with fresh, clear ocean water.

Photograph from pole-mounted camera, looking west across the Skagit River delta and one of several large sediment fans that are moving 1-2 meters per day across the tidal flats. These fans threaten to bury the last intact stands of eelgrass in Skagit Bay, an important rearing habitat for juvenile salmon, crab, and other marine wildlife.

Man walks on rocky beach holding a pole high above his head with a small camera mounted to it.

Eric Grossman walks with a pole-mounted camera on a rocky area near Skagit Bay.

Geologically young coastal mountains and steep active volcanoes characterize the Pacific Northwest, and experience lots of erosion from some of the highest rainfall in the country. Forecasts for this area indicate even more rainfall and stronger and more frequent river flooding, which can increase erosion. Moreover, a rising snowline and glacier melt across the Pacific Northwest—now evident from climate change—expose a greater surface area to erosion. A larger quantity of sediment flowing down this “sediment superhighway” is expected to fill stream channels and increase flood risk, especially when a rising sea level slows the flow of fresh water near the river mouth and pushes the ocean-river convergence farther upstream. This convergence also traps sediment, sometimes clogging channels and river mouths, and makes the river system more likely to overtop its banks and levees during times of high flow. This clogging can also cause the river to change course and amplify the flood risk to nearby developed areas.

Man walks in shallow water up to his mid-calves, wearing waders and backpack, carrying small hand-held device.

Visiting scientist from Delft University measuring land surface elevations with a very precise GPS device.

Aside from contributing to a greater flood risk, sediment shapes estuarine environments critical to fish spawning and rearing; several species of aquatic vegetation such as eelgrass; valued shellfish like crab, clams, and oysters; shorebirds; and a diverse set of small invertebrates that feed the rest of the food web. Shellfish and salmon are firmly entrenched in the culture of the indigenous peoples and those who identify with the Pacific Northwest. Indigenous people have already lost many stocks of fish and shellfish, and concern grows that a changing climate and rising sea level will continue to adversely impact indigenous people tied to coastal reservations.

Land-use managers and farmers are concerned about the combined effects of sea-level rise and coastal floods, which hamper drainage. These managers want to know, for instance, where the shoreline will be in future decades, and the extent of flooding in coastal lowlands. As sea level rises, wetlands essential for salmon recovery could become submerged, and important farmland for national seed crops could be lost to pooling groundwater and saltwater intrusion. These are significant reasons to investigate how estuarine areas will evolve, and what risks people and aquatic species face—particularly as sediment flow fluctuates. Sophisticated models need to be developed to forecast coastal change, and they require data that capture a dynamic and ever-changing environment.

Map shows the state of Washington in relief, with darker outlined region showing the Puget Sound watershed and study sites in it

USGS research of estuaries and river deltas covers these six major watersheds of Puget Sound.

What the USGS is doing

USGS research covers six of the major watersheds in Puget Sound. By gathering high-resolution coastal elevation and habitat data using lidar, sonar, underwater photography, and an ultra-precise GPS, scientists reconstruct how shorelines and estuaries have shifted through time. They also take a series of overlapping photographic images and create seamless onshore-offshore elevation models in 3D, revealing landscape and habitats that can influence and be influenced by storm surge and waves.

They gather detailed measurements of river and ocean levels to map how the annual water flow from tides, rivers, and storms fluctuates up and down the coast. For the first time in Washington State, USGS scientists are placing river-monitoring instruments in sections of estuary and beach environments to capture a comprehensive picture of what transpires when rising seas meet flooding rivers.

Aerial view of the Skagit River where the two folks branch off of the main river.

A small sample of a digital elevation model of the Skagit River system derived from USGS bathymetry data, showing the complete shape of the channel bottom for the first time.

Sediment traps, current meters, wave and acceleration sensors, sonar, and underwater video also record how much and what type of sediment moves with specific tides, currents and wave conditions. Sedimentologists work with biologists and ecologists to study how sediment disturbs habitats and organisms, and its cascading effects throughout the food web.

USGS also helped create an online tool (Puget Sound Coastal Resilience) for the region’s six watersheds to visually demonstrate current and future effects from the joint occurrence of projected sea-level rise, storm surge, and river flooding. Additionally, USGS developed tools with the Swinomish Indian Tribal community and Skagit River System Cooperative to understand how future sea-level rise will impact their natural food resources and overall community well being.

Plot shows tall grass stalks from a side-on perspective.

Example of side-on photography of marsh vegetation reprocessed into a binary image to extract vegetation traits, such as biomass, shoot height, and shoot width, which affect water flow and sediment trapping.

To inform salmon recovery efforts, USGS modeled how water moves through the Nisqually Delta National Wildlife Refuge, the largest estuary restoration project in the Pacific Northwest. Similar models show how oyster larvae disperse in Fidalgo Bay Aquatic Reserve, and how marsh vegetation influences waves and traps sediment in Port Susan Bay.

To model future wave energy and its potential impacts on coastal communities and ecosystems, the scientists use an innovative photographic method to capture how marsh vegetation influences water flow and sediment. Instead of spending hours in the field measuring individual plants, they photograph plants from the side to capture such traits as plant heights, leaf widths, shoot densities, and biomass, all of which impede the flow of water and sediment across the marsh. Hundreds of photographs can be taken in the short 2- to 3-hour window of low tide and analyzed overnight. Documenting the intimate ways that vegetation influences water flow and sediment helps highlight the value of restoring natural habitat to combat coastal hazards.

Many people in colorful clothing stand and sit holding canoe paddles on shore, long wooden canoe in the water with passengers.

Participants in the 2008 Coast Salish Tribal Canoe Journey.

USGS researchers have teamed up with Coast Salish Tribes and First Nations on two projects aimed at understanding and ameliorating the pressures that culturally important species like salmon and shellfish face. The first project is a wave model that forecasts storm surge and waves to examine their influence on habitats for juvenile salmon and shellfish. The second project involves tribes collecting water quality data across the entire Salish Sea—which encompasses Puget Sound, the Strait of Georgia, and the Strait of Juan de Fuca—by towing water quality probes behind traditional ocean-going canoes during their annual Tribal Canoe Journey. These probes measure such aspects as temperature, salinity, and pH throughout the water column and down to the seafloor. This unusual approach reveals variations in water quality conditions today across the vast area of the Salish Sea, and will track indicators of climate change in the coming years.

Small probe with wires attached to yellow waterproof box sitting on gravel.

Water quality probes that are affixed to several canoes during the Coast Salish Tribal Canoe Journey.

To read more about other studies in Puget Sound and how they inform ecosystem restoration, visit Coastal Habitats in Puget Sound.

What the USGS has learned

Man stands in calm tidal channel wearing safety equipment holding a rod to measure stream flow.

Chris Curran, USGS hydrologist, measures stream flow through a recently restored tidal channel in an estuary in Washington.

Flooding rivers in the Pacific Northwest bring tons of sediment to the coast each year. In fact, more sediment flows into the basin here—enough to cover a football field to the height of six Space Needles—than flows into the larger Chesapeake Bay. With projections of rising air temperatures due to climate change, USGS studies indicate that sediment moving downstream from the glacial area of the North Cascade Range during larger floods will increase 3 to 6 times by 2080, potentially leading to more flood damage, greater costs to furnish clean water, and impacts to wildlife habitat and ecosystem restoration. In addition, the increase in rain and temperatures could also weaken steep mountain slopes and glaciers, delivering additional sediment from landslides.

“Replumbing” the rivers with dikes and levees means sediments no longer build up in areas like floodplains and marshes, where extending the land would help reduce vulnerability to sea-level rise. Moreover, seawalls built along the coast to defend against ocean waves block sediment that would otherwise supply those marshes and beaches. Instead, sediment accumulates in channels, increasing flood risk, or is transported offshore, where it buries fish habitat and disrupts food webs.

Working with several indigenous communities, USGS has installed a network of sensors to monitor how sediment moves through rivers and estuaries, and calculate how much arrives on beaches. By integrating coastal inundation models with studies of shellfish and traditional harvesting practices, the USGS has determined that future sea-level rise is likely to reduce suitable shellfish areas by 20 to 25 percent by 2100 in some areas where seawalls disturb the shoreline.

New analysis reveals that storm surge raises water levels in the Salish Sea 1 to 3 feet above predicted tides 10 to 13 percent of the time, most often when king tides coincide with high river flow. Other research illustrates that marsh restoration reduces the impact of those waves and storm surge in coastal lowlands. Green infrastructure like marsh restoration and rebuilding oyster reefs helps counteract the local impacts of climate change while restoring essential ecosystems for juvenile marine species like salmon, forage fish, and Dungeness crab.

To help promote societal awareness, USGS has recently joined the Washington State Coastal Hazards Resilience Network and leads a community citizen science effort. Washington’s shoreline is not always publicly accessible for gathering data or placing instruments, so in the spirit of engaging locals and landowners, nearly 50 volunteers help document the effects of coastal flooding. After USGS scientists survey the area, both USGS and citizen-collected information help validate and shape the models that provide a predictive snapshot of how vulnerable or how resilient the coast will be.


Two men look at computer screens on a boat, one man is seated at the keyboard and the other looks over his shoulder.

Eric Grossman and Rob Wyland reviewing bathymetry data as it’s being collected on research vessel Parke Snavely.

Water is Life for the Swinomish Indian Tribal Community, USGS News, June 2017

Washington river warmingEverett Herald, June 2015

Sediment in Puget Sound Rivers, USGS news release, Sept 2012

Canoe Families Play Starring Role in Study of Salish Sea ConditionsIndian Country Today Media Network, July 2011

Science and Native Traditions Merge to Monitor Water Quality in Salish Sea, USGS news, July 2011

Ancient Canoes, Modern Science To Track Water Quality,, July 2008

Tribal Canoes Towing Underwater ProbesSound Waves, 2008

You Tube videos showing the Tribal Canoe/USGS collaboration, 2008

USGS Workshop on Sea-Level-Rise ImpactsSound Waves, 2008