Chinook Salmon Use of Eelgrass Habitats

Skagit River Delta, Washington

A Pacific Northwest icon, Puget Sound is the second-largest estuary in the United States. Its unique geology, climate, and nutrient-rich waters produce and sustain biologically productive coastal habitats. USGS is conducting research in the region as part of the Coastal Habitats in Puget Sound program, an interdisciplinary collaboration to coordinate, integrate, and link USGS studies with the Puget Sound Nearshore Ecosystem Restoration Project goals and objectives. Natural resource managers look to the USGS as a critical science resource needed to solve problems in this important ecosystem.

Study Overview

The degree to which eelgrass on river deltas provides critical habitat for estuarine fishes, especially out‐migrating juvenile salmon, is an important scientific and management issue that bears on efforts to conserve and restore both eelgrass and fish. In a journal article published in Marine and Coastal Fisheries, we report on spatiotemporal variation in abundance and body size of juvenile Chinook Salmon and three forage fish species in relation to eelgrass on a large river delta in Puget Sound and consider how diking and river channelization potentially influenced eelgrass use by these fish. Fish–eelgrass associations were unique for each species. Puget Sound Chinook Salmon are currently listed as threatened under the U.S. Endangered Species Act. The river delta selected has abundant populations of all forage fish species.

Importance of Eelgrass to Puget Sound

In the Puget Sound region, seagrasses, such as Eelgrass, form complex habitats that support other aquatic organisms by providing attachment substrate, food, refuge from predation, and nursery areas. Eelgrass can form extensive meadows on Puget Sound river deltas. The extent to which these meadows provide critical rearing habitat for local estuarine fishes, especially out‐migrating juvenile salmon, is not well understood. Delta eelgrass also has been impacted by diking and river channelization with unknown consequences for fish. Current issues facing eelgrass include:

  • For the past 40 years, eelgrass abundance in Puget Sound has been stable at the scale of the entire region, but there have been losses in several localities.
  • Eelgrass was recently established as an indicator of the health of Puget Sound, and in 2011 a goal was set to increase eelgrass extent in Puget Sound by 20% by 2020.
  • There is considerable interest in further defining whether eelgrass constitutes essential estuarine habitat for fish and shellfish species of management concern.

Coastal Habitats in Puget Sound (CHIPS)

CHIPS current studies have three themes:

  • Effects of urbanization on nearshore ecosystems
  • Restoration of large river deltas
  • Recovery of nearshore ecosystems

The primary focus within these themes is on developing information on the physical, chemical, and biological processes—as well as human dimensions—associated with the restoration or rehabilitation of the nearshore environment. Puget Sound partners and citizens will receive USGS results through databases, geospatial models and analyses, technical reports, and formal publications.


  • Investigate the use of eelgrass on a Puget Sound river delta by juvenile Chinook Salmon and forage fish.
  • Examine combined effects of eelgrass characteristics (meadow size and morphology) and oceanographic conditions (temperature and salinity), which covaried according to location on the delta with respect to channelized distributary outlets, diked shorelines, and a jetty.


The study was conducted in the Skagit River delta in Puget Sound during April–September, when juvenile salmon were out‐migrating, juvenile forage fish were resident in the area and growing and eelgrass standing crop was at its seasonal maximum. Eelgrass growing on the outer margins of large river deltas may be particularly important to salmon because it forms extensive meadows in this setting and is the first eelgrass encountered by out‐migrating juveniles. Eelgrass also has been found to continue to support high abundances of juvenile Chinook Salmon in July and August, after they had mostly vacated other nearshore habitats.

Analyses were focused on four fish species occurring most frequently in the catch:


  • Four zones were selected for examining fish use of eelgrass based on proximity to Skagit River outlets, eelgrass meadow morphology, and grain size of underlying sediments. Fish were netted at sites in eelgrass meadows and unvegetated habitat within each zone.
  • Four to eight sites were sampled in each habitat (eelgrass or unvegetated) in each zone each month during neap tides from April to September, 2008–2010 (in 2008 we did not sample unvegetated habitat).
  • Site locations were selected randomly, except for seven sites in zone 4 that were sampled every trip because of the lack of enough information to delineate eelgrass and unvegetated habitat boundaries.

Map showing Skagit Bay study area.

The Skagit River is the largest river entering Puget Sound, accounting for 35% of the freshwater and 40% of the sediment entering the sound. This river retains important salmon populations including Chinook Salmon runs that are relatively healthy compared with other Puget Sound populations. The Skagit River delta has been extensively diked and the river channelized to develop farmland and protect it from flooding and saltwater intrusion, and a jetty was constructed to maintain a navigation channel.

Hypotheses and Data Visualization

Five null hypotheses were developed concerning abundance and body size of Chinook Salmon, Pacific Herring, Surf Smelt, and Shiner Perch in relation to eelgrass and water column properties. Specific information about each hypothesis is available in the journal of Marine and Coastal Fisheries.

The interactive visualizations below show the results of the hypothesis testing.

Hypotheses 1 and 2

Hypothesis 1: Abundance of each species does not differ between eelgrass and unvegetated habitat. This test used data from paired eelgrass and unvegetated habitat from 2009–2010 and zones 2–4.

Hypothesis 2: Abundance of each species in eelgrass does not differ among zones 1–4. This test used data from all sampling years (2008–2010).

This visualization functions as a representation for both scenarios proposed by hypotheses 1 and 2. The interactive capabilities of the visualization allow for specific selections to be made to represent each hypothesis.

Hypothesis 3

Abundance of each species is not related to water column depth, water temperature, or salinity.

Hypothesis 4

Body size (length) of each species does not differ between eelgrass and unvegetated habitat.

Hypothesis 5

Body size (length) of each species in eelgrass does not differ among the four zones.


Results suggest that conservation and restoration of delta eelgrass would benefit all four species and help to identify the settings in which these actions would be most beneficial.

Chinook Salmon

Chinook Salmon were more abundant in eelgrass than in unvegetated habitat in June–July and were relatively more abundant in eelgrass compared with unvegetated habitat in regions with intact eelgrass than offshore from a channelized distributary outlet.

Forage Fish

Abundances of Pacific Herring and Shiner Perch were consistently severalfold higher in eelgrass than in unvegetated habitat. Surf Smelt were more abundant in eelgrass than in unvegetated habitat at some locations, but never less abundant in eelgrass.

Find the Data

Juvenile Chinook Salmon and Forage Fish Use of Eelgrass Habitats in a Diked and Channelized Puget Sound River Delta

Read the Journal Article

Data collected in 2008-2010 to evaluate juvenile salmon and forage fish use of eelgrass on the Skagit River Delta, Washington State, USA

Download the Data