Habitat use by juvenile salmon, other migratory fish, and resident fish species underscores the importance of estuarine habitat mosaics

A new paper demonstrates critical role that connectivity plays in the health of the Fraser River estuary and the fish, including salmon, that rely on it.

Pacific salmon, especially Chinook and Chum, reside and feed in estuaries during downstream migrations. But the extent to which they rely on estuaries, and which habitats within estuaries, is not well understood. We need to understand this complexity if we are going to enact effective conservation policies. This is especially important in urban systems where habitat loss is ongoing, and at different rates across the estuarine mosaic.

The Fraser River estuary, for example, supports a multitude of fish species, and is a crucial stopover for juvenile salmon from throughout the Fraser watershed. Currently however, more than 70% of the habitat historically accessible to these salmon has been lost or disconnected. Estuaries are also comprised of different types of habitats, including seagrasses, marshes and sand flats. Researchers from the Raincoast Conservation Foundation and the University of Victoria studied how different fish use these distinct but connected habitats within the Fraser River estuary to help understand their relative importance for different fish species. Over two years they caught more than 55,000 fish from 40+ different species, including almost 9,000 juvenile salmon.

Their study, published in the journal Marine Ecology Progress Series, demonstrates that each habitat is required if the overall fish biodiversity of the estuary is to be conserved.

“Estuarine fish communities exhibit complex spatiotemporal variation in habitat use, and multiple habitat types are required to conserve overall fish species richness and abundance. Focusing on a single habitat or species risks underestimating the value brought to the system by each component—in the case of the Fraser River estuary, focusing habitat remediation efforts solely on eelgrass could lead to further declines in salmon populations with the loss of remaining marsh. This supports the premise that connected seascapes of different habitat types main- tain greater biodiversity and productivity, and we suggest that estuaries be managed as such.”

Read the research


Interfacing with land and sea, estuaries support a mosaic of habitats that underpin the production of many coastal fisheries. These ecosystems are threatened by multiple stressors, including habitat loss and climate change, but the relative importance of estuarine habitat types for different fish species remains poorly understood since direct habitat comparisons are rare. This knowledge gap is exemplified in temperate estuaries by salmon—ecologically and commercially important species that use estuaries during their migrations to and from the ocean. Here, we tested for species-specific habitat use by sampling fishes in 3 interconnected estuarine habitats (brackish marsh, eelgrass, and sand flat), across seasons and temperature regimes. We quantified fish species richness, community distinctness, and catches (of Chinook and chum salmon, other migratory fishes, and resident fishes) in the Pacific Northwest’s heavily urbanized Fraser River estuary, the terminus of what was once the world’s most productive salmon basin. Overall, eelgrass habitat supported the greatest fish species richness (n = 37) and catches (37402 fish), exceeding that of both the marsh (19 species, 7154 fish) and sand flat (22 species, 6697 fish). However, the majority of salmon were caught in the marsh (61%). These differences, coupled with our finding that at least one unique fish species inhabited each habitat (eelgrass = 15, marsh = 8, sand flat = 1), demonstrate species-specific habitat use and underscore the importance of connected seascapes for biodiversity conservation.


Chalifour L, Scott DC, MacDuffee M, Iacarella JC, Martin TG, Baum JK (2019) Habitat use by juvenile salmon, other migratory fish, and resident fish species underscores the importance of estuarine habitat mosaics. Mar Ecol Prog Ser 625:145-162. https://doi.org/10.3354/meps13064

Things to know about the Fraser River estuary

  • Largest contributor of freshwater to the Salish Sea
  • Supports majority of BCs human population
  • Fraser Valley Regional District produces 39.4% of BC’s agricultural revenue on 2.3% of the land base (Ministry of Agriculture 2017)
  • Fraser estuary hosts Canada’s most active port
  • Fraser Estuary supports more than 100 species that are recognized as “at-risk” (threatened, endangered or of concern) either provincially or federally
  • Fraser Estuary is rearing habitat for 21 salmonid populations in 4 different species that are listed as threatened or endangered by COSEWIC (Committee on the Status of Endangered Wildlife in Canada)

Select figures

Figure 1, map of sites sampled from research paper.
Fig. 1. Sites sampled in 2016 and 2017 within the Fraser River estuary, British Columbia, Canada: 5 marsh sites (white triangles; M1−M5), 6 sand flat sites (black squares; S1−S6), and 6 eelgrass sites (grey circles; E1−E6). All sites were sampled each year, with the exception of E6, which was replaced by E7 in 2017. Habitat polygons are approximations from the 2002/2003 Fraser River Estuary Management Program Habitat Inventory of the Lower Fraser River Estuary, and boundaries may vary. Sand flat habitat extends seaward beyond the shown polygons to a drop-off between 5 and 6 km from shore.
Figure 2, graphs of species richness by habitat.
Fig. 2. (A) Rarefied species richness curves for marsh (blue triangles), eelgrass (green circles), and sand flat (yellow squares) habitats, combining data across seasons and years, and (B−D) species richness curves by season for marsh (B), eelgrass (C), and sand flat (D) habitats. Symbols reflect ob- served species richness, solid lines represent interpolated values, and dashed lines represent extrapolated values. Shading represents 95% confidence intervals.
Figure 3, charts of fish species caught in 2016 and 2017.
Fig. 3. Top 10 fish species caught in 2016 and 2017 by habitat: (A) marsh channel, (B) eelgrass meadow, and (C) sand flat sites in the Fraser River estuary. Migratory species, including Chinook and chum salmon, are shown on a red scale, resident fishes on a blue scale. Numbers above bars for shiner surfperch and three-spined stickleback indicate total catch when catch scale was exceeded.

Author Affiliations

Department of Biology, University of Victoria, Victoria, BC, Canada
Raincoast Conservation Foundation, Sidney, BC, Canada
Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, BC, Canada
Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada

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Raincoast’s in-house scientists, collaborating graduate students, postdoctoral fellows, and professors make us unique among conservation groups. We work with First Nations, academic institutions, government, and other NGOs to build support and inform decisions that protect aquatic and terrestrial ecosystems, and the wildlife that depend on them. We conduct ethically applied, process-oriented, and hypothesis-driven research that has immediate and relevant utility for conservation deliberations and the collective body of scientific knowledge.

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Coastal wolf with a salmon in its month.
Photo by Dene Rossouw.