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New study shows importance of estuary habitats for threatened Chinook salmon in the Fraser River

Lia Chalifour stands in the waters and tall grass of the Fraser River estuary taking measurements.
Photo by Michael O. Snyder.

Sidney BC. A new study from Raincoast and its partners used salmon ear bones (otoliths) and genetic fingerprinting to confirm the importance of the Fraser estuary for juvenile Chinook salmon. Previous estuary researchers suspected these habitats were of high importance to young Chinook, but this study confirms that Harrison River Chinook, which migrate quickly to the estuary after emerging from the gravel, remain there for an average of six weeks. Most juvenile Chinook resided in the estuary for 30-50 days, and one even extended its stay for 89 days. This work underscores the need for protection of the Fraser estuary as Chinook rearing habitat.

“The Fraser estuary is an expansive, silty ecosystem, which makes it difficult to study fish movements. Using modern techniques, we were able to confirm that this threatened population of Chinook salmon rely heavily on the estuary during their emigration to the ocean, which is a critical period that influences their future survival,” said lead author Lia Chalifour.

With support from Raincoast Conservation Foundation biologists, the research team led by PhD Student Lia Chalifour in the Baum Lab at the University of Victoria, applied a technique that used the tiny ear bone (an otolith) and the patterns of trace elements imprinted on it as the young fish swims from fresh to saltwater, to understand each fish’s journey through the river and estuary. This information was then combined with genetic fingerprinting that indicated where in the Fraser watershed the salmon came from, i.e. their natal home stream. In this way, the team was able to understand the importance of estuary habitat to specific Fraser populations. 

The team captured hundreds of juvenile Chinook salmon in the estuary in 2016 and 2017. They focused on fish captured from the Harrison River for the otolith analysis. This allowed them to determine when fish entered the estuary, how long they stayed and how much they grew during their stay.  The team also found that juvenile Chinook relied on marsh habitats more than sand flats and eelgrass habitats, although much of the marsh dewaters at low tide, and the fish then move to deeper areas for refuge.

“This study shows that young Harrison River Chinook rely heavily on the estuary, and in particular the fresh and brackish marsh on the Fraser delta, before they enter the ocean” said Dave Scott, Raincoast biologist and co-author on the paper. “Since the vast majority of these habitats have already been lost or degraded, this stage may be a bottleneck that reduces their productivity”.

The study provides insight to managers wanting to rebuild Fraser River Chinook salmon runs that have declined sharply.  The Committee on the Status of Endangered Wildlife in Canada has now listed 14 of 16 Fraser River Chinook populations as threatened or endangered, with low numbers resulting in contentious fishing closures in recent years. Harrison River Chinook salmon, which were the Fraser’s most productive Chinook population through the 80s and 90s, were listed as “threatened” following low returns over the last decade. Protecting Fraser Chinook is also crucial to the recovery of endangered Southern Resident killer whales that rely heavily on them as their preferred prey. 

“Industrial projects such as the proposed expansion of Terminal 2 on Roberts Bank would further impact juvenile Chinook in the estuary, lowering their productivity and chances for recovery. On the other hand, investments in restoration and protection could enhance their recovery, helping to sustain and rebuild this important population,” added biologist Misty MacDuffee, Wild Salmon Program Director at Raincoast and co-author on the paper.

A graphic abstract of Lia Chalifour's research: early migrating ocean-type Chinook salmon  are in the Fraser estuary throughout the emigration period.
Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary. Lia Chalifour, David C. Scott, Misty MacDuffee, John F. Dower, Terry D. Beacham, Tara G. Martin, and Julia K. Baum. CJFAS – 2020 – DOI: 10.1139/cjfas-2020-0247.