Estuary use, physiological status and response to connectivity restoration in juvenile Chinook salmon in the Lower Fraser River and estuary

Juvenile salmon depend on estuaries to complete the transition to marine habitats, yet they face growing pressure from human modification and climate change driven changes in hydrology, temperature, and other dynamics. Understanding how variation in estuary use within and among populations shapes individual habitat use and condition is therefore increasingly important for conservation and management. Here, I investigated differences in estuary use, smoltification and potential stressors in juvenile ocean-type Chinook salmon (Oncorhynchus tshawytscha) while assessing the potential effectiveness of estuary restoration actions through field research across eight years in the Fraser River estuary. Early migrating Harrison River Chinook arrived at the smallest sizes and showed the highest reliance on brackish marsh habitats, while South Thompson Chinook arrived later and at larger sizes with shorter estuarine residence, and stream-type populations showed limited estuarine habitat use. I then used biomarker panels to examine salinity tolerance and screened for stressor responses and pathogens. Early migrating Harrison River ocean-type Chinook salmon took advantage of lower salinities migrating downstream while undergoing smoltification with many arriving in the estuary in a pre-smolt condition. Later migrating South Thompson Chinook salmon may be exposed to higher degrees of stressors as they arrive later, when temperatures can reach levels which lead to thermal stress. Ocean-type Chinook salmon were commonly infected with several pathogens during this outmigration period, with potential health and survival outcomes. Lastly, juvenile salmon access to estuarine habitats was evaluated at two major jetty breach projects which restored estuary connectivity. I found that juvenile salmon responded strongly to jetty breaching efforts, with high capture rates of small subyearling Chinook and chum (O. keta) salmon. Chinook salmon from numerous Fraser River populations utilized the jetty breaches, demonstrating the potential broad benefits of restoration actions in large estuaries. Overall, while estuaries are sensitive to human impacts and climate change, they may also provide important opportunities for managers to reduce stressors, given they have the necessary population specific information they require. Management and mitigation activities which aim to reduce the impacts of stressors in a higher temperature future will be crucial to protect productivity of these important salmon habitats.