Factors Affecting Spatiotemporal Variation in Survival of Endangered Winter‐Run Chinook Salmon Out‐migrating from the Sacramento River

Abstract

AbstractAmong four extant and declining runs of Chinook Salmon Oncorhynchus tshawytscha in California’s Central Valley, none has declined as precipitously as the Sacramento River winter run. Migratory winter‐run Chinook Salmon employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. Migratory winter run, on their way from freshwaters to the ocean, employ a life history strategy to reside and feed in stopover habitats that have been affected by anthropogenic disturbance. Using acoustic telemetry, we examined conditions that influenced reach‐specific movement and survival of out‐migrating juveniles during a prolonged, multi‐year drought from 2013 to 2016, followed by one of the wettest years on record (2017). We modeled how time‐varying individual riverine covariates and reach‐specific habitat features influenced smolt survival. Model selection favored a model with mean annual flow, intra‐annual deviations from the mean flow at the reach scale, reach‐specific channel characteristics, and travel time. Mean annual flow had the strongest positive effect on survival. A negative interaction between mean annual flow and intra‐annual reach flow indicated that within‐year deviations at the reach scale from annual mean flow had larger effects on survival in low‐flow years. These factors resulted in higher survival during years with pulse flows or high flows. Changes in movement behavior in response to small‐scale changes in velocity were negatively associated with survival. Covariates of revetment and wooded bank habitat were positively associated with survival, but the effect of these fixed habitat features changed depending on whether they were situated in the upper or lower part of the river. Fish exhibited density‐dependent stopover behavior, with slowed downstream migration in the upper river in the wet years and extending to the lower river in the most critically dry year. This paper contributes two key findings for natural resource managers interested in flow management and targeted habitat restoration. The first is new insight into how the magnitude of pulse flows in dry and wet years affects survival of winter‐run fish. The second is that density dependence influences where stopover habitat is used. Despite this, we identified an area of the river where fish consistently exhibited stopover behavior in all years.