Among four extant and declining Chinook salmon (Oncorhynchus tshawytscha) runs in California’s Central Valley, none have declined as precipitously as Sacramento River winter-run Chinook Salmon. In addition to habitat loss, migratory winter-run employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. This life history strategy is widely considered to be a key factor in the continued decline of winter-run. Using acoustic telemetry, we examined conditions that influenced reach-specific movement and survival of outmigrating juveniles during a prolonged, multi-year drought from 2013-2016, followed by one of the wettest years on record in 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 in 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 to how the magnitude of pulse flows in dry and wet years affect survival of winter-run. 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.