1. Seasonal variation in river water levels creates a shifting mosaic of habitat conditions associated with variables such as water temperature, chemistry and prey availability to consumers. Previous work has shown that fishes can exploit spatial variation in water temperature, but less is known about how they respond to shifts in the spatial arrangement of habitat conditions through time. 2. Juvenile coho salmon (Oncorhynchus kisutch) are the numerically dominant fish species in many southwest Alaskan streams, which exhibit seasonal variation in water level and temperature due to changes in precipitation and snowmelt. We assessed the degree to which juvenile coho salmon exploit the associated shifting mosaic of water temperature by monitoring the spatial distribution of water temperatures and juvenile coho salmon in the lake-influenced reaches of a southwest Alaskan stream. We also monitored the diets of juvenile coho salmon relative to the spatial distribution of prey taxa. 3. Juvenile coho salmon exhibited two scales of movement to track spatiotemporal variation in habitat conditions. First, over the course of 6 weeks, individuals moved among off-channel units, tracking shifts in the location of warm water habitat caused by receding water level. Second, individuals moved at diel time scales, foraging on benthic macroinvertebrates in the cold thalweg of the stream at night and then digesting prey in warmer off-channel habitats during the day. 4. Seasonally asynchronous variation in water temperature among off-channel habitat units produced portfolio effects in habitat conditions, such that coho salmon had continual access to warm habitat for digestion despite its ephemeral availability at discrete locations. 5. Our study demonstrates that behavioural thermoregulation by juvenile fishes can be important throughout the growing season and is not restricted to ephemeral events such as resource pulses or heat stress. Our results have implications for the conservation of highly connected, heterogeneous landscapes, and their ability to support economically and ecologically important species such as coho salmon.