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Spatial and temporal variation in thermal conditions are important dimensions of aquatic landscapes, yet we do not understand how this heterogeneity will respond to climate change. Snowpack in many regions is declining but impacts on aquatic thermal regimes remain poorly understood. Our analyses of summer stream temperatures across a complex river basin in southwest Alaska show that loss of snowpack has disproportionate effects on water temperatures in streams that are cold under typical conditions, thereby homogenizing stream temperatures across the landscape during low snow conditions. Streams draining steep watersheds warmed from a summer average of 4–8°C between high and low snow years and became more responsive to variation in regional air temperature (as proxy for solar radiation), while streams draining flat watersheds changed negligibly. Our results suggest that conservation strategies for aquatic landscapes that focus on snow‐dominated cold‐water refugia may not be robust to future climate warming and changes in snowpack.