How local geomorphic and hydrologic features mediate the sensitivity of stream thermal regimes to variation in climatic conditions remains a critical uncertainty in understanding aquatic ecosystem responses to climate change. We used stable isotopes of hydrogen and oxygen to estimate contributions of snow and rainfall to 80 boreal streams and show that differences in snow contribution are controlled by watershed topography. Time series analysis of stream thermal regimes revealed that streams in rain-dominated, low-elevation watersheds were 5–8 times more sensitive to variation in summer air temperature compared to streams draining steeper topography whose flows were dominated by snowmelt. This effect was more pronounced across the landscape in early summer and less distinct in late summer. Thus, the impact of climate warming on freshwater thermal regimes will be spatially heterogeneous across river basins as controlled by geomorphic features. However, thermal heterogeneity may be lost with reduced snowpack and increased ratios of rain to snow in stream discharge.