This study clarifies how climate change affects stream temperatures in snowy cold regions, where groundwater impacts vary with geological conditions. We developed a physics-based water circulation model that incorporates an atmospheric and land surface process model considering snow processes, a runoff model, and a water temperature estimation model. Small watersheds in the mountainous area of Hokkaido formed the study area, and the runoff model was assigned different parameters depending on the geological characteristics. Using these parameters, changes in water temperature were calculated with respect to changes in the meteorological data in historical and future simulations. Current water temperatures were effectively reproduced by the model, and following the IPCC RCP 8.5 scenario, future water temperatures in the distribution area for new pyroclastic flows were predicted to remain lower in summer than in the distribution area of older formations. The findings of this study will be useful in informing conservation measures for river ecosystems, including the prioritization of streams where cold-water fish need to be conserved.