Conserving climate-change refugia is a crucial adaptation strategy for reducing the impacts of global warming. Here, we used the dominance of volcanic rocks in the watershed as a landscape-scale surrogate for cold groundwater inputs to clarify the importance of underlying geology in stream ecosystems along climate gradients. Japan provides an ideal study area for this purpose due to its diverse geology and climate. First, using monitoring stations distributed across multiple catchments in Japan, we explored the relationship between watershed geology and the mean summer water temperature of mountain streams along climate gradients in the Japanese archipelago. We found that mean summer water temperature was explained by the interaction between the watershed geology and climate in addition to independent effects. Surprisingly, the cooling effect supported by volcanic rocks reached up to 3.3°C among study regions. Next, we examined the function of volcanic streams as cold refugia. Community composition analyses showed that volcanic streams hosted distinct stream communities composed of more cold-water species than nonvolcanic streams. Scenario analyses based on multiple global climate models and Representative Concentration Pathways (RCPs) revealed a geology-related pattern of thermal habitat loss for cold-water species. Unlike volcanic streams, nonvolcanic streams rapidly declined in thermally suitable habitats for lotic sculpins, even under the lowest emission scenario (RCP 2.6). These findings highlight that geology, climate variability, and their interaction should be considered simultaneously to manage climate-change refugia in mountain streams effectively.