Long-term water temperature records are necessary for better understanding climate change impacts on freshwaters. We reconstruct summer water temperatures from three climatically sensitive mountain lakes in Austria using paleolimnological methods aiming to examine long-term thermal dynamics and lakes' responses to regional climate variability since the Little Ice Age. Our results indicate divergent trends for the lakes. In two of the lakes, which are located at the sunny southern slope of mountains, water temperature has increased several degrees concurrent with the observed air temperature increase. In contrast, no change is observed in the reconstructed water temperatures of a shaded lake, located at the northern slope, where also the ecological and thermal changes are most subtle. The results indicate the importance of cold water inputs, such as snowmelt and groundwater, on lakes' thermal conditions and suggest that watershed characteristics and lake stratification play a major role in defining the lake-specific thermal regime.