There is increasing interest in using waterbodies as renewable energy sources to heat and cool buildings and infrastructure. Here, we estimate the potentials for heat extraction and disposal for the main lakes and rivers of Switzerland based on acceptable temperature changes in the waterbodies, and compare them to regional demands. In most cases, the potentials considerably exceed the demand, and minor impacts on the thermal regime of the waterbodies are expected. There are, however, critical situations: rivers crossing densely-populated areas, where demand often exceeds the potential, and heat disposal in summer into lowland rivers and shallow lakes, where temperatures may exceed ecological criteria. To assess the impacts of a realistic thermal use, we model the temperature effects in two lakes: Upper Lake Constance, a large lake with relatively low population density, and Lower Lake Zurich, a smaller lake with high regional demand. The estimated mean temperature alterations are −0.05 to +0.02 °C for Lake Constance, and −0.60 to +0.22 °C for Lake Zurich. Based on the model results, we discuss the effects of operating parameters on the efficiency and impacts of thermal use. Our analysis demonstrates that waterbodies provide real alternatives for heat/cold production in many regions of the world.