The assessment of ecological impacts of pumped-storage (PS) hydropower plants on the two connected water bodies is usually based on present climatic conditions. However, significant changes in climate must be expected during their long concession periods. We, therefore, investigate the combined effects of climate change and PS operations on water temperature and quality, as well as extent and duration of stratification and ice cover, using a site in Switzerland. For this purpose, a coupled two-dimensional hydrodynamic and water quality model for the two connected water bodies is run with 150 years long synthetic stochastic meteorological forcing for both current and future climate conditions under two PS and two reference scenarios. The results show relevant synergistic and antagonistic effects of PS operations and climate change. For example, hypolimnion temperatures in September are projected to increase by < 0.6 °C in a near-natural reference scenario and by ~ 2.5 °C in an extended PS scenario. Ice cover, which occurs every year under near-natural conditions in the current climate, would almost completely vanish with extended PS operation in the future climate. Conversely, the expected negative impacts of climate change on hypolimnetic dissolved oxygen concentrations are partially counteracted by extended PS operations. We, therefore, recommend considering future climate conditions for the environmental impact assessment in the planning of new or the recommissioning of existing PS hydropower plants.