Changes in water temperature and stratification dynamics can have a significant effect on hydrodynamics and water quality in reservoirs. Therefore, to assess future climate impacts, projections of three regional climate models for Europe, under the IPCC A1B emission scenario (2081–2100), were used with the CE-QUAL-W2 water quality model to evaluate changes in the thermal regime of 24 Portuguese reservoirs, representing different geographic regions, morphologies, volumes and hydrological regimes. Simulation results were compared with reference simulations for the period 1989–2008 and changes in water temperature and thermal stratification characteristics were evaluated. Future inflow scenarios were estimated from precipitation-runoff non-linear correlations and outflows were estimated considering present water uses, including hydropower, water supply and irrigation. Results suggest a significant increment in the mean water temperature of the reservoirs for the entire water volume and at water surface of 2.3 and 2.5 °C, respectively, associated with a runoff reduction of approximately 23%. Overall, variations in annual stratification patterns are characterized by changes in the mean annual length of stratification anomaly that ranged from −21 to +39 days. Results also show the influence of depth and volume over the reservoir's temperature anomaly, highlighting the importance of future water uses and operation rule curves optimization for reservoirs.