The global climate change effect on the hydrodynamic characteristics of the southern part of Aswan High Dam (AHD) reservoir, Lake Nubia, was investigated in this work. The investigation was conducted for the 21st Century by using the outputs of eleven Global Climate Models (GCMs) for two global emissions senarios combined with hydrological modeling. To investigate the hydrodynamics in the water column, a model was presented using a two-dimensional, laterally averaged, finite difference hydrodynamic and water quality code, CE-QUAL-W2. The model was calibrated and verified with measured data series from the years 2006 and 2007, respectively. Three hydrodynamic characteristics of the reservoir were investigated with respect to climate change: water surface levels, evaporation water losses, and thermal structure. The results show that the evaporation water losses are higher than the base case for all scenarios, while water surface levels and water temperature are higher for most of the scenarios.