Climate change (CC) directly affects crops’ growth stages or level of maturity, solar radiation, humidity, temperature, and wind speed, and thus crop evapotranspiration (ETc). Increased crop ETc shifts the fraction of discharge from groundwater aquifers, while long-term shifts in discharge can change the groundwater level and, subsequently, aquifer storage. The long-term effect of CC on the groundwater flow under different values of ETc was assessed for the Nile Delta aquifer (NDA) in Egypt. To quantify such impacts, numerical modeling using MODFLOW was set up to simulate the groundwater flow and differences in groundwater levels in the long term in the years 2030, 2050, and 2070. The model was initially calibrated against the hydraulic conductivity of the aquifer layers of the groundwater levels in the year 2008 from 60 observation wells throughout the study area. Then, it was validated with the current groundwater levels using an independent set of data (23 points), obtaining a very good agreement between the calculated and observed heads. The results showed that the combination of solar radiation, vapor pressure deficit, and humidity (H) are the best variables for predicting ETc in Nile Delta zones (north, middle, and south). ETc among the whole Nile Delta will increase by 11.2, 15.0, and 19.0% for the years 2030, 2050, and 2070, respectively. Zone budget analysis revealed that the increase of ETc will decrease the inflow and the groundwater head difference (GWHD). Recharge of the aquifer will be decreased by 19.74, 27.16, and 36.84% in 2030, 2050, and 2070, respectively. The GWHD will record 0.95 m, 1.05 m, and 1.40 m in 2030, 2050, and 2070, respectively when considering the increase of ETc. This reduction will lead to a slight decline in the storage of the Nile Delta groundwater aquifer. Our findings support the decision of the designers and the policymakers to guarantee a long-term sustainable management plan of the groundwater for the NDA and deltas with similar climate conditions.