Groundwater-dependent cultivation is imperative to meet the ever-increasing food demands in Egypt. To explore the Moghra aquifer’s potential, where a large-scale rural community is being established, a finite element groundwater flow (i.e., FEFLOW®) model was invoked. The developed model was calibrated against the observed water levels. GRACE-based groundwater storage was incorporated into the tuning procedure of the developed model. Eight abstraction rates from 1000 wells, changing from 800 to 1500 m3/day/well, were simulated for a 100-year test period. The maximum resulting drawdown values, respectively, ranged from 59 to 112 m equating to about 20–40% of the aquifer’s saturated thickness. The implications of the climate change from gradual sea level rise and an increase in crop consumptive water use were investigated. Extending seawater invasion into the aquifer caused a slight increase in the piezometric levels within a narrow strip along the seaside. Applying a chronologically increasing withdrawal rate to meet the projected increment in crop water requirements raised the maximum resulting drawdown by about 7.5%. The sustainable exploitation regime was defined as a time-increasing withdrawal rate adequate to reclaim 85,715 acres (34,688 ha). The recommended development scheme is compatible with the withdrawal rationing rule, aiming to maintain that the resulting drawdown does not exceed one meter a year.