An arid climate accompanied by a freshwater shortage plagued Egypt. It has resorted to groundwater reserves to meet the increasing water demands. Fossil aquifers were lately adopted as the sole water source to provide the irrigation water requirements of the ongoing reclamation activities in barren areas. Yet, the scarcity of measurements regarding the changes in the aquifers’ storage poses a great challenge to such sustainable resource management. In this context, the Gravity Recovery and Climate Experiment (GRACE) mission enables a novel consistent approach to deriving aquifers’ storage changes. In this study, the GRACE monthly solutions during the period 2003–2021 were utilized to estimate alterations in terrestrial water storage (TWS) throughout Egypt. Changes in groundwater storage (GWS) were inferred by subtracting soil water content, derived from the GLDAS-NOAH hydrological model, from the retrieved TWS. The secular trends in TWS and GWS were obtained using the linear least square method, while the non-parametric technique (Mann–Kendall’s tau) was applied to check the trend significance. The derived changes in GWS showed that all aquifers are undergoing a significant loss rate in their storage. The average depletion rate over the Sinai Peninsula was estimated at 0.64 ± 0.03 cm/year, while the depletion rate over the Nile delta aquifer was 0.32 ± 0.03 cm/year. During the investigated period (2003–2021), the extracted groundwater quantity from the Nubian aquifer in the Western Desert is estimated at nearly 7.25 km³. The storage loss from the Moghra aquifer has significantly increased from 32 Mm³/year (2003–2009) to 262 Mm³/year (2015–2021). This reflects the aquifer exposure for extensive water pumping to irrigate newly cultivated lands. The derived findings on the aquifers’ storage losses provide a vital source of information for the decision-makers to be employed for short- and long-term groundwater management.

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.

Egypt has recently inaugurated a mega development project aiming to alleviate the overpopulation along the Nile River and to meet the looming food gap. Toshka is a promising area where groundwater-dependent activities are being expanded adjacent to Lake Nasser. Thus, it is of utmost importance to provide a sustainable development approach and to assess the resulting environmental implications. Accordingly, a coupled groundwater flow and transport model was invoked. The generated model was successfully calibrated for the observed water levels and salinity. The proposed exploitation regime of 102 wells each pumping 1000 m³/day was simulated for a 100-year test period. The maximum resulting drawdown was about 25 m, compatible with the advocated sustainable restriction limit. Climate change (CC) impacts of reducing the lake’s storage and increasing the crops’ water requirements were investigated. The lake’s water level fluctuations were a key factor in the aquifer hydraulics and flow direction. The drawdown breakthrough considering the CC catastrophic scenario (RCP8.5) has increased by about 20%. The developed solute transport model was utilized to simulate the salinity spatial distribution and the lateral movement of leaking pollutants from the underway activities. Cultivation activities were found feasible up to 80 km away from the lake border where salinity does not exceed 2000 ppm. Yet, a protection strip of not less than 4.8, 6.0, and 7.2 km according to the lake operating condition is inevitable to ensure that pollutants do not intrude into the lake. These findings will assist the decision-makers in scheming environmental impact assessment criteria for sustainable development.