Groundwater has been identified as one of the major freshwater sources that can potentially meet the growing demands of Egypt’s population. Gravity data (from 381 ground gravity stations) were collected, processed, and analyzed together with the available aeromagnetic (800 line-km) data to investigate the hydrogeologic and structural settings, areal distribution, geometry, and water storage of the aquifers in El Qaa coastal plain in the southwest Sinai Peninsula, and to assess their longevity given projected extraction rates. Findings include (1) complete Bouguer anomaly and total magnetic intensity maps show two connected sub-basins separated by a narrow saddle with an average basin length of 43 km and an average width of 12 km; (2) two-dimensional modeling of both gravity and magnetic data indicates basin fill with a maximum thickness of 3.5 km; (3) using anomalous residual gravity, the volume of water in storage was estimated at 40–56 km3; and (4) progressive increases in extraction rates over time will deplete up to 40 % of the aquifers’ volume in 200–230 years and will cause the water quality to deteriorate due to seawater intrusion in 45 years. Similar geophysical exploration campaigns, if conducted over the entire coastal plains of the Red Sea and the Gulfs of Suez and Aqaba, could assist in the development of sound and sustainable management schemes for the freshwater resources in these areas. The adopted techniques could pave the way toward the establishment of sustainable utilization schemes for a much larger suite of similar aquifers worldwide.