Study regionThe Miocene Fluvial Moghra Aquifer in the North Western Desert of Egypt Study focusThe study integrates stable isotope analyses with aeromagnetic and hydrogeological datasets to accomplish the following: (1) define the primary source(s) of recharge to the Moghra aquifer, (2) assess aquifer connectivity with the Nile River aquifer, and (3) investigate the vertical connectivity of the Moghra aquifer with the underlying Nubian Aquifer System (NAS) through subvertical faults. New hydrological insights for the regionThe findings reveal (1) significant heterogeneity in groundwater isotopic compositions (Group A: δ18O: 1.1–13.8 ‰; δD: 4.6–73.5 ‰, B: δ18O:−0.99 to 0.85; δD: −7.58 to 4.38 ‰; and C: δ18O:−1.1 to −3.4; δD: − 6.3 to −18.2 ‰) indicative of variability in recharge sources. (2) Groundwater compositions west (up to 30 km) of the Nile River (Group A) resemble enriched modern Nile waters following the Aswan High Dam (AHD) construction that give way further west to relatively depleted groundwater (Group B) resembling historical pre-AHD Nile water compositions. (3) Further west from Group B depleted Group C samples occur along intersections of multiple fault systems (NW and NE-oriented faults) interpreted as mixtures of rising highly-depleted paleo Nubian Aquifer System (NAS) waters and pre-AHD Nile waters. (4) The advocated structural control is reported in similar settings in Egypt, suggesting that intersections of multiple fault systems provide regional connections between deep and shallow aquifers in northeast Africa, recharge overlying shallow aquifers, and should be considered in groundwater management scenarios.