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Wadi Qena basin represents one of the most promising regions for future development in Egypt. Fresh water supplies are crucial for such plans. We provide an integrated remote sensing (Landsat, ASTER DEM, Geoeye-1), geophysical (aeromagnetic), isotopic (δ 18 O, δ 2 H), field (stratigraphic and structural interpretation) and geochemical (major dissolved ions) approach to delineate zones of potential groundwater resources in Wadi Qena basin. Four water-bearing horizons were sampled: fractured crystalline aquifer, Nubian Aquifer System (NAS), Post Nubian Aquifer System (PNAS) and the Quaternary aquifer. Findings include: (1) spatial analysis of remote sensing data in a GIS environment indicates extensive structural deformation by dextral faults trending NE-SW (i.e. Qena-Safaga shear zone [QS]) and sinistral faults trending NW-SE (i.e. Najd shear zone) and sufficient surface water supply from the east through Wadi Fattera sub-basin; (2) analysis of geophysical data indicates that these faults control the water-bearing horizons in the subsurface; (3) isotopic analysis reveals four isotopic groups including two end members, one mixed group and one mixed and evaporated group: group (I) highly depleted fossil Nubian waters (range: δ 18 O from − 6.39 to − 6.74‰ and δ 2 H from − 48.21 to − 52.46‰); group (II) modern waters in fractured basement (range: δ 18 O from − 1.41 to − 1.51‰ and δ 2 H from 5.46 to − 6.04‰); group (III) a mixed cluster between NAS and modern waters (range: δ 18 O from − 4.82 to − 5.05‰ and δ 2 H from − 33.28 to − 38.54‰); and group (IV) samples which have both mixing between the Nubian and meteoric waters and also have a considerable deviation from the Global Meteoric Water Line (GMWL) (range: δ 18 O from − 0.58 to − 4.69‰ and δ 2 H from − 19.59 to − 38.68‰), (4) samples with a mixed isotopic signature (in group III), which tap the NAS and are located along the main channel of Wadi Fattera (area 3600 km 2 ) provide evidence for modern recharge along surface exposures of the NAS and enhanced infiltration along deep-seated faults; (5) samples with a mixed isotopic signature (in group IV), which tap the Quaternary and PNAS aquifers and are located along deep-seated faults provide evidence of artesian upward leakage from the deep NAS into the shallower Quaternary and PNAS aquifers. The present study improves our understanding of the role of structural control and modern recharge in exploration for aquifer potential in arid environments.