AbstractThe role of faults in controlling groundwater flow in the Sahara and most of the hyper‐arid deserts is poorly understood due to scarcity of hydrological data. The Wadi Araba Basin (WAB), in the Eastern Sahara, is highly affected by folds and faults associated with Senonian tectonics and Paleogene rifting. Using the WAB as a test site, satellite imagery, aeromagnetic maps, field observations, isotopic and geochemical data were examined to unravel the structural control on groundwater flow dynamics in the Sahara. Analysis of satellite imagery indicated that springs occur along structurally controlled scarps. Isotopic data suggested that cold springs in the WAB showed a striking similarity with the Sinai Nubian aquifer system (NAS) water and the thermal springs along the Gulf of Suez (e.g., δ18O = −8.01‰ to −5.24‰ and δD = −53.09‰ to −31.12‰) demonstrating similar recharge sources. The findings advocated that cold springs in the WAB represent a natural discharge from a previously undefined aquifer in the Eastern Desert of Egypt rather than infiltrated precipitation over the plateaus surrounding the WAB or through hydrologic windows from deep crystalline basement flow. A complex role of the geological structures was inferred including: (1) channelling of the groundwater flow along low‐angle faults, (2) compartmentalization of the groundwater flow upslope from high‐angle faults, and (3) reduction of the depth to the main aquifer in a breached anticline setting, which resulted in cold spring discharge temperatures (13–22°C). Our findings emphasize on the complex role of faults and folds in controlling groundwater flow, which should be taken into consideration in future examination of aquifer response to climate variability in the Sahara and similar deserts worldwide.