An integrated [very low frequency (VLF) electromagnetic, magnetic, remote sensing, field, and geographic information system (GIS)] study was conducted over the basement complex in southern Sinai (Feiran watershed) for a better understanding of the structural controls on the groundwater flow. The increase in satellite-based radar backscattering values following a large precipitation event (34 mm on 17–18 January 2010) was used to identify water-bearing features, here interpreted as preferred pathways for surface water infiltration. Findings include: (1) spatial analysis in a GIS environment revealed that the distribution of the water-bearing features (conductive features) corresponds to that of fractures, faults, shear zones, dike swarms, and wadi networks; (2) using VLF (43 profiles), magnetic (7 profiles) techniques, and field observations, the majority (85 %) of the investigated conductive features were determined to be preferred pathways for groundwater flow; (3) northwest–southeast- to north–south-trending conductive features that intersect the groundwater flow (southeast to northwest) at low angles capture groundwater flow, whereas northeast–southwest to east–west features that intersect the flow at high angles impound groundwater upstream and could provide potential productive well locations; and (4) similar findings are observed in central Sinai: east–west-trending dextral shear zones (Themed and Sinai Hinge Belt) impede south to north groundwater flow as evidenced by the significant drop in hydraulic head (from 467 to 248 m above mean sea level) across shear zones and by reorientation of regional flow (south–north to southwest–northeast). The adopted integrated methodologies could be readily applied to similar highly fractured basement arid terrains elsewhere.