An integrated hydro-geophysical and hydrochemical investigation was conducted to delineate aquifer geometry, assess groundwater potential, and evaluate water quality in the southern part of Wadi Qena, Eastern Desert, Egypt. Eighteen time-domain electromagnetic (TDEM) soundings, ground magnetic profiles, pumping-test data, and six groundwater chemical analyses were jointly interpreted. The integrated datasets reveal five geo-electrical layers and identify two main aquifer systems: a shallow Quaternary aquifer (50-300 m depth; 4.9-86 Omega m) and a deeper Nubian Sandstone aquifer (300-650 m depth; 4.7-17.6 Omega m). Magnetic modeling delineates a variable basement surface (350-850 m) that controls aquifer thickness and the spatial distribution of transmissive zones. Areas of deep basement lows coincide with high-transmissivity wells (655-1170 m2/day) and low resistivity, indicating thick, well-connected sandstone bodies. Hydrochemical data (TDS: 1447-1607 mg/L; Na-Cl facies) indicate increasing salinity toward the northwest, consistent with upward leakage along magnetic lineaments and the dissolution of salt-bearing formations. The integrated interpretation demonstrates that combining TDEM, magnetic, and geochemical approaches provides a robust framework for identifying productive aquifers, understanding salinity sources, and optimizing groundwater development in arid terrains.