It is of great importance to evaluate simple methods to identify mineral occurrence for the future development of society. Applying a reconnaissance magnetic data analysis can help detect the main structural trends mounted to the occurrence of minerals. In this study, geological and geophysical data were analyzed to evaluate the main structural trends affecting mineralization in the area of Wadi El-Nakheel. Geomagnetic data were processed to remove the earth’s magnetic field and reduce the magnetic pole. Some mathematical filters related to detecting and enhancing boundaries between rock units, depending on their magnetization affinity, were applied, including the first vertical derivative, the analytic signal, and 3D Euler deconvolution. After structural analysis of these data, we reached the following findings: The main structural trends from the surface and subsurface estimations were the northwest–southeast trend and the northeast–southwest trend. The orientation and origin of Wadi El-Nakheel are aligned with the main structural trend affecting the area that formed during the Red Sea Rift movement and the Pan-African orogeny. The depth of the deep-seated structure controlling the valley is 1500 m and all mineral occurrence is mainly structurally controlled in the studied area; phosphate ore outcrops are usually aligned with the northwest–southeast geological trend, and metallic ores are related to basement rock succession and the main dominant geological structures in the studied area. Finally, the magnetic method was demonstrated to be a reliable tool for detecting the subsurface boundary between geologic units.