Wadi El Khariq has a vast area that can be reclaimed. Upper Jurassic carbonates represent the main aquifer. The Desert Research Center has a pilot station in Wadi El Khariq that suffers from water deficiency. Therefore, the drilling of new wells is needed. As fault zones make fracture conduits for groundwater, detecting these faults is a vital process. Therefore, this study aims to trace the existing subsurface structures and their impact on groundwater occurrence. The interpretation of the results of the vertical electrical soundings leads to the detection of five geoelectrical layers. The third and fourth layers correspond to fractures and argillaceous limestone represents the water-bearing layers. The interpretation of the results of the eight 2D electrical resistivity tomography profiles gave more illustrative information about the lateral facies changes, the structures effect along the study area, distribution of the different types of water-bearing limestone, and the depth to their top. The deduced structures from electrical study are represented by the faults F1–F6. The faults F1 and F2 are confirmed from both 1D and 2D imaging profiles. The fault plains of F1, F2, F5, and F6 are continuous between the measured imaging profiles. The 2D imaging profiles revealed that the clay content increase eastwards. The correlation results of the natural gamma and lithological logs of the drilled wells as well as the constructed hydrogeological profiles revealed that the area of study affected by another group of faults (F6–F12). These faults affect on the groundwater occurrence and quality. These faults lead to the formation of graben and horst structures, lateral facies changes, variation in layers thickness, and the occurrence of the fractured limestone layer lying beneath the calcareous clay at variable depths. Most of the detected faults in the study area have NW–SE trends coinciding with the lineation analyses of the faults and fractures of El Khariq basin. The fractured limestone aquifer in the study area is recharged via the percolation of the surface runoff water of local precipitation on Gable El Maghara catchment area through the fracture lines, fault planes and bedding planes besides paleowater of the paleo-rainy seasons. The depth to water varies from 60 to 114 m. The groundwater salinity of the wells drilled in El Khariq plain varies greatly due to the effect of the lithological nature of the water-bearing formation and the well design. It varies from 2335 to 12548 mg/l. The discharge value (Q) varies from 60 to 12 m3/h. This variation is related to the extension and type of the effective fracture system affecting the concerned aquifer.