Scarcity of water in arid and hyper-arid environments is one of the main challenges that hinder the development of such areas. Therefore, the main study objective is to introduce a comprehensive scientific approach based on remote sensing data and geoinformatic applications in combination with field investigations to extract inferences for groundwater exploration in a remote data-scarce pilot area (El-Kubanyia basin). The measured composite section has thickness 410 m where the geologic exposures are represented from Upper Cretaceous to Quaternary age. The Quaternary aquifer has limited exploration where it was penetrated by 16 wells (depths ranging between 23 and 210 m, salinity between 775 and 3142 mg/l), while Nubian sandstone does not explored yet. The porosity and permeability are evaluated for Nubian group through blue dye staining thin sections and reveal high capabilities to bear and sore groundwater. The photogeologic structural lineaments of El-Kubanyia basin include sets of fracture and/or faults (NE-SW, NW-SE and E-W) where two faults are connecting between Naser Lake and Nubian group in El-Kubanyia basin. The magnetotelluric and gravity data clarified that the basin outlet is a graben filled with post-Cretaceous sedimentary rocks. The integration between the obtained geological structures with data derived from remote sensing investigations, are used to design five conceptual models simulate the opportunities for recharging the Quaternary and Nubian sandstone aquifers and identify the different recharge sources such as; Nile River, Nasser Lake, and paleo-precipitation in past wet periods. Finally, a future perspective strategy for groundwater exploration was presented.