We used multi-map analysis of remote sensing and ancillary data to identify potentially accessible sites for groundwater resources in the Kharga Basin in the Western Desert of Egypt. This basin is dominated by Cretaceous sandstone formations and extends within the Nubian Sandstone Aquifer. It is dissected by N-S and E-W trending faults, possibly acting as conduits for upward migration of groundwater. Analysis of paleo-drainage using Digital Elevation Model (DEM) generated from the Shuttle Radar Topography Mission (SRTM) data shows that the Kharga was a closed basin that might have been the site of a paleo-lake. Lake water recharged the Nubian Sandstone Aquifer during the wetter Holocene time. We generated the following layers for the multi-map analysis: (1) Fracture density map from the interpretation of Landsat Operational Land Imager (OLI), SRTM DEM, and RADARSAT data. (2) Thermal Inertia (TI) map (for moisture content imaging) from the Moderate Resolution Imaging Spectroradiometer (MODIS) data. (3) Hydraulic conductivity map from mapping lithological units using the Landsat OLI and previously published data. (4) Aquifer thickness map from previously published data. We quantitatively ranked the Kharga Basin by considering that regions of high fracture density, high TI, thicker aquifer, and high hydraulic conductivity have higher potential for groundwater accessibility. Our analysis shows that part of the southern Kharga Basin is suitable for groundwater extraction. This region is where N-S and E-W trending faults intersect, has relatively high TI and it is underlain by thick aquifer. However, the suitability of this region for groundwater use will be reduced significantly when considering the changes in land suitability and economic depth to groundwater extraction in the next 50 years.