Shallow aquifer mapping and large-scale characterization of groundwater dynamics in the Saharan-Arabian Desert is largely impeded by the limited hydrological datasets from sparse and unevenly distributed well logs. Today, as these aquifers are depleting at alarming rates in response to climatic and anthropogenic stresses, accurate knowledge of their dynamical characteristics is not only essential for understanding the water deficit in these increasingly populated areas but also to understand the regional and global environmental impacts of such changes. Herein, we suggest that groundwater mounding can be used for assessing aquifer connectivity in hyper-arid deserts. Using the shallow Post Nubian Aquifer System (PNAS) in Egypt as a test site, we integrate remote sensing, isotopic, hydrochemical and geoelectrical methods to characterize the Saharan groundwater mounds, examine the structural control on groundwater dynamics and discuss the potential of future satellite missions to characterize aquifer connectivity. The results suggest that groundwater mounding in the PNAS is attributed to artesian discharge of the deep Nubian Aquifer System (NAS) along the intersection of WNW and E-W major faults. This is evident by the dominant isotopic signature (δ18O: −9.93‰; δ2H: −79.05) of the deep NAS in the shallow PNAS with a percentage of up to 85% in the faulted zone. The 2D-Electrical Restively Imaging (ERI) delineate multiple small-scale mounds, atop of faults, that can attain 37 m height above average water table creating a relatively steep hydraulic gradient and deviating the groundwater flow direction. Future orbital radar sounding missions can benefit from characterizing the geometry of these mounds to define the measurement requirements of such hydrological features. The large-scale time-coherent subsurface mapping of the Saharan-Arabian aquifers can provide unique insights to examine the aquifer connectivity and the response of aquifers to climatic and anthropogenic stresses in desert areas that otherwise cannot be addressed using existing sporadic well-logs.