The ambitious agricultural development projects in Egypt and the associated horizontal expansion
into the core desert lands and desert fringe zones around the Nile Valley primarily depend on water
availability. This study investigates the vertical recharge from the deep Nubian Aquifer System (NAS)
toward the shallow aquifers, including the Carbonate and Quaternary aquifers in southern Egypt.
While this connectivity has been studied locally through case studies, the present study integrates
stable isotope data from all previous studies, together with analyses from vastly distributed new
groundwater samples, remote sensing, and geophysical methods to better understand groundwater
dynamics and aquifer connectivity over a regional domain. Findings show that: (1) the depths to the
basement surface range from 350 to 4700 m below the land surface, (2) the major structural trends
are E-W, NW–SE, NE-SW, ENE, NNW, and WNW trends, (3) the contribution ratios from the deep
NAS to the overlying aquifers range between 10 and 98% as estimated using isotope mass balance
calculations, and (4) the intersection of NW, ENE, and NE structural trends, which show similar trends
between surface faults and deep faults, indicating vertical continuity, plays a major role in aquifer
connectivity along the western desert fringes of the Nile River, particularly south of latitude 26°30′N.
These findings indicate that the relatively thin sedimentary cover overlying the NAS south of latitude
26°30′N facilitates the upwelling of the NAS groundwater along with the intersection of the NW,
ENE, and NE fault systems. Given the consensus of high hydraulic heads of the NAS compared to the
overlying aquifers, the study suggests that a large-scale vertical upwelling at the deduced intersecting
structural trends throughout the entire Limestone Plateau is worthy of further investigation. Such
vertical upwelling could bring significant groundwater resources to shallow levels, as long as the NAS
maintains its higher heads, and thus supports desert greening projects in Egypt. The findings also
highlight the necessity of examining similar mechanisms in other desert environments with multiple
aquifer systems.