Investigating groundwater resources in Egypt is crucial, particularly in light of the water scarcity issues in this hyper-arid region and the ongoing climatic challenges. The replenishment of shallow aquifers by deep mega aquifers is significant because it supports the heavily utilized and easily accessible shallow aquifers. This replenishment occurs via vertical and sub-vertical faults. In this study aeromagnetic
data were utilized to reveal subsurface deep-seated major faults and to infer their relation to major surface faults that were traced from the published geological maps of Egypt. The analysis and interpretation of the present data revealed that the main subsurface structural trend is extending NE-SW, while the main surface fault trend runs in an opposite position extending NW-SE. This discrepancy in the extension of surface and subsurface faults indicates lack of a vertical and/or subvertical continuity. Consequently, no interconnection exists between the deep Nubian Sandstone Aquifer System (NSAS) and the shallow Carbonate Aquifer System (CAS), implying no upward feeding from the NSAS towards the CAS in the study area. This anticipation is confirmed from the stable isotopic analyses for some representing groundwater samples which were carried out and published in a literature.