Investigating groundwater resources in Egypt is crucial, particularly in light of the water scarcity issues in the hyper-arid region and 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. This study aims to predict the connection status between the deep Nubian Sandstone Aquifer System (NSAS) and the shallow Carbonate Aquifer System (CAS) from Sohag to Assiut Governorates (the Western border), Upper Egypt. In this study aeromagnetic data was utilised to reveal the subsurface deep-seated major faults, however, the major surface faults were traced from the published geological maps of Egypt. The analysis and interpretation of the data revealed that the main subsurface structural trend is extending NE-SW, while the main surface fault trend is extending NW-SE. This discrepancy in the extension of surface and subsurface faults indicating lack vertical and/or subvertical continuity. Consequently, no interconnection between the deep NSAS and the shallow CAS. Therefore, the upward feeding from NSAS towards the CAS do not occur 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.