Studying groundwater resources in Egypt is essential, especially under the water scarcity issue we face nowadays in our hyper-arid region. The recharge from deep mega aquifers towards shallow aquifers is important because it feeds the easily accessible and highly consumed shallow aquifers, this feeding is achieved via vertical and sub-vertical faults. The present study aims to predict the connection status between the deep Nubian Sandstone Aquifer System (NSAS) and the shallow Quaternary Aquifer System (QAS) in Upper Egypt in the western bank of the Nile River from Aswan to Sohag governorates. Aeromagnetic data was analysed to reveal the subsurface deep-seated major faults and major surface faults were traced from the published geological maps of Egypt. The analysis and interpretation of the aeromagnetic data and surface faults revealed that the main structural trends prevailing are extending in the E-W, NW-SE and NE-SW directions for deep and surface faults. It was deduced that these faults are regional and extends from the deep subsurface to the shallow surface. The continuity between the deep-seated and surface faults forecasts the vertical connection between the deep NSAS and the QAS. In the meantime, the isotopic analyses of previous published works supports this connection.