The Gaafour and El Aroussa basins (Northern Tunisian Atlas) are predominantly agricultural areas that face increasing water scarcity due to prolonged droughts and the intense exploitation of its shallow aquifer. Situated within a complex geological context, the area holds promising deep aquifers that could serve as strategic reserves for water supply under severe climatic conditions. In this context, the present study aims to assess the hydro-geological potential of the Gaafour and El Aroussa plains and to define the subsurface structure of the deep untapped Eocene aquifer. The use of advanced gravity filters and the seismic data analysis enabled the identification of buried sub-basins separated by a NW-SE horst, named as the "Oued Mihoub high", which separates the plain of Gaafour from that of El Aroussa. These two basins are bounded by significant NE-SW and NW-SE fault systems, which control the sedimentary infill and the aquifer geometry. The gravity modeling techniques revealed the configuration and the extent of the various basins and horst structures, highlighting the crucial role of the horst in the hydrogeological dynamics by controlling the direction of groundwater flow, as it diverts it from both sides. In addition, the NE-SW and the NW-SE fault systems play a key role in improving the hydro-geological potential of the aquifer by enhancing porosity and permeability, facilitating infiltration and promoting groundwater recharge. This specific approach provides valuable insights into the subsurface architecture and hydrogeological characteristics of these regions, aiding future groundwater exploration and resource management of an arid region.