Groundwater is the main water resource in Tunisia, especially in the Tunisian Sahel (the arid region of the Mediterranean). The increasing scarcity requires an understanding of the interactions between the Sfax deep aquifer of the Upper Miocene and the Regueb aquifer of the same age. In this paper, we study the hydrogeophysical relationship between these two deep aquifers. The method involves seismic, gravity and piezometric data collected during periods of high and low water tables to better understand the hydrogeological connection, groundwater flow mechanisms and recharge zones. Lithostratigraphic correlation of the NW-SE direction shows the thickness of geological formations across the study area, with the Regueb aquifer exceeding 800 m in depth and the Sfax aquifer over 1000 m, indicating a strong hydrogeological connection. Seismic reflection data suggest that the two aquifers are tectonically shaped by a Cretaceous heritage. Gravity filters for the Bouguer anomaly, horizontal gradient magnitude, Euler deconvolution, tilt angle and a three-dimensional gravity model, for example, were created to delineate the structurally controlled boundary between the two deep aquifers and to highlight the subsurface structures and fault networks with their depths and their directions. Finally, this integrated study, for the first time, reveals a structure that controls the boundary and flow between the deep aquifers of Regueb and Sfax.