Sisseb El Alem-Nadhour Saouaf (SANS) basin, is located in the Northeastern Tunisia, where groundwater systems are often exposed to rapidly reserve overexploitation, changing recharge amounts and quality degradation. A three-dimensional (3D) regional hydrogeological model of SANS basin was developed in order to understand the geometry of subsurface and its implications on groundwater dynamics. The 3D model was built by the interpretation of 2D seismic reflection profiles, calibrated by wire line logging data of oil wells, hydraulic wells and geologic field sections. After checking efficiency of interpolation methods by geostatistical tools, validated model highlighted the impact of faults system on the aquifer geometry and structure. Thus, Plioquaternairy and Oligo-Miocene aquifers in the study area represent important geometric variations and cumulated thickness affected by intensive fractures which divided the system into 4 sub-basins (Bled Ktifa, Sisseb, El Alem and Nadhour Saouaf). Moreover, vertically, geological modeling shows 11 hydrogeological layers, with different hydrodynamic characteristics. This study was benefic to propose a conceptual model for the SANS system and to identify the recharge zones and the over-pumped areas which are affected by a significant evaporation rates and reveal large fluctuations of flow dynamic. These results suggest the critical importance of building a various GIS database and testing numerical geological models on groundwater flow dynamic assessment.