The Oued Gueniche aquifer system, represented by plio-quaternary silico-clastic layers, is considered one of the most important groundwater reservoirs in the Bizerte region (northern Tunisia). It is the only source of water supply for a variety of purposes, particularly agriculture. Unfortunately, overexploitation of these resources has led to their gradual depletion, which has been exacerbated by years of deficient rainfall. This situation has prompted decision makers to explore possible resources in deeper layers, especially those of the Mio-Pliocene. Although some of these have proved to be good aquifers, the available data is insufficient to develop a strategy for their rational exploitation. It is against this backdrop that this study aims to characterize, for the first time, the geometry of the deep Mio-Pliocene aquifer via a multidisciplinary approach integrating surface and subsurface data. Existing geological maps, lithological logs from four oil wells, and twenty-eight seismic lines were used to track variations in sedimentary facies both laterally and vertically and to highlight subsurface structures such as folds, horsts, grabens, and controlling faults. As a result, isobath and isopach maps of the Mio-Pliocene formations were produced. These clearly show the geometry (thickness, depth, lateral extensions, etc.) of the aquifers and aquitards. For greater precision, a 3D image of the Mio-Pliocene aquifer system was constructed. Above all, it highlighted the various groundwater flow paths. The results obtained, which can be improved by further studies, underline the importance of integrating various data sources and analytical techniques to characterize the Oued Gueniche aquifer system, providing valuable insights for developing long-term solutions to address the water scarcity in this region of Tunisia.