This study aims at identifying the sources and fate of salinity in the Djebeniana basin (Tunisia) aquifers. Groundwater samples from the shallow Plio-Quaternary (PQ) phreatic aquifer and deep Miocene aquifer were analyzed for major/minor ions, trace elements, and stable isotopes of the water molecule (δ18OH2O - δ2HH2O), chlorine (δ37Cl) and bromide (δ81Br). Two clusters of samples with distinct chemical compositions were identified. Cluster I samples correspond to Na–Cl mineralized waters with δ37Cl from −0.3‰ to 0.16‰ and δ81Br from 0.21‰ to 0.39‰. Cluster II samples correspond to Ca–SO4 waters presenting a lower salinity than Cluster I, with δ37Cl from −0.3‰ to 0.09‰ and δ81Br from 0.28‰ to 0.54‰. When plotted in a δ2HH2O vs δ18OH2O graph, most of Cluster I groundwater samples tend to align on a mixing line with seawater whereas Cluster II samples appear to define a local evaporation line. The spatial distribution of samples associated with these clusters allows for evaluating the hydrogeochemical processes associated with groundwater salinization: 1) recent recharge from rainwater dissolving salts and entailing the downward migration of saltwater in the higher reaches of the groundwater flow system, 2) upward leakage of mineralized waters from the deep Miocene aquifer, 3) seawater intrusion in the lower reaches of the coastal aquifer, and 4) ion-exchange reactions prompted by seawater intrusion. A conceptual model of groundwater salinization is proposed as a tool for better managing groundwater resources in the Djebeniana basin.