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Coastal aquifers are considered as major sources for freshwater supply worldwide, especially in arid zones. The weak rainfall as well as the intensive extraction of groundwater from coastal aquifers reduce freshwater budget and create local water aquifer depression, causing both seawater intrusion and a threat to groundwater. This phenomenon was observed in the Jerba Island which is located in southeast Tunisia. Jerba’s unconfined aquifer shows high values of groundwater salinity reaching, locally, 17 g/l and a strong contrast between some zones of the aquifer. High pumping rates and weak recharge disturb the natural equilibrium between fresh and saline water causing water salinization in most areas of the island. This study aims at establishing the salinity map of the aquifer and identifying the origin of groundwater salinization. The salinity map shows that zones characterized by low groundwater salinity are located in the center of the study area. High groundwater salinities are observed near the coast and in some parts having low topographic and piezometric levels. Groundwater geochemical characterization, and Br/Cl and Na/Cl ratios suggest that the origin of abnormal salinity is seawater intrusion. Considering groundwater salinity values and Br concentrations, a seawater intrusion map is established. It shows that many areas of the unconfined aquifer are contaminated by mixed groundwater and seawater. The statistical analysis demonstrates that high mineralization of the groundwater is due to gypsum and carbonate dissolution coupled with the mixed groundwater and seawater in many areas.