Geochemical analyses of groundwater samples from the Djeffara confined aquifer (Southern Tunisia) were performed. The distribution of saline waters was investigated to identify the origin of the groundwater contamination. The aquifer was shown to be affected by an abnormal increase in groundwater salinity. Near the recharge zone, the groundwater salinity does not exceed 2.5 g l−1 but reaches 7 g l−1 in the northeast of the study area. Due to over pumping, groundwater level decline is so important that it disturbs the equilibrium between fresh and saline waters. The salinity distribution coupled with the structure and geology of the Djeffara aquifer suggest current seawater intrusion is possible through the deep fault systems affecting the zone. The groundwater level was shown to be highly correlated with the sea level fluctuation in the area near the fault systems, suggesting a communication between the sea and the confined aquifer. Groundwater salinization is probably related to infiltration of seawater through the faults. However, an intrusion on the side of the discharge area of the aquifer may also be possible. The bromide and chlorine analyses coupled with the SO4/Cl ratio confirmed that the mixing between fresh and saline waters is the main origin of groundwater salinization.