The Djeffara plain, extending over Tunisia and Libya (48,000 km 2 ), experiences unsustainable exploitation of groundwater, the severity of which needs to be determined. Here, we used data from Gravity Recovery and Climate Experiment (GRACE) and Global Land Data Assimilation System (GLDAS) to assess the groundwater storage variation (∆GWS) for the period 2002-2016. ∆GWS values, downscaled over a 0.5°× 0.5°grid using pumping wells spatial distribution and rates, were introduced in a discrete set of groundwater and salt budget equations to ascertain the recharge and the coastal fluxes. An average recharge of 4.3 ± 2.7 mm•yr −1 representing 2.2 ± 1.4% of the domain-averaged annual rainfall was obtained. A saline intrusion of 147.3 × 10 6 and 46.9 × 10 6 m 3 •yr −1 was calculated for the Tripoli (Libya) and Djerba (Tunisia) areas, respectively. The overall Submarine Groundwater Discharge (SGD) of freshwater along the 450 km long Djeffara coast represents about 339.6 × 10 6 m 3 •yr −1 for the 2002-2016 period.