The North Western Sahara Aquifer System (NWSAS) is characterized by unsustainable groundwater exploitation whose magnitude depends on the still unclear recharge value. It is extending over Libya, Tunisia, and Algeria, with an area of 10⁶ km². Here, we proposed an integrated approach combining Gravity Recovery and Climate Experiment (GRACE) and Global Land Data Assimilation System (GLDAS) data to reconstruct groundwater storage variations (ΔGWS) between April 2002 and July 2016. ΔGWS values are then introduced in a regional water budget equation accounting for the temporal evolution of withdrawals and natural discharge to calculate the time variations of the recharge. Yearly reconstruction of the recharge shows a large variability with alternation of net positive recharge and periods of net diffuse discharge associated with evaporation. The temporal average effective recharge value for the period of interest is 1.76 ± 0.44 mm yr⁻¹. Lag-times for the recharge to reach the water table of 45 and 100 yrs characteristic of a diffuse recharge and corresponding vadose thickness in the range 3.90 ± 3.60 and 8.60 ± 8.10 m were identified using a cross-correlation analysis between reconstructed annual recharge and annual rainfall (AR). Statistical interpretation of the relation between ΔGWS, AR, and withdrawals shows that the anthropogenic effect (groundwater extraction) is the main controlling factor (99% of explained variance) in comparison to AR variations for the ΔGWS time series under consideration. A relation between long-term recharge and average annual rainfall (AAR) suggests a recharge representing 1.8 ± 0.3% of AAR in transboundary aquifers of the Saharan belt.