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The high groundwater salinity of crystalline aquifers in semiarid areas is generally attributed to the dissolution and leaching of meteoric salts that have been progressively evapoconcentrated in the different hydrological compartments under dry climate conditions. A numerical model, simulating water and salt balances, was developed from a case study in Northeast Brazil to: (1) test the validity of this hypothesis, through the quantification of all relevant water cycle processes in the studied watershed, and (2) demonstrate how changes in land cover can impact groundwater salinity. Computations showed that the aridity and the high evapo(transpi)ration rates from the unsaturated zone and/or surface water (ponds, reservoirs) cannot lead to the observed aquifer salinization levels, but only to concentrations of a few tens or hundreds of mg L–1 (Cl–). The only process that can induce a high groundwater salinity, with chloride concentrations up to several g L–1, is the transpiration of groundwater by the deep roots of the vegetation, with a rate reaching 100% of the annual recharge. In this case study, the vegetation involved is the native Caatinga forest. Simulations of the long-term dynamics of groundwater salinity indicate that aquifer areas with high salinity are relicts of the Caatinga pre-colonization period during which subterranean endorheic conditions were prevailing. Following the Caatinga deforestation linked to colonial agricultural development, aquifer recharge increased and endorheism ceased. Consequently, these aquifers may have now been experiencing a desalination process for about three centuries. The desalination spatial variability drivers are explained in the paper. [ABSTRACT FROM AUTHOR]