Unpublished chemical and isotopic data taken in November 1992 from the three major Saharan aquifers, namely the Continental Intercalaire (CI), the Complexe Terminal (CT) and the phreatic aquifer (Phr), were integrated with original samples in order to chemically and isotopically characterize the largest Saharan aquifer system and investigate the processes through which groundwaters acquire their mineralization. Instead of classical Debye–Hückel extended law, a specific interaction theory (SIT) model, recently incorporated in PHREEQC 3.0, was used. Inverse modeling of hydrochemical data constrained by isotopic data was used here to quantitatively assess the influence of geochemical processes: at depth, the dissolution of salts from the geological formations during upward leakage without evaporation explains the transitions from CI to CT and to a first end member, a cluster of Phr (cluster I); near the surface, the dissolution of salts from sabkhas by rainwater explains another cluster of Phr (cluster II). In every case, secondary precipitation of calcite occurs during dissolution. All Phr waters result from the mixing of these two clusters together with calcite precipitation and ion exchange processes. These processes are quantitatively assessed by the PHREEQC model. Globally, gypsum dissolution and calcite precipitation were found to act as a carbon sink.