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The shallow Plio-Quaternary (PQ) water table, present over almost the whole Djerid and Chott El Gharsa basins (southern Tunisia), is used as a complement of oases irrigation, especially in summer season. The simplicity of the Plio-Quaternary lithology is confronted to the complexity of the mineralisation mechanisms and the water origin in this aquifer. An approach combining the use of water-dissolved chemical species and isotopic contents has been used to better understand the PQ behaviour under severe increasing exploitation and to determinate the origin of its different water bodies. In southern Tunisia, the aquifer system is composed of the upper unconfined PQ aquifer, the intermediate semi-confined/confined Complexe Terminal (CT) and the deeper confined Continental Intercalaire (CI). Chemical analyses highlighted an origin of mineralisation in close relationship to the dissolution of both sulphated salts (MgSO4 and Na2SO4) and chlorinated salts (NaCl and MgCl) abundant in the surface and subsurface gypsum crust. Positive correlations between gypsum anhydrite, mirabilite, thenardite and halite saturation indexes with respective mineral species, confirm evaporites dissolutions. Isotopic data showed that in addition of sporadic rainfall events, there is a contribution from the CI and the CT Saharan groundwaters, recharging the PQ aquifer in the study area. Return flow irrigation is partly affected by evaporation, before recharging the shallow aquifer, in oases limits.