Abstract Assessment of the recharge is of strategic importance for a sustainable development of the aquifer resource, especially in arid and semi-arid areas. This study synthesizes and compares the results of isotope hydrology investigations obtained for different aquifer systems in Tunisia. The δ2H, δ18O values and 14C, and 3H contents are distinct in unconfined and confined groundwater and vary from northern to southern parts of Tunisia reflecting different recharge conditions. Low δ2H and δ18O values of deep confined groundwater in the southern and central parts agrees with groundwater residence times that suggest an important phase of recharge during the Holocene and Pleistocene under paleo-climatic conditions that are quite humid from the current. The study of paleo-groundwater signals of these aquifers indicates that the transition from the end of the Pleistocene to the Holocene is associated with a much humid climate to give a widespread age signal in southern and central deep groundwater in Tunisia. Furthermore, the current climatic conditions are the determining factors in the recharge process of Tunisia aquifers. So, they allow only very low recharge rates of most aquifers. As a result, paleo-water is dominating in many groundwater basins particularly where the extraction of water exceeds the present recharge.