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The expansion of irrigated agriculture and the overexploitation of groundwater aquifers are leading to saltwater intrusion, severe deterioration of groundwater quality and soil subsidence at arid areas. The geochemical processes taking place along an 800 km flow line in the non-carbonate Continental Intercalaire aquifer (CI) in North Africa are described using chemical (major and trace element) and isotopic indicators. The aquifer is hydraulically continuous from the Atlas Mountains in Algeria to the Chotts of Tunisia and the geochemical evidence corroborates this. The CI aquifer of North Africa is one of the largest confined aquifers in the world. The aquifer is hydraulically continuous from the Atlas Mountains in Algeria (recharge area) to the Chotts of Tunisia (discharge area) and the geochemical evidence corroborates this. The isotopic study (Delta(18)O, Delta(2)H) permits classifying groundwater into three groups. The first group is characterized by low H-3 concentrations, low C-14 activities and depleted stable isotope contents. It corresponds to an old end-member in relation with palaeoclimatic recharge which occurred during the Late Pleistocene and the Early Holocene humid periods. The second group is distinguished by high to moderate H-3 concentrations, high C-14 activities and enriched heavy isotope signatures. It corresponds to a modern end-member originating from a mixture of post-nuclear and present-day recharge in relation to return flow of irrigation. The third group is characterized by an average composition of stable and radiogenic isotope signatures. It provides evidence for the mixing between the upward moving palaeoclimatic end-member and the downward moving present-day end-member. Rainfall, originating from a mixture of Atlantic and Mediterranean air masses.