Abstract The geochemical processes taking place along an 800 km flow line in the non-carbonate Continental Intercalaire aquifer (CI) aquifer 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 highest discharge temperature is 73 °C but silica geothermometry indicates a maximum temperature of 94 °C at depth. Chloride concentrations increase from 200 to 800 mg l −1 and the Br/Cl ratios confirm the dissolution of non-marine evaporites or interstitial waters as the main source of salinity. Fluoride concentrations are low and are likely to be derived from rainfall, recording oscillations in source. Radiocarbon ages, except near outcrop, are at or near detection limits and the δ 18O and δ 2H values indicate a cooler recharge regime with rainfall having lower primary evaporation than today. This is shown by the fact that mean isotope ratios of CI waters are around 3‰ lighter than the present-day weighted mean value for rain. Major ion ratios and most trace elements indicate that despite the complex structure and stratigraphy, uniform evolution with continuous water-rock interaction takes place along the flow lines, which are only disturbed near the Tunisian Chotts by groundwater converging from additional flow lines. The ageing of the water can also be followed by the smooth increase in several indicator elements such as Li, K and Mn which are least affected by solubility controls. Similarly the influence of marine facies in the Tunisian sector may be recognised by the changing Mg/Ca and higher Br/Cl as well as trace element indicators. The groundwaters are oxidising up to 300 km from outcrop (dissolved O 2 has persisted for at least 20 ka) and within this zone the concentrations of several elements forming oxy-anions, such as U and Cr, increase and NO 3 remains conservative. Beyond 300 km from outcrop, the groundwaters are reducing and contain high Fe concentrations. The basin contains huge reserves of fresh/brackish waters but these need careful development due to the limiting high salinity and scaling tendency resulting from the high temperatures and mineral super-saturation caused during abstraction as well as high concentrations of some harmful elements such as Cr in the oxidising section.