The Okavango Delta in North Botswana is a hot-spot of biodiversity within the semi-arid central part of the South African plateau. This endorheic ecosystem is highly dependent on the annual flood that brings freshwater from the highlands of Angola to the North. However, in many places, the groundwater of the Delta is saline and contains very high concentrations of metal and metalloid elements, making it toxic to the flora and fauna. These saline waters have been largely studied and their formation is generally explained through evaporation and evapotranspiration processes. However, no studies have investigated the geochemical composition of the sediments that host the aquifers. Here, we provide a complete sedimentological and geochemical investigation (major, traces and rare earth elements, carbon and oxygen stable isotopes ratios, Sr and Nd isotope ratios) of the various geomorphological and ecological compartments that form the landscape of the SW Okavango Delta. We demonstrate that the non-connected underground aquifer is capped by a clay layer corresponding to a major event of dust deposition from the Makgadikgadi pan. We suggest that this aquifer may extend outside the island, below the floodplain and that the hydrological structure of the Nxaraga area is indeed composed of two non-connected aquifers of different origins. Challenging the model based on evaporation and evapotranspiration, we propose that the composition of that allochtonous clay and the in situ reactions between sediment, water and organic matter in a confined aquifer explain the geochemical enrichment of the water.