The Okavango Delta in North Botswana is one of the few active alluvial mega-fans developing in an endorheic setting (Assine & Soares, 2004;McCarthy, 2013) (Figure 1). This fan forms a vast swamp flooded annually by water from the highlands of Angola to the North and it supports an exceptional ecosystem in the middle of the semi-arid Kalahari Desert. Due to their isolation, endorheic ecosystems result from tight coupling between climatic, topographic and geologic settings. Changes in one or several of these controlling factors have dramatic effects on the fragile equilibrium of the ecosystems, especially in semi-arid or arid climate contexts (Yapiyev et al., 2017). In the context of rapid climate change and of a regionally increasing anthropogenic pressure, especially on water resources (Ministry of Mineral, Energy and Water Affairs, Republic of Botswana, 1997), improving our knowledge of the structure and functioning of the sensitive Okavango geo-ecosystem is a fundamental challenge. Among the major threats to the ecosystem of the Delta, a decrease in the amount and quality of the water is probably the most important. In order to evaluate the impact of global change on the ecosystem, it is thus necessary to fully understand the hydrology of the Delta. In that respect, describing the geometry, sedimentological structure and geochemical pattern of the various aquifers is essential to understand the geochemical exchanges between the surface and groundwater, the soil and the biosphere.Many studies have already addressed the sedimentation, the hydrology and the vegetation dynamics of the fan in terms of sediment input or water dynamics. A majority of these studies also deal with the effects of anthropogenic activity such as, water pumping, or those of tectonic activity along the faults bordering the rift (Ellery