The people in the semi-arid north of Namibia suffer from an inadequate water supply, both in quantity and quality, exacerbated by repeated drought seasons. Geologically, the region is comprised mostly of the Cubango Megafan, a very large fluvial inland delta (54,000 km²). Both sediment and groundwater recharge stem from the Angolan Highlands in the north. The megafan contains three aquifer systems, a shallow perched system of low yield and dubious water quality and two transboundary regional aquifers. The latter are also in part saline. An analysis of the distribution of salinities and water types in the upper regional aquifer showed that groundwater with higher salinities, of the NaCl-type, occurs mostly at the terminal (downstream) parts of the fan. Lower-salinity groundwater dominates further upstream, at first as NaHCO3-type and finally the CaHCO3-type. Analyses of drill cores revealed that the pore waters of the megafan material must have been saline initially. Since fresh groundwater recharge comes from the highlands up north, we therefore postulate that that the freshwater pushes the saline waters out (freshening), thereby creating the classical ion exchange sequence described by the water types mentioned above. A 2D areal numerical flow and reactive transport model was set-up to emulate the observed variations in water qualities across the south-west of the megafan. Groundwater flow was modeled using available groundwater levels to approximate present-day flow conditions, despite poorly defined boundary conditions and limited, often unreliable data. Despite using time-invariant flow to reconstruct paleo-hydrogeological conditions the model produced a good fit to the spatial hydraulic head and hydrochemistry data obtained in the field. The results confirm our conceptual model of a freshening front advancing from the north and provides time-averaged recharge volume estimates needed to recreate present-day observations. These findings may offer valuable insights for future groundwater exploration in this vast system.