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The multi-layered transboundary Kalahari aquifer system spanning across Namibia, Botwswana, South Africa, and Zimbabwe, comprises the transboundary Stampriet basin (A005, according to the classification of the International Groundwater Resources Assessment Center IGRAC). This aquifer system reaching from the foothills of the Great Escarpment in Namibia south-east into South Africa, forms a complex and partly artesian multi-aquifer system that is used for drinking water supply, irrigation agriculture and is prospected for in situ-leaching mining. In order to establish functional and geochemical baselines for the major large-scale transboundary aquifer, an integrated hydrological, hydrogeological, geochemical and isotopic assessment has been carried out. The system boundaries have been re-assessed to integrate the contributing hydrological basins outside of the aquifer system proper that constitute the dominant source of indirect recharge by transmission losses from ephemeral streams. A coupled surface-groundwater model provided the direct and indirect recharge sources for the Stampriet groundwater model. The study has shown that at a basin scale of about 10.000 km² indirect recharge by transmission losses becomes the predominant recharge mechanism, establishing the importance of analysing this recharge source in large groundwater basins, especially in arid zone groundwater systems. The currently available data on hydrochemical and isotopic groundwater composition have been collected, combined with existing databases from previous projects on the Kalahari/Stampriet basin and re-assessed to derive geochemical baselines. Geochemical baselines have been established for the main aquifer units based on a geochemical groundwater classification. The geochemical analysis has been supported by sampling of trace element and isotopic geochemical indicators for the groundwater evolution in the aquifer system to delineate the development, establishment and stability of geochemical and redox-reaction zones. A re-analysis of residence time tracers has been being carried out to derive and evaluate flow paths and travel times in different aquifers. Based on these data an open source large scale compartment model has been developed to construct groundwater flow patterns based on residence time tracers and geochemical end members. The compartment model calculates the quantitative flow rates between aquifer units based on an a series of hypothetical a priori conceptual models. Closure of hydrological and geochemical mass balances and coherence with available residence time data (tritium, carbon-14) are used to validate the flow model. Results of the study indicate indirect recharge plays a larger role than previously assumed. The unconfined/confined transition zones control recharge and exchange mechanisms and geochemical zonation. The compartment model provides a quantitative assessment of recharge, flow and inter-aquifer exchange rates that is independent from previous numerical groundwater modeling and constitutes, in combination with residence time tracers and geochemical indicators, an additional source of information for the study of complex aquifer systems.