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The identification of potential recharge areas and estimation of recharge rates to the confined semi-fossil Ohangwena II Aquifer (KOH-2) is crucial for its future sustainable use. The KOH-2 is located within the endorheic transboundary Cuvelai-Etosha-Basin (CEB), shared by Angola and Namibia. The main objective was the development of a strategy to tackle the problem of data scarcity, which is a well-known problem in semi-arid regions. In a first step, conceptual geological cross sections were created to illustrate the possible geological setting of the system. Furthermore, groundwater travel times were estimated by simple hydraulic calculations. A two-dimensional numerical groundwater model was set up to analyze flow patterns and potential recharge zones. The model was optimized against local observations of hydraulic heads and groundwater age. The sensitivity of the model against different boundary conditions and internal structures was tested. Parameter uncertainty and recharge rates were estimated. Results indicate that groundwater recharge to the KOH-2 mainly occurs from the Angolan Highlands in the northeastern part of the CEB. The sensitivity of the groundwater model to different internal structures is relatively small in comparison to changing boundary conditions in the form of influent or effluent streams. Uncertainty analysis underlined previous results, indicating groundwater recharge originating from the Angolan Highlands. The estimated recharge rates are less than 1% of mean yearly precipitation, which are reasonable for semi-arid regions.