The most important water resource in drylands such as Namibia is groundwater and its recharge including temporal and spatial variations need to be assessed reliably for sustainable water management. In this paper, a grid-based conceptual water balance model with a simplification at the catchment scale level is used to assess groundwater recharge. The reliability of the model predictions are verified by the independent chloride mass balance method. The distributed, process-oriented, physically based water balance model MODBIL used in this study considers the major water balance components and calculates a spatially differentiated water balance by simulating water fluxes and storages at temporal and spatial resolutions based on meteorological, topographic, soil physical, land cover and geological input parameters. In this study it is set up for the upper Khaudum and Nhoma catchments in the Kalahari of north-eastern Namibia and northwestern Botswana at a spatial resolution of 500 x 500 m, calculated daily for a period of 22 years. A mean annual area groundwater recharge of 11.5 mm a−1 is calculated for the catchments, but spatial variations between 0 and 17.5 mm a−1 occur depending on the variability of vegetation, soil and geomorphology. Groundwater recharge only occurred on a few days during the simulation period. Keywords: Soil water balance model, Namibia, Groundwater recharge, Kalahari, Chloride Mass Balance.