In 2009, 78 locations were sampled in the catchment areas of the ephemeral Swakop River and the tributary Khan River within the framework of a strategic environmental assessment (SEA) prior to new uranium mining activities. Samples were analysed for main components, dissolved uranium, and trace elements. Alluvial groundwater in the upper Khan and Swakop River catchments is freshwater of drinking water quality, whereas groundwater in the lower river catchment is saline. Nitrate concentrations are elevated yet below the WHO guideline value apart from a few exceptions. Potentially toxic trace element concentrations are without critical implications for drinking water quality. Drinking water samples from the municipalities of Swakopmund and Walvis Bay meet the requirements of the Namibian and the WHO drinking water standards. Process and seepage water samples from uranium mines have elevated concentrations of uranium, arsenic and fluoride, manganese and a number of other trace elements like lithium, nickel and cobalt. Uranium is a common trace element in the groundwater of the catchment and mostly present at elevated concentrations. Only 21 % of analysed groundwater samples have uranium concentrations below the provisional WHO guideline value of 15 µg/L. Six groundwater samples in the vicinity of the Rössing and Langer Heinrich Uranium Mines and the lower Swakop River Valley have uranium concentrations above the regional background level. The chemical composition of water samples alone is insufficient and inconclusive to identify the source for the high uranium level in the respective groundwater samples. Keywords: ephemeral river, geogenic background, groundwater, mine discharge, Namibia, uranium.