In arid and semi-arid regions the population, livestock, vegetation and wildlife are highly dependent on the water resources of ephemeral streams. In order to assure effective and sustainable water management in these heavily-used and sensitive environments, thorough investigations of the hydrological system are required. In case of the Swakop River in Namibia, water for human consumption is stored in two surface dams, built in the 1970s, and abstracted from boreholes in the alluvial aquifer. This study aims at identifying the impacts of the construction of the Swakoppoort and Von Bach Dam on the downstream groundwater quantity and quality of the alluvial aquifer.