Semiarid regions are often affected by water scarcity and poor water quality. Seasonal changes in precipitation and drought events increase the pressure of use on water bodies and their pollution. In Central Northern Namibia, a high seasonal intra- and inter-annual variability of precipitation caused a 5-year lasting drought period. In the semiarid region, ephemeral channels and water pans represent the main water source, besides the institutionalized water supply. No systematic analysis of its quality has been conducted so far. The states of the surface waters at the end of the dry season in 2017 and the end of the rainy seasons in 2018 and 2019 were characterized by the analysis of physical–chemical parameters, focusing on usability. The first results show coarse contamination of the waters, which results in high turbidity values. Salt concentrations, such as Ca2+and Na+, greatly increased due to evaporation. Al is present in high concentrations in solid and liquid phases, which indicates direct anthropogenic pollution. Spatial differences are evident in the study area and based on the precipitation gradient, land use, and population density. The waters cannot be used as drinking water without prior treatment.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10661-023-11505-1.