Water samples of precipitation and different surface waters were collected between 2016 and 2021 in southern Africa using narrow-neck bottles of 300 ml volume. The bottles were stored in a refrigerator until measurements. The stable isotope ratios of oxygen (18O/16O) and hydrogen (2H/1H) of the water samples were measured using a PICARRO L1102-i isotope analyzer (WS-CRDS). Calibration of the measurements was done with VSMOW, SLAP and GISP standards from the IAEA. A total of six replicate injections were performed for each sample and mean and standard deviations (1 sigma) were calculated, resulting in a reproducibility of the replicate measurements of generally better than 0.1 ‰ for oxygen and 0.5 ‰ for hydrogen. The aim of this data collection is to fill a gap in southern Africa, where isotopic data on precipitation and surface waters do not have sufficient spatial coverage and are mainly sampled before 2013. Regional studies of meteorology, hydrology, environmental geochemistry and paleoclimate may benefit from this dataset.