Since 1973, Kunene River water has been carried from the Calueque reservoir in Angola along a 160 km open concrete canal to the town of Oshakati in the central part of the Cuvelai-Etosha Basin and has been supplying drinking water to the most densely populated rural area of Namibia. Despite its importance for the region, intra-seasonal water quality and the technical condition of the canal are not routinely checked. Water samples were collected during four field campaigns right before the onset of the rainy season (November 2013 and 2014), and after the rainy season (June 2014 and May 2015), at 16 sites along the canal for stable water isotopes (deuterium, oxygen-17 and oxygen-18) and hydrochemical analyses. The isotope patterns and chemical composition of the canal water is discussed in comparison to local rain, Kunene source water, surface water and groundwater. Clear isotope enrichment indicates evaporative loss of water. A Craig–Gordon model was used to estimate water loss. The loss increases with distance from the source with a maximum of up to 10 %, depending on the season. The results are discussed in context of water availability, vulnerability and water resources management in this water-scarce area.