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The stable water isotope deuterium (H-2) was applied as an artificial tracer ((H2O)-H-2) in order to estimate groundwater recharge through the unsaturated zone and describe soil water movement in a semi-arid region of northern central Namibia. A particular focus of this study was to assess the spatiotemporal persistence of the tracer when applied in the field on a small scale under extreme climatic conditions and to propose a method to obtain estimates of recharge in data-scarce regions. At two natural sites that differ in vegetation cover, soil and geology, 500ml of a 70% (H2O)-H-2 solution was irrigated onto water saturated plots. The displacement of the H-2 peak was analyzed 1 and 10 days after an artificial rain event of 20 mm as well as after the rainy season. Results show that it is possible to apply the peak displacement method for the estimation of groundwater recharge rates in semi-arid environments via deuterium labelling. Potential recharge for the rainy season 2013/2014 was calculated as 45 mm a(-1) at 5.6 m depth and 40 mm a(-1) at 0.9 m depth at the two studied sites, respectively. Under saturated conditions, the artificial rain events moved 2.1 and 0.5 m downwards, respectively. The tracer at the deep sand site (site 1) was found after the rainy season at 5.6 m depth, corresponding to a displacement of 3.2 m. This equals in an average travel velocity of 2.8 cm d(-1) during the rainy season at the first site. At the second location, the tracer peak was discovered at 0.9 m depth; displacement was found to be only 0.4 m equalling an average movement of 0.2 cm d(-1) through the unsaturated zone due to an underlying calcrete formation. Tracer recovery after one rainy season was found to be as low as 3.6% at site 1 and 1.9% at site 2. With an in situ measuring technique, a three-dimensional distribution of H-2 after the rainy season could be measured and visualized. This study comprises the first application of the peak displacement method using a deuterium labelling technique for the estimation of groundwater recharge in semi-arid regions. Deuterium proved to be a suitable tracer for studies within the soil-vegetation-atmosphere interface. The results of this study are relevant for the design of labelling experiments in the unsaturated zone of dry areas using (H2O)-H-2 as a tracer and obtaining estimations of groundwater recharge on a local scale. The presented methodology is particularly beneficial in data-scarce environments, where recharge pathways and mechanisms are poorly understood.