Background Site-vegetation relations of Vachellia erioloba, Faidherbia albida, Euclea pseudebenus and Tamarix usneoides in two contrasting locations in the Namib Desert (Namibia) were evaluated with the goal to relate soil water availability to the occurrence of trees under hyper-arid conditions. Methods Plant water potentials were measured using a pressure chamber in the field. Pre-dawn water potentials were assessed to reflect the soil water potential of the rhizosphere. Midday water potentials were measured to assess the strongest negative water potential applied by the sample trees. Results Pre-dawn water potentials and midday water potentials indicated access to soil water in the rhizosphere and by this, provide an explanation for an occurrence of V. erioloba within the extreme environmental conditions of sand dunes in the Namib Desert. Diurnal ranges seem to reflect more and less suitable stands, in terms of soil water availability, within the sampling sites. While the impact of the ephemeral Kuiseb river on soil water availability was assessed through the four species’ plant-internal water relations, comparable pre-dawn water potentials of V. erioloba at both sites indicate soil water availability also in the dunes of Namibrand. The extreme midday water potentials of the dune plants possibly show the upper limit of tolerance for V. erioloba. Conclusions The preliminary data provide an explanation of the occurrence and distribution of the investigated species in beds of ephemeral rivers and on dunes under the hyper-arid climatic conditions of the Namib Desert and qualify suitability within the assessed sites. Understanding the plant-physiological processes and assessing the plant-internal water potential provides a valuable tool to evaluate soil water availability within the rhizosphere and to describe an adaptation potential of investigated species. The comparability of pre-dawn water potentials at both sites indicates unexpected soil water availability within lower parts of the dunes of Namibrand. Further research needs are derived concerning the origin and distribution of such soil water. These species in these specific tree-environments are understudied and little published, thus the results support an improved understanding of the ecology in arid environments. Keywords: Water potential, Arid land, Soil water availability, Namibia, V. erioloba.