In this paper, a modelling approach is presented which is able to analyze a water-supply regime in order to comprehend health-related aspects in water resources management. The area of investigation is the Cuvelai-Etosha Basin in central northern Namibia. Major health hazards for the rural and peri-urban population stem from the usage of unsafe water sources. In the systems analysis, the variable Health turned out to be one of the major sustainability indicators. Furthermore, the identification of cause–effect chains revealed that education is a key factor in improving users’ health situation, whereas poverty significantly degrades it.