Short of affordable and clean potable water poses high risk to health of human beings globally. Water scarcity is a challenge that affects all countries across the globe and this is more prominently felt in rural communities of poorer countries. In recent years, South Africa has faced severe droughts limiting portable water supply to rural areas of the country. Developing an alternate water security strategy for rural communities in South Africa can assist local government to manage water systems successfully. This paper illustrates the process of building a water supply strategy using the case of water management in Limpopo and Mpumalanga provinces of South Africa. These provinces experience a high challenge of water supply and access due to lack of water services, and challenge of building stakeholder support for resource management strategies. A number of rural communities were visited, water samples collected from boreholes, rivers, dams and taps around the two provinces. From chemical and other test, we established the quantity and quality of water sources around the two provinces. System dynamics and system analysis approach are used in this paper to model the existing water resource management and map out its frailties and limitations. A model to connect a system of boreholes and nearby water sources was then developed. The results, it is observed that the reliability and improvement of water system for rural areas was achieved through these approaches. The results show enhanced abstraction of water from sources within the communities that can secure water in these rural communities.