Recent advances in analytical techniques have allowed hydro-geochemical databases to form an essential component of animal and human epidemiological studies. Geographically localised communities and livestock production systems have a higher incidence of risk factors, and therefore baseline concentrations of key health elements are required to assess the quality of the water. Risk assessments conducted for drinking water for indigenous goats in rural communal livestock production systems for three separate communities found several trace elements (As, Br, Cd, F, Pb, Hg, Mo and Se) occurring as localised anomalies in the aquatic environment at concentrations exceeding local and international guidelines (at times by several orders of magnitude). The watering points assessed are capable of contributing significantly to the mineral requirements of the indigenous goats thus exposed. Potential hazards were identified that impact on the norms of health, palatability and product quality for human consumption. Hydro-geochemical correlations were noted that increase both the risk associated with exposure and the likelihood of incomplete diagnosis of mineral related disorders. Recommendations are also made with regard to a programme monitoring water quality and the need to include water chemistry when formulating rations, mineral supplements and diagnosing disorders or diseases across different production environments.