Geothermal springs are natural geological phenomena that occur throughout the world. South Africa is blessed with several springs of this nature. Limpopo province contains 31% of all geothermal springs in the country. The springs are classified according to the residing mountain: Soutpansberg, Waterberg and Drakensberg. This study focused on the geothermal springs within the Soutpansberg region; that is, Mphephu, Siloam, Sagole and Tshipise. The study was aimed at assessing the occurrence and potential health risk associated with drinking water from geothermal springs within Soutpansberg. Geothermal springs and boreholes were sampled for a period of 12 months (May 2017–May 2018) to accommodate two major seasons in the study areas. The physicochemical and trace metal compositions of the geothermal springs and boreholes (tepid and hot) were analyzed using ion chromatography (IC) (Dionex Model DX 500) and inductively coupled plasma-mass spectrometer (ICP-MS). Trace metal concentrations of the geothermal springs and boreholes were within permissible drinking water guidelines by the South African National Standards (SANS) and World Health Organisation (WHO), with exception of mercury (Hg), which is high in summer season. The bioaccumulation from regular consumption could, however, result in negative effects. Pearson’s correlation revealed that there is a direct relationship between temperature and pH, and some of the trace metals (V, Zn, Hg, Pb). This implies dissolution of minerals (rock-water interaction) under slightly high temperature. Multivariate statistics further elucidate the relationship and possible sources of the trace metals. Therefore, it can be inferred that the rock-water interaction is the main geochemical process governing the release of trace metals in groundwater. Hazard Index values for both children and adults were higher than 1, and this implies that the communities are at high risk of non-cancer health effects. Further, As, Cr and Cd were found to be the highest contributors to the potential cancer risk in the study areas, with children having a higher risk than adults. Therefore, there is a need for clinical/epidemiological study, and regular monitoring and control measures, to verify actual prevalence of cancer and protect human health, particularly the children, within the study areas.