The contamination of natural mineral bottled drinking water with trace, heavy metals and rare-earth elements is a growing concern globally, especially in regions with limited access to safe drinking water sources. In South Africa, the safety of bottled water remains a critical issue due to potential health risks associated with heavy metal exposure. This study aimed to evaluate physicochemical parameters alongside to assess the health risks due to heavy metals in natural mineral bottled drinking water available in South Africa, using inductively coupled plasma mass spectrometry analysis. A total of 21 bottled water samples from different brands were collected and analysed for heavy metal concentrations including Pb, Cd, As, Cr, Ni, Ba and Hg, as well as physicochemical parameters such as pH, conductivity, dissolved oxygen and total dissolved solids among others. The results revealed physicochemical parameters were within acceptable ranges, indicating overall water quality. Varying levels of heavy metals across different brands observed with concentrations of Al, Fe, Mg, Ca, K and Mn in some samples exceeding permissible limits set by WHO and SAWQG for drinking water quality. The mean concentration of the heavy metals is in the decreasing toxicity order of Sr > Al > Ba > Mn > Cu > Cr > Zn > Fe > As > Co > U > Ni > Cs > Pb > Cd > Hg. The mean values of the chronic daily intake (CDI) for the concentration of heavy metals for adults are in the order of Cr > Fe > Sr > Ba > Mn > Cu > Zn > Li > V > As > Ni > Be > Pb > Hg > Cd and were below acceptable limits. The estimated values of both HQ and HI (with mean of 2.07E−03 and range of 0.00 to 1.76E−02) for the heavy metals are all found to be less than 1. The total mean value of ILCR is 4.67E−06, and range of 0.00 to 2.76E−05, which is insignificant and within the permissible level of the cancer risk guidance limit of 1.00E−06 to 1.00E−04. The results show that consumption of natural mineral bottled drinking water of South Africa is safe and may not cause any significant health risk to the populace. However, the long-time potential effects due to the few exceeded metals levels needed to be considered. Our findings contribute to the ongoing discourse on water quality assurance, offering insights into the overall integrity of the natural mineral bottled water supply chain in South Africa. This research not only serves as a foundation for regulatory measures but also underscores the significance of maintaining high-quality standards in the bottled water industry for public health and environmental sustainability.