To investigate the presence of metal elements and assess their health risk for the populace in the Nandong Underground River Basin (NURB), we conducted an analysis of eleven common heavy metals in the water body. A Health risk assessment (HRA) model was employed to analyze 84 water samples from the NURB. The detection results revealed the following order of heavy metals concentrations: Fe > Al > Mn > Zn > As > Cd > Pb > Cr > Ni > Cu > Hg. Correlation analysis indicated a certain similarity in material source and migration transformation among these eleven metal elements. Our study identified that the health risks for local residents exposed to metal elements in the water of NURB primarily stem from carcinogenic risk (10⁻⁶–10⁻⁴ a⁻¹) through the drinking water pathway. Moreover, the health risk of heavy metal exposure for children through drinking water was notably higher than for adults. The maximum health risks of Cr in both underground and surface water exceeded the recommendation standard (5.0×10⁻⁵ a⁻¹) from ICRP, surpassing the values recommended by the Swedish Environmental Protection Agency, the Dutch Ministry of Construction and Environment and the British Royal Society (5.0×10⁻⁶ a⁻¹). The results of the health risk assessment indicate that Cr in the water of NURB is the primary source of carcinogenic risk for local residents, followed by Cd and As. Consequently, it is imperative to control these three carcinogenic metals when the water was used as drinking water resource.