<p>This study investigated heavy metal pollution in water bodies of metal mining areas in the Han River Basin (Shaanxi section), a critical water source for China’s South-to-North Water Diversion Project. Water samples were collected from mining-affected areas, transition zones, and the main stem. Pollution levels, ecological risks, and health risks were assessed using the Nemerow Comprehensive Pollution Index, Potential Ecological Risk Index, and Health Risk Assessment models. The most severe pollution was found in mining-affected waters, where average Fe and Mn concentrations exceeded China’s Class III standard by 4.8 and 3.5 times, respectively, and the maximum Cd concentration exceeded the standard by 2.9 times. The Nemerow index indicated moderate to severe pollution in mining areas (P_N up to 4.21), transitioning to no pollution in the mainstream (P_N &lt; 0.7). Cd and Tl were identified as the primary ecological risk factors, with potential ecological risk indices (E_i) reaching 128.32 and 44.0, respectively. The health risks associated with drinking water ingestion were significantly higher than those from dermal contact, with Cd-induced carcinogenic risks for children as high as 5.12 × 10⁻⁵ a⁻¹, far exceeding the acceptable level (1 × 10⁻⁶ a⁻¹). Children were particularly vulnerable to elevated risks. Correlation and PCA analyses indicated that Cd, Pb, Fe, Mn, Be, and Ni originated mainly from mining activities, while Sb and Tl were influenced by both geological background and industrial sources. This study provides a foundation for targeted pollution control in high-risk areas.</p>