Acid mine drainage (AMD), characterized by its acidity and high content of heavy metals, is a significant global environmental problem that harms human health through its impact on rivers. Therefore, this study aims to identify heavy metals in both surface and underground AMD-polluted karst rivers, focusing on the Zhijin River area which is severely affected by AMD, and assess their health risks to residents. Through the collection of 30 surface water samples and 16 groundwater samples from both wet and dry seasons, the study examines the concentration, sources of pollution, and health implications of six heavy metals (Fe, Mn, Cr, Cd, As, and Hg). The results showed that Fe and Mn levels in surface water were highly polluted during both seasons, especially during the wet season, with Fe levels reaching 20.0 mg/L and Mn levels reaching 1.9 mg/L. Further correlation and principal component analyses revealed that mining activities are the primary contributors to the contamination in this region. Health risk assessments and Monte Carlo simulation, including both deterministic and probabilistic, showed that the noncarcinogenic health risk indices for surface water and groundwater were within acceptable limits for both seasons. However, groundwater poses a higher carcinogenic risk to children, with As levels during the wet season and Cr levels during the dry season warranting close monitoring. Factors such as body weight and intake rate played a crucial role in health risk evaluations. This study underscores the need for further attention to groundwater risk, temporal heterogeneity in the Zhijin River.