Heavy metal pollution is a critical issue affecting the safety of drinking water sources. However, the impact of human activities on heavy metal risk levels in water-carrying lakes remains unclear. This study aims to explore the risk mechanisms of heavy metals in Luoma Lake, an important water-carrying lake for the South-to-North Water Diversion Project. We explored the spatial and temporal differences in the distribution of heavy metals in Lake Luoma using methods such as the heavy metal pollution index (HPI) and assessed the risk variations using a health assessment model. The results indicated that heavy metal concentrations in water-carrying lakes generally decreased during the dry season, with Mn and Zn levels decreasing by 89.3% and 56.2%, respectively. The comprehensive score of HPI decreased by 13.16% following the retreating polder compared to the control area (Non-retreating polder area). Furthermore, the HPI at the drinking water intake was lower, which is closely associated with the elevated dissolved oxygen (DO) and oxidation–reduction potential (ORP) resulting from water diversion. The annual average health risk across the entire lake was not significant, with higher levels observed in the control area. The annual non-carcinogenic risk levels of Mn, Ni, Cu, Zn, and Pb range from 10−13 to 10−9, which are considered negligible risk levels. Notably, the carcinogenic risk posed by arsenic (As) through the drinking pathway reached 10−5 a−1, exceeding the maximum levels recommended by certain organizations. These findings provide a critical foundation for managing heavy metals in water-carrying drinking water sources.