The West Coast New Area is a typical city in China where water supply is predominantly sourced from reservoirs. Heavy metal pollution in these reservoirs directly impacts the safety of drinking water and human health. Therefore, this study comprehensively evaluated the status of heavy metal pollution in the water environment and sediment of the main water supply reservoir in the study area, revealing the interaction relationship and pollution sources, as well as assessing the probabilistic health risks to human beings. The results show that there are different degrees of pollution in the main water supply reservoirs in the study area, and the pollution increases with the increase of water depth. The heavy metal pollution index was up to 2681, indicating heavily pollution. The main polluting elements were Mn and Fe, and the maximum contents were 4.11 mg L−1 and 0.68 mg L−1, respectively, which far exceeded the Class III standard limit of drinking water in China. The main source of pollution is human activities, and Mn release from sediment aggravates deep water pollution. The non-carcinogenic risk index of heavy metals in the reservoir, ranging from 4% to 14%, is higher than 1, indicating a potential non-carcinogenic threat. Furthermore, heavy metals have a much greater impact on children compared to adults, among which Mn is the main contributor to human non-carcinogenic risk, contributing more than 60%. Therefore, controlling the content of Mn and Fe can effectively reduce the heavy metal pollution of reservoir and human health risk. The research results are of great significance for the utilization of reservoir water resources and the protection of the ecological environment in the study area.