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Although mercury (Hg) mining activities in the Wanshan area have ceased, mine wastes remain the primary source of Hg pollution in the local environment. To prevent and control Hg pollution, it is crucial to estimate the contribution of Hg contamination from mine wastes. This study aimed to investigate Hg pollution in the mine wastes, river water, air, and paddy fields around the Yanwuping Mine and to quantify the pollution sources using the Hg isotopes approach. The Hg contamination at the study site was still severe, and the total Hg concentrations in the mine wastes ranged from 1.60 to 358 mg/kg. The binary mixing model showed that, concerning the relative contributions of the mine wastes to the river water, dissolved Hg and particulate Hg were 48.6% and 90.5%, respectively. The mine wastes directly contributed 89.3% to the river water Hg contamination, which was the main Hg pollution source in the surface water. The ternary mixing model showed that the contribution was highest from the river water to paddy soil and that the mean contribution was 46.3%. In addition to mine wastes, paddy soil is also impacted by domestic sources, with a boundary of 5.5 km to the river source. This study demonstrated that Hg isotopes can be used as an effective tool for tracing environmental Hg contamination in typical Hg-polluted areas.