Sediments serve as a crucial accumulation site for pollutants, and the source and sink effects of sediment pollutants significantly influence the overlying water. In this research, the concentrations of heavy metals in the sediments of Jinmucuo Lake were investigated. The pollution levels and ecological risks of the heavy metals were assessed via the geoaccumulation index and potential ecological risk index, and the potential sources were identified via multivariate statistical methods. Results revealed that the mean concentrations of cadmium, chromium, copper, zinc, nickel, arsenic and mercury exceeded the soil background values in Tibet, and each element generally tended to increase with decreasing depth in the sediment cores. Heavy metals were mainly distributed in the estuaries of the western part of the lake. Moreover, the geoaccumulation index revealed that mercury pollution was severe, followed by nickel and copper. The potential ecological risk index revealed that Jinmucuo Lake was a highly strong ecological risk and that mercury was the most important ecological risk factor. Multivariate statistical analysis indicated that chromium and nickel pollution was influenced by natural factors and anthropogenic activities, while geothermal activity, river inputs and atmospheric transmission were the main sources of mercury and arsenic. Moreover, cadmium, lead, copper and zinc pollution was mainly affected by transportation and high background values. The results provide an important reference for the ecological and environmental protection of Jinmucuo Lake.