Tibetan Plateau lakes have high ecological value and play a crucial role in maintaining ecological balance. This research aimed to study the pollution characteristics, ecological risk, and potential sources of eight heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) in the surface sediments of 12 Tibetan Plateau lakes. The results of the toxicity risk index (TRI) showed that only Gongzhu Tso (28.09) and La’ ang Tso (20.25) had heavy metals that could pose a very high risk of toxicity to aquatic organisms. Hg posed the highest potential ecological risk to aquatic organisms. Based on the results of multiple analyses, we inferred that the contents of Cr, Cu, Hg, and Ni in sediments of Tibetan lakes were influenced by industrial and agricultural development; Cd, Pb, and Zn were influenced by transport and atmospheric transport; and As was derived from geothermal activity and rock weathering.