Plateau wetlands provide important wintering habitats for migratory waterbirds, making the assessment of environmental contamination relevant to their conservation. Characterizing potentially toxic elements in lake sediments provides a basis for identifying contamination patterns and prioritizing environmental monitoring in these habitats. Here, we assessed potentially toxic element contamination in surface sediments and potential ecological risks in three plateau lakes supporting wintering black-necked cranes (Grus nigricollis) in Shangri-La, Yunnan, China. In January 2025, 131 composite sediment samples (0–20 cm) were collected from Bitahai, Shudu, and Napahai lakes. Concentrations of Cu, Zn, Pb, As, Hg, and Cd were determined by inductively coupled plasma mass spectrometry. Contamination and potential ecological risks were evaluated using the geo-accumulation index (I_geo) and potential ecological risk index (PERI), respectively. Potential sources were investigated using EPA PMF 5.0. Sediments were generally unpolluted to slightly polluted. Mean PERI values were 65.2, 62.7, and 76.5, respectively, indicating low potential ecological risk, with Cd and Hg contributing most. PMF resolved four factors tentatively associated with traffic/domestic emissions, agricultural/combustion inputs, localized inputs, and natural/regional sources. These findings provide a baseline for sediment monitoring and environmental management of black-necked crane wintering habitats, with particular attention to Cd, Hg, and As.