Abstract: Rapid urbanization, industrial expansion and population growth pose potential threats to the fragile aquatic ecosystems in the oasis areas in Xinjiang. As a typical emerging pollutant, in-depth research on the environmental behavior of per- and polyfluoroalkyl substances (PFASs) was significant for understanding their potential impact on ecosystem stability and ecological balance. This study focused on the Sangong River and Qira River basins in Xinjiang, employing high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to quantify the concentrations of PFASs in surface water. The sources were identified and quantified using a principal component analysis-multiple linear regression (PCA-MLR) model, and the ecological risks were characterized using the risk quotient (RQ). The results showed: (1) In July-August 2019, The total concentration of PFASs ranged from 0.9 to 17.8 and 0.8 to 16.2 ng/L in the surface water of the Sangong River and the Qira River. (2) Short-chain perfluoroalkyl carboxylic acids were the primary pollutants, with perfluorobutanoic acid (PFBA) accounting for 59.4% to 65.0% of the total PFASs. (3) The multiple receptor models identified that domestic sources (47%), atmospheric transport and wet deposition, as well as pesticide use (41%), and precursor degradation (12%) were three major sources of PFASs in the Sangong River. For the Qira River, the main sources of PFASs were textile treatment and pesticide use. (4) The RQ values of PFASs in the Sangong River and Qira River were well below 0.1, indicating that the ecological risks of PFASs were relatively low. The results showed that the overall pollution level of PFASs in the Sangong River and Qira River basins was relatively low, and the resulting ecological risks were negligible.