Due to environmental sensibility and fragility, the water chemistry revolution and heavy metals accumulation influenced by natural and anthropogenic processes in the rivers on the Tibetan Plateau have recently become a global concern. However, targeted studies in small watersheds on the Tibetan Plateau are relatively limited. A study of surface waters in Duilong Qu (DLQ), a small watershed located on the Tibetan Plateau, have been conducted to assess the impact of natural and anthropogenic activities on the water environment of the DLQ by analyzing the major ions and heavy metals (Cd, Cr, Mn, Fe, Ni, Cu, Zn, Pb, and As) in the river waters. The results of the analysis of major ions showed that and were the dominant anions and Ca2+ was the dominant cation, indicating that the water chemistry of the river waters was mainly of the HCO3-Ca type. The results of Piper diagram and Gibbs diagram analysis indicate that the water solute is mainly controlled by the weathering of carbonate rocks, followed by the influence of geothermal water confluence. Compared to the world river average, the concentrations of Cr, Pb, and As in the studied rivers were relatively high. The heavy metal concentrations satisfy the standards of WHO and GB (Chinese national standard) guidelines. The PCA-APCS-MLR model has been employed and evidenced as a reliable tool to identify the sources of the heavy metals in this study. The results revealed that the heavy metals in the DLQ are caused by natural sources, geothermal water, and mining operations. The primary sources of As (93.63%), Cr (93.07%), Mn (73.53%), Fe (59.54%), and Pb (58.28%) in the DLQ were geothermal water, while Zn (91.41%), Mn (20.67%), Fe (40.46%), and Pb (26.15%) originated mainly from natural sources. Additionally, Cu (91.41%) was primarily influenced by mining operations, and Ni originated from mining (53.61%) and geothermal water sources (46.39%), while Cd (97.88%) originated from unknown sources. In the high-flow season periods from 1992 to 2017, the As concentrations in the DLQ decreased significantly, which might result from increasing precipitation and runoff. Overall, the results of this study suggest that both natural and anthropogenic activities have jointly affected the solutes in small rivers on the Tibetan Plateau, and heavy metal pollution should be emphasized in the future.