Abstract: Abnormally high arsenic concentrations in the water bodies of the Bangong Lake Basin, located on the northwestern Qinghai-Tibet Plateau, may pose significant health risks. This study aims to characterize the arsenic content and identify the factors influencing its distribution across various water bodies within the Bangong Lake Basin, thereby providing a scientific basis for drinking water safety assessment in this region. A total of 56 representative water bodies, including rivers, lakes, groundwater in lake shore zones, and springs, were systematically sampled across the Bangong Lake Basin. Arsenic concentrations and major hydrochemical parameters were analyzed using multivariate statistics, Piper diagrams, Gibbs plots, correlation analysis, and hydrogen-oxygen isotope analysis. The results indicate pronounced differences in arsenic concentrations among different water body types. Groundwater arsenic levels ranged from 1.0 to 8.4 μg/L, with an average of 3.1 μg/L; river water ranged from 2.2 to 11.0 μg/L, averaging 5.0 μg/L; and lake water ranged from 4.5 to 91,700.0 μg/L, with an average of 4,159.4 μg/L. There is considerable spatial variation in arsenic content in groundwater and river water. Elevated arsenic levels are associated with weak hydrodynamic conditions and intense evaporation, which also account for the extremely high arsenic concentrations observed in western Bangong Lake and other lakes. Additionally, arsenic content in lake water is strongly correlated with the replenishing river water. High-arsenic water predominantly belong to the Cl–Na and Cl–Na•Mg hyodrochemical types. Arsenic concentrations show a significant positive correlation with salinity indicators such as Cl^–, Na⁺, and K⁺, indicating that these waters have undergone intense evaporation. The hydrogen and oxygen isotope regression line for the water samples is δ²H = 4.79δ¹⁸O − 36.36. Compared to the local atmospheric precipitation line in Ali Prefecture, the lower slope and more negative intercept indicate strong evaporation effects, confirming that weak hydrodynamic evaporation or evaporation-driven karst decomposition significantly influences arsenic enrichment in these water bodies.