Abstract: The abnormal arsenic content 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. These findings are crucial for ensuring the safety of drinking water for local residents. Samples were systematically collected and analyzed from 56 major water bodies within the basin, including rivers, lakes, groundwater in lake shore zones, and springs. Analytical methods employed included multivariate statistics, Piper diagrams, Gibbs plots, correlation analysis, and hydrogen-oxygen isotope analysis. The results reveal substantial variation in arsenic concentrations among different water body types. (1) 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. 1. There is considerable spatial variation in arsenic content in groundwater and river water. Elevated arsenic levels are associated with slow hydrodynamic conditions in certain river sections and intense evaporation environments. These factors also contribute to the high arsenic concentrations observed in Bangong Lake on the western side and other lakes. Additionally, arsenic content in lake water is strongly correlated with the replenishing river water. (2). High-arsenic waters predominantly belong to the Cl–Na and Cl–Na·Mg chemical 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 and concentration. (3) The hydrogen and oxygen isotope regression line for the water bodies is δ²H = 4.79δ¹⁸O − 36.36. Compared to the local atmospheric precipitation line in Ali Prefecture, this line has a smaller slope and a slightly negative intercept, confirming that weak hydrodynamic evaporation or evaporation-driven karst decomposition significantly influences arsenic enrichment in these water bodies.