Many xenobiotic compounds can threaten human health and natural ecosystems. The ability to predict the level of human activities and identify major impact factors is crucial for the design of pollutant risk-reduction plans. In this study, a total of 25 volatile organic compounds (VOCs) including eight alkenes, six alkanes, and eleven aromatics were identified at 11 monitoring locations along the Huangshui River of the Tibetan Plateau. GC-MS analysis was applied to detect the concentrations of the VOCs. The results showed that the alkene, alkane, and aromatic concentrations in the sediment were significantly higher than in the water in all seasons (p < 0.001). The VOC concentrations in summer were significantly higher than in spring and winter (p < 0.01). In addition, several VOCs were found to surpass the national standard, i.e., bromoform reached 312.43 μg/L in water during the summer (the national standard is 100 μg/L), carbon tetrachloride was 209.58 μg/L (the national standard is 2 μg/L), and vinyl chloride was 10.99 μg/L (the national standard is 5 μg/L), which were all related to human activities. Principal component analysis (PCA) was used to comprehensively evaluate the water quality and the VOCs. The total organic carbon (TOC) was found to be responsible for the presence of the VOCs in the river, accounting for 77.93%, 81.97%, and 82.13% of the total variance in the datasets in spring, summer, and winter, respectively.