Danjiangkou Reservoir has been widely concerned as the water source of the world’s longest cross basin water transfer project. Biogenic elements are the foundation of material circulation and key factors affecting water quality. However, there is no comprehensive study on the biogenic elements in tributaries of Danjiangkou Reservoir, hindering a detailed understanding of geochemical cycling characteristics of biogenic elements in this region. Guanshan River, one of the main tributaries that directly enter the Danjiangkou Reservoir, was token as the research object. Spatiotemporal distribution characteristics of basic water quality parameters and biogenic elements were studied. Water quality was comprehensively evaluated through water quality index (WQI). Absolute principal component score-multiple linear regression (APCS-MLR) model was adopted to explore the main sources of biogenic elements. Results showed that, in terms of season, the concentrations of TN, TP, and DOC were significantly higher in wet season than in dry season, while no significant differences were found for DIC and DSi. Spatially, the concentrations of DC, DIC, TN and TP in the middle and lower reaches were higher than that in the upstream. DOC concentration peaked in the middle reaches, while DSi showed higher concentrations in the upstream. WQI values indicated that the river water quality was between good and excellent, although the water quality in wet season was slightly worse than that in the dry season. PCA extracted five potential sources, which accounting for 84.12% of the total variance, including rock weathering, mixed source of sewage discharge and agricultural non-point source pollution, dissolved soil CO2, seasonal factor and agricultural non-point source pollution. These sources contributed 38.96%, 12.33%, 13.54%, 23.95% and 11.21% to river water quality parameters, respectively. Strengthening the monitoring of biogenic elements, controlling pollutant discharge and exploring the relationship between biogenic elements and other pollutants are important for the water environment management in this basin.