Eutrophication has become a severe environmental problem in some tributaries of the Three Gorges Reservoir (TGR) in China. A two-year field investigation of nutrients, oxygen stable isotopes (δ¹⁸O), and hydrogen stable isotopes (δD) was performed from January 2010 to December 2011 to determine the sources of nutrients in Xiangxi Bay (XXB). The results showed that nitrogen, phosphorus and silicon varied seasonally depending on hydrodynamic changes. The bottom-layer intrusive density current decreased nitrogen and silicon concentrations and increase phosphorus concentrations in XXB, while the middle-layer intrusive density current increased nitrogen and silicon concentrations and decrease phosphorus concentrations. The differences in δ¹⁸O and δD among the Yangtze River (YR), XXB and the region upstream of XXB were significant, and according to the tracer method, the estimated contribution ratios of nitrogen, phosphorus and silicon from the YR to XXB were much larger than those from the region upstream of XXB. These findings suggest that water quality in the TGR can be improved by reducing the pollution load throughout the upstream basin of the YR but not through decentralized efforts in only one or two tributary basins.