Identification of nitrate sources and its transformations are important for the management of large lakes and reservoirs. The Three Gorges Reservoir (TGR) in China is one of the largest reservoirs around the world. In this study, stable isotopes of nitrogen (δ15N-NO3-) and oxygen (δ18O-NO3-) of nitrate in water were used to gain insights into nitrate sources and transformations in the tail area of the TGR. Bayesian mixing model has been conducted to estimate the proportional contribute of nitrate sources. The mixing modelling results indicated that NH4+ fertilizer (range 7-54%) and soil organic nitrogen (range 2-45%) were the dominant NO3--N sources in the tail area of the TGR during the three season study period. Nitrification contributed a part of NO3--N in the river water during the dry season. The nitrate from soil solution in the riparian zone with denitrified NO3- might be another major reason for the enrichment of δ15N-NO3- and δ18O-NO3- during the normal season. Reducing the use of chemical nitrogen fertilizers, especially NH4+ fertilizers, and protecting soil from erosion may be effective measures to improve water quality in the TGR.