Based on monitoring data of water quality and river runoff from 2007 to 2008, the dynamics of TN and TP transported into the backwater region of the Linjiang River were investigated and fluxes of TN and TP were also estimated. It was shown that the dynamic changes of TN and TP were significant. The concentration of TP in rainy seasons was higher than that in dry seasons, while the cases for TN was contrary. The fluxes of TN and TP were significantly higher in rainy seasons than those in dry seasons. On average, there were about 4 142 t TN and 455 t TP transported into the backwater region of the Linjiang River every year. And TN flux decreased by 32.7% from 2007 to 2008, while TP flux increased by 34.3%, which was in agreement with the interannual variation of the concentrations of TN and TP. TN flux was primarily influenced by river runoff, whereas TP flux was affected by both concentration and runoff. Further analyses indicated that TN was mainly caused by point source pollutants(dominated by NH3N, and then DON). On the contrary, TP was mainly caused by plane source pollutants(dominated by PO34P). It was also indicated that it was critical to control the point source pollution in the basin to promote the water quality of the backwater region of the Linjiang River.