Based on the hydrological and water quality data in the main monitoring sections of Dongting Lake from 2013 to 2017, influxes of TN and TP from the four upstream branches (Xiang River, Zi River, Yuan River and Li River) and three water inlets (Songzi, Taiping and Ouchi) of Dongting Lake, as well as the outflux of Chenglingji outlet were estimated to analyze the spatio-temporal characteristics and retention effect of the two pollutants. The results show that the annual nitrogen and phosphorus fluxes into Dongting Lake showed an overall increasing trend during 2013-2016; but in 2017, influenced by the synchronous change of water quality and water quantity, the nitrogen and phosphorus influxes decreased by 19.93% and 23.14%, respectively, compared with 2016. Controlled by seasonal variation of water quantity, the nitrogen and phosphorus influxes distributed unevenly in the year, with more than 70% from April to September. In terms of spatial distribution, the nitrogen and phosphorus influxes mainly came from the four upstream branches, accounting for 78.48% and 71.77%, with the greatest contribution from the Xiang and Yuan Rivers. The four upstream branches were affected by the comprehensive effect of point and non-point source pollution whereas the three water inlets were mainly influenced by non-point source pollution. Apart from these, pollutant retention rate of these two pollutants in Dongting Lake were low, so the concentration of phycophyta was not high, but the nitrogen and phosphorus concentrations in the lake (1.73 and 0.075 mg/L ) were still much higher than the critical value of algae outbreak (0.2, 0.02 mg/L). In order to reduce the risk of water bloom, it is vital to maintain the connectivity of the lake, pay attention to the risks of TP in the three water inlets and the control of pollutants around the lake.