Based on overlying water and sediment samples collection from fifteen sites during July, September, November 2018 and January 2019 in hydro-fluctuation belt of Danjiangkou reservoir China – the variation of nitrogen (N) was studied. And the concentrations of NH4+-N, NO3−-N and NO2−-N in the sediment, pore water and overlying water were determined to evaluate the diffusion flux across the water-sediment interface. The results showed that the lowest sediment N concentrations was 36.54 mg/L in July, and the highest one was 145.93 mg/L in November. Spatially, the sediment N concentrations were higher in tidal soil and loam than sandy soil. According to diffusion fluxes of NH4+, NO3− and NO2−, sediments at all sites tend to release N to the overlying water except sampling month of November, where sediment act as a sink of NO3−. The highest release rates of NH4+-N and NO3−-N were 17.66 mg m−2·d−1 and 80.15 mg m−2·d−1, respectively, which is much higher than the release rate of NO2−-N (0.29 mg m−2·d−1). The findings indicate that hydro-fluctuation belt sediment contributes a lot to the nitrogen contents in the overlying water, and internal pollution is a main reason for the water quality deteriorate even eutrophication.