Nitrogen and phosphorus contents are analyzed in the overlying waters and pore waters taken from the Changjiang Estuary and Shanghai coastal tidal flats in this study. In addition, the diffusion fluxes of nitrogen and phosphorus across the sediment-water interface in tidal flats are estimated according to the nutrient concentration gradients at the interface. It has been indicated that the concentrations of ammonium, nitrite, nitrate and dissolved phosphorus in overlying waters range from 0.0082~2.56, 0.03~0.58, 0.69~5.38 and 0.035~0.53 mg/L, respectively, while 0.0025 ~ 1.35 mg/L for NH4+-N, 0. 0055 ~ 0.20mg/L for NO2--N, 0.61~1.14 mg/L for NO3--N and 0.11~0.53mg/L for DP insurface pore waters.The findings have revealed that ammonium, nitrite, nitrate and dissolved phosphorus diffusion fluxes across the sediment-water interface are between -0.024~0.99, -0.39~ -0.0019, -3.09~the source of phosphorus and an important sink for nitrogen in the waters.