The chemical and physical properties of nitrogen and phosphorus as well as their concentrations in the overlying water, pore-water and sediments in Huainan segment of the Huaihe river were analyzed. The chemical forms of phosphorus in sediments were differentiated by a sequential fraction method. The results revealed that the NH4+-N content in pore-water of 6 surface sediments is obviously higher than that in overlying water, indicating that there is a dynamic tendency of releasing NH4+-N from sediment into overlying water. Chemical compound of nitrogen differs among segments of the river, while phosphorus has no such difference. Calcium bound phosphate (Ca-P) and iron bound phosphate (Fe-P) accounts for 60 % of the total phosphorus, and occluded-P (O-P) accounts for less than 20 %. Our findings indicate that 1) industrial waste water and domestic sewage have contributed to the excessive nutrient salts in Huaihe river, 2) decreased water flow during low water periods, and the interaction between sediments and overlying water disturbed by transport ships accelerate nutrient salt releasing into overlying water, which results in eutrophication of the river.