Water and sediment samples were collected from Caohai basin. The distribution of nitrogen and phosphorus concentrations in water and the release characteristics of nitrogen and phosphorus from the sediment were analyzed. The results showed that total nitrogen and total phosphorus concentrations of most inflow river water were higher than those of outflow river water during wet and dry seasons. Affected by the exotic input, total nitrogen and total phosphorus concentrations of the waters in emerged plants zone were higher than that of submerged plants zone, which were decreasing along the water flow direction. In wet season, the concentrations of total nitrogen and total phosphorus in sediment interface water were higher than those of surface water, while such a pattern was not obvious in dry season. The release flux of total nitrogen from sediment was between 5.244 and 362.506 mg·m^-2·d^-1, which was considered as “source” of total nitrogen. The release flux of total phosphorus from sediment ranged from -3.081 to 3.009 mg·m^-2·d^-1, which was considered as “sink” in emergent plants zone and “source” in submerged plants zone, indicating that endogenous release is an unneglectable source of nitrogen and phosphorus in Caohai waters.