In order to find out the difference in absorbability of different aquatic plants on nitrogen (N) and phosphorus (P) existing in surface water, and even to explore its mechanism, the simulated ditch experiment and pot experiment were conducted using 8 different aquatic plants. And the plants with great difference on absorbing N and P were selected to make further exploration on root physiological characteristics and microbiological changes of sediment. The results showed that the concentrations of N and P in ditch water decreased significantly after planting aquatic plants, among 8 aquatic plants, the greater biomass was observed in Pontederia cordata, watermifoil, Sorbaria sorbifolia, Zizania and thalia dealbata, which could absorb more nutrients, resulting in consequently, the decreased nutrients in ditch water. Compared with the treatment of no aquatic plants, nutrient residual in ditch water decreased significantly, total N decreased by 22.4%~44.0%, ammonium nitrate decreased by 24.5%~36.8%, nitrate decreased by 13.6%~51.6%, total P decreased by 15.6%~34.6% and water-soluble P decreased by 26.3%~41.3%, respectively. Aquatic plants could absorb more nutrients was due to their stronger root activity, more xylem sap or higher SAP nutrient concentration. But these advantages could not exist in one specific aquatic plant, for example, Zizania had the stronger root activity, while the N and P concentrations in xylem sap were higher in watermifoil, Pontederia cordata and Sorbaria sorbifolia. In the ditch water planted aquatic plants, where the decreased proportions of N and P were larger, the total number of microorganisms, nitrobacteria and denitrifying bacteria, even the microbial biomass C, N and P were also higher, and vice versa.