A field experiment was conducted to remove the potential eutrophication effect of N and P from rural wastewater (RW) during the whole rice growing season of 2010. Commercial fertilizer and RW were applied to furnish 40 kg P ha-1except CK. Results showed TN concentration of the floodwater in the paddy wetland system decreased quickly after transplanting, rosed significantly (P ≤ 0.05) after two N topdressings, and then decreased gradually as the following sequences: SW > GW > DW > BW > CK. Total P (TP) concentration had significantly declined after P application, from October 15 there were no significant increases in TP concentration in the floodwater. Meanwhile, the yield for CK was significantly less (P ≤0.05) than SW, GW, DW, and BW, with the yield of BW significantly greater (P ≤ 0.05) than other treatments. It is feasible to remove N and P from RW by the paddy wetland system and can be widely used to improve the yield of rice.