In the Taihu Lake region, the neighboring eutrophied river water is widely used to irrigate the paddy field. Both refilled and monolith lysimeter experiments were adopted to simulate the irrigation system to study the contribution of eutrophied irrigation water to nitrogen (N) and phosphorus (P) in a paddy soil. In the repacked soil column experiment with regular irrigations, N leaching losses were high in the beginning of the flooding period, and decreased gradually to around zero indicating that N leaching at the beginning flooding stage came mostly from native soil N not N in the irrigation water. The dissolved organic nitrogen (DON), however, was steadily detected throughout the whole flooding period indicating that the leaching loss of DON was mainly from the input from river water irrigation. Contrary to the N leaching pattern, an obvious P leaching loss was observed only after a long time of flooding indicating that continuous P input from eutrophied irrigation water led to saturation of soil P absorption after a long time flooding treatment. In comparison to the repacked soil column experiment, with local fertilizer application rate, the leaching losses of N and P were lower in the undisturbed lysimeter experiment and the contributions of eutrophied irrigation water were higher to the N and P in paddy soil. Among the 56.3 kg N/hm2 of input from irrigation water, there was totally 55.8 kg N/hm2could be attributed to soil retention and rice plant uptake, indicating that paddy soil might serve as an environmentally friendly ecosystem in N and P absorption as eutrophied irrigation water in Taihu region concerned. Furthermore, N and P fertilizer application rate could be decreased accordingly to optimize fertilizer management when contributions from eutrophied irrigation water were taken into consideration.