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While many controlled irrigation and drainage techniques have been adopted in China, the environmental effects of these techniques require further investigation. This study was conducted to examine the changes of nitrogen and phosphorus of a flooded paddy water system after fertilizer application and at each growth stage so as to obtain the optimal drainage time at each growth stage. Four treatments with different water level management methods at each growth stage were conducted under the condition of ten-day continuous flooding. Results show that the ammonia nitrogen ( NH -N+ ) concentration reached the peak value once the fertilizer was applied, and then 4 decreased to a relatively low level seven to ten days later, and that the nitrate nitrogen ( NO -N? ) 3 concentration gradually rose to its peak value, which appeared later in subsurface water than in surface water. Continuous flooding could effectively reduce the concentrations of NH -N+ , 4 NO -N? , and total phosphorus (TP) in surface water. However, the paddy water disturbance, in the process of soil surface adsorption and nitrification, caused 3 NH -N+ to be released and increased the 4 concentrations of NH -N+ and 4 NO -N? in surface water. A multi-objective controlled drainage 3 model based on environmental factors was established in order to obtain the optimal drainage time at each growth stage and better guide the drainage practices of farmers. The optimal times for surface drainage are the fourth, sixth, fifth, and sixth days after flooding at the tillering, jointing-booting, heading-flowering, and milking stages, respectively.