Abstract: To reduce agricultural non-point source pollution and improve nitrogen use efficiency, the research on the changes of concentrations of NH4+-N and NO3--N in surface and ground water after fertilizer application and changes of that at each growth stage was conducted based on experimental test in flooding paddy field under different leakage rates by use of lysimeter. Results showed that after fertilizer application, the concentrations of NH4+-N in both surface and ground water increased significantly and then decreased, and their peak values both appeared at the 5th day after fertilizer application, they were 17.75 and 10.34mg/L, respectively in surface water and ground water. Results also showed that the concentration of NO3--N in surface water decreased after a brief increment, and its peak value appeared at the 2nd day after fertilizer application. While the concentration of NO3--N in ground water gradually rose and then decreased, its peak value appeared at the 5th day after fertilizer application (3.25mg/L). Compared with the value at the 1st day, the concentrations of NO3--N in ground water increased to 249.4% at 6th day. Water was supplied in the paddy and soil in paddy was disturbed and the process that absorption of NH4+-N in the surface soil and nitrification process were promoted. Then the concentrations of NH4+-N and NO3--N in surface water was increased and concentrations of that gradually decreased with the flooding time increasing. Different leakage (2 and 4mm/d) had a certain influence on the changes of nitrogen, but the difference between each treatment was not significant. Therefore, drainage should be avoided after fertilizing, immediate drainage should be avoided after rain and surface irrigation.