Field experiments were carried out in Huantai County from 2006 to 2008 to evaluate the effects of different nitrogen (N) fertilization and irrigation management practices on water leakage and nitrate leaching in the dominant wheat–maize rotation system in the North China Plain (NCP). Two N fertilization (NF1, the traditional one; NF2, fertilization based on soil testing) and two irrigation (IR1, the traditional one; IR2, irrigation based on real-time soil water content monitoring) management practices were designed in the experiments. Water and nitrate amounts leaving the soil layer at a depth of 2.0 m below the soil surface were calculated and compared. Results showed that the IR2 effectively reduced water leakage and nitrate leaching amounts in the two-year period, especially in the winter wheat season. Less than 10 percent irrigation water could be saved in a dry winter wheat season, but about 60 percent could be saved in a wet winter wheat season. Besides, 58.8 percent nitrate under single NF2IR1 and 85.2 percent under NF2IR2 could be prevented from leaching. The IR2 should be considered as the best management practice to save groundwater resources and prevent nitrate from leaching. The amounts of N input play a great role in affecting nitrate concentrations in the soil solutions in the winter wheat–summer maize rotation system. The NF2 significantly reduced N inputs and should be encouraged in ordinary agricultural production. Thus, nitrate leaching and groundwater contamination could be alleviated, but timely N supplement might be needed under high precipitation condition.