In spite of the importance of N management in agricultural production, closing the full nitrogen balance remains a challenge, mainly due to the uncertainties in both fluxes of nitrogen input and output. We analyzed N deposition and its influence on crop productivity and field nitrogen balance based on data from three of 15 years (1990–2005) of experiments in North China. The results showed that the average annual nitrogen deposition was 76, 80, and 94 kg N/ha at Changping, Zhengzhou, and Yangling in a wheat-maize rotation system, respectively. The deposited N could support a corresponding total biomass production (wheat plus maize) of 9.6, 10.6, and 8.8 Mg/ha with a total grain yield of 3.8, 4.8, and 3.7 Mg/ha, however, that did not cause a further decline in soil organic matter. N fertilizer application could increase total biomass (grain) by 244% (259%) and 74% (119%) for wheat and maize, respectively. Under optimal N management, N deposition accounted for 17–21% of the total N inputs, which affected significantly the recovery efficiency of applied N. N deposition showed a significant spatial variation in terms of the fraction of dry and wet depositions. On an annual average, N deposition roughly balanced out N losses due to NH3 volatilization and N2O loss from nitrification and denitrification. NH3 volatilization and NO3−-N leaching each accounted for 16–20% of the total N outputs. A system modeling approach is recommended to investigate the spatial variation of N leaching as affected by climatic conditions, and to fully account for the nitrogen fluxes. The N deposition derived from this study can be used as the background N input into the wheat-maize double cropping system for N balance.