The excessive use of chemical fertilizers or manure in agriculture sometimes causes environmental problems, such as inland water pollution. In this study, we used a database for the estimation of the nitrogen how associated with agricultural practices in each prefecture in Japan. We also estimated the amount of residual N in farmland and non-utilized livestock waste N, as indices of environmental risk (i.e., possibility of inland water pollution). The amount of residual N in Japan was estimated of 445,985 t N (92 kg N ha(-1)), represented the difference between the total input (1,282,824 t N; 266 kg N ha(-1)) and total output (836,838 t N; 174 kg N ha(-1)) in farmland. It was estimated that 71% of the residual N was associated with chemical fertilizer application. The effective use of chemical fertilizers is important for reducing residual N in Japan. Non-utilized livestock wastes were estimated to amount to 82,832 t N (17 kg N ha(-1)). These values were higher in prefectures in which larger amounts of livestock feces were produced. Therefore, a mitigation plan for reducing environmental risk should be designed depending on the characteristics of the prefectures.