Dairy farming regions are important contributors of nitrogen (N) to surface waters. We evaluated the N budget and relationships to riverine N exports within the Shibetsu River catchment (SRC) of a dairy farming area in eastern Hokkaido, Japan. Five drainage basins with variable land-cover proportions within the SRC were also evaluated individually. We quantified the net N input (NNI) to the catchment from the difference between the input (atmospheric deposition, chemical fertilizers, N fixation by crops and imported food and feed) and the output (exported food and feed, ΔSliv and ΔShu, which are the differences between input and output in livestock and human biomass, respectively) using statistical and measured data. Volatilized ammonia (NH3) was assumed to be recycled within the catchment. The riverine export of N was quantified. Agricultural N was a dominant source of N to the SRC. Imported feed was the largest input (38.1 kg N ha−1 year−1), accounting for 44% of the total inputs, followed by chemical fertilizers (32.4 kg N ha−1 year−1) and N fixation by crops (13.4 kg N ha−1 year−1). The exported food and feed was 24.7 kg N ha−1 year−1 and the ΔSliv and ΔShu values were 7.6 and 0.0 kg N ha−1 year−1, respectively. As a result, the NNI amounted to 54.6 kg N ha−1 year−1. The riverine export of total N from the five drainage basins correlated well with the NNI, accounting for 27% of the NNI. The fate of the missing NNI that was not measured as riverine export could possibly have been denitrified and/or retained within the SRC. A change in the estimate of the deposition rate of volatilized NH3 from 100 to 0% redeposited would have decreased the NNI by 37%, although we believe that most NH3 was likely to have been redeposited. The present study demonstrated that our focus should be on controlling agricultural N to reduce the impact of environmental pollution as well as on evaluating denitrification, N stocks in soil and the fate of NH3 volatilization in the SRC.