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The nitrogen (N) budget was developed for Jiulong River Watershed (JRW), an agricultural watershed in a warm and humid area of southeast China. Water quality monitoring, field surveys, modelling and GIS techniques were applied to estimate N flux of atmospheric deposition, mineralization, runoff, denitrification, and ammonia volatilization. Over the whole watershed, fertilizers, import of animal feeds, biotic fixation, mineralization and atmospheric deposition contributed 67.1%, 16.5%, 2.1%, 4.9% and 9.5%, respectively, of total N input (129.3 kg N ha−1 year−1). Runoff, sale of production, denitrification, and ammonia volatilization contributed 7.3%, 24.4%, 10.5% and 57.8% of total N output (72.9 kg N ha−1 year−1), respectively. The N budget for the JRW suggested that more than 50% of the N input was lost to the environment, and about 14% was discharged as riverine N, which indicated that agricultural and human activities in the watershed substantially impacted the estuary and coastal water quality, and so altered the N biogeochemistry process. [ABSTRACT FROM AUTHOR]