To assess the fate of the large amounts of nitrogen (N) brought into the agricultural environment by human activities in the Changjiang River basin, we used [China's county level agricultural database of 1980 and 1990. National Resources and Environmental Data Center, China] and published conversion data to set up a complete N budget for the Changjiang River basin. Sources considered include imported N such as atmospheric deposition, inorganic fertilizer, biological fixation and manure. Dominant losses considered include crop harvests, denitrification of soil nitrate and NH3 volatilization, and the budget was estimated from the difference between all inputs and all outputs. Therefore, the geographic distribution of excess N, considered as lost, by N storage in farmland and N transported to water bodies in Changjiang River basin was analyzed. In the Changjiang River basin, the anthropogenic reactive N has far exceeded the terrestrial bio-fixed N in nature, and human activities have significantly altered the N cycle in this region. The total inputs of N in 1980 and 1990 were 8.0 and 12.9 Tg N, respectively. The total N outputs are 4.41 Tg N in 1980 and 6.85 Tg N in 1990. Thus, the excess N that was stored in farmland was 1.51 Tg N at 1980 and 2.67 Tg N at 1990, respectively, and losses through transportation to water bodies in 1980 was 2.08 and 3.38 Tg N in 1990, respectively. Our research shows that from 1980 to 1990, cultivated land increased 5.9%, grain production increased 30% and N fertilizer-use increased 106%, but the N fertilizer-use efficiency decreased 36%, and the variations in the distribution of N fertilizer-use efficiency, N budgets and N transport to water bodies tended to coincide with each other geographically.