To evaluate the effect of human activities on the amount of nitrogen (N) transported to the Three Gorges Dam (TGD), we have developed and applied a model to estimate the riverine N transport from watersheds draining into the upper Changjiang River basin. By using this model and a database of agricultural statistics, we study the temporal and spatial changes in N inputs to watersheds and surface waters. The total amount of N transported to the surface drainage waters from the agro-ecosystem in 2000 showed a 2.9-fold increase over that in 1980. Considering a constant (37%) loss rate from the river, the annual amount of N transported to the TGD from the agro-ecosystem of the Changjiang river upper basin was about 0.35 × 106, 0.47 × 106, 0.59 × 106, 0.64 × 106 and 1.01 × 106 t in 1980, 1985, 1990, 1995, and 2000, respectively. Further, the transported amount of new anthropogenic reactive N approximately quadrupled in 2000, while the amount of riverine N due to rural human waste varied slightly. Of the total N transported to surface drainage waters in 10 watersheds in 2000, the Jialingjiang watershed accounted for 35%; the TGD region, 15%; and the Toujiang, Wujiang and Minjiang watersheds, 11% each. In 1980, the N sources were concentrated in the rural areas surrounding Chendu City and Chongqing City; however, these sources considerably expanded in the 1990s. The increased use of synthetic fertilizers and the decrease in the fertilizer N-use efficiency are implicated as major causal factors of increased riverine N transport; the calculated amount of N transported to the main tributaries agrees well with previously reported data.