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Based on the mass balance approach, a detailed quantification of nitrogen (N) cycling was constructed for an urban–rural complex system, named the Greater Hangzhou Area (GHA) system, for this paper. The GHA is located in the humid climatic region on the southeastern coast of China, one of the earliest regions in the Yangtze Delta to experience economic development. Total N input into the GHA was calculated at 274.66 Gg/yr (1 Gg = 10 9 g), and total output was calculated at 227.33 Gg/yr, while N accumulation was assessed at 47.33 Gg/yr (17.2% of the total N input). Human activity resulted in 73% of N input by means of synthetic fertilizers, human food, animal feed, imported N containing chemicals, fossil fuel combustion, and other items. More than 69.3% of N was released into the atmosphere, and riverine N export accounted for 22.2% of total N output. N input and output to and from the GHA in 1980 were estimated at 119.53 Gg/yr and 98.30 Gg/yr, respectively, with an increase of 130% and 131%, respectively, during a 24‐year period (from 1980 to 2004). The N input increase was influenced by synthetic fertilizers (138%), animal feed (225%), N‐containing chemicals (371%), riverine input (311%), and N deposition (441%). Compared to the N balance seen in the arid Central Arizona–Phoenix (CAP) system in the United States, the proportion of N transferred to water bodies in the humid GHA system was found to be 36 times higher than the CAP system. Anthropogenic activity, as it typically does, enhanced the flux of N biogeochemistry in the GHA; however, a lack of an N remover (N pollutant treatment facilities) causes excess reactive N (N r ; such as NH 3 , N 2 O, NO x ), polluting water bodies and the atmosphere within the GHA. Therefore many challenges remain ahead in order to achieve sustainable development in the rapidly developing GHA system.