The rapid development of aquaculture has sustained aquatic food production but has also led to a host of environmental problems, ranging from eutrophication of aquatic ecosystems to global acidification. China has become the world's largest producer and consumer of aquaculture products. Nitrogen is an essential nutrient in aquaculture ecosystems, and the quantitative environmental fate and impact of nitrogen during aquaculture processes have notable environmental consequences but have received little attention. Here, we established a nitrogen cycling model for China's aquaculture ecosystem to investigate the creation and fate of reactive nitrogen over a decadal time scale. A nitrogen balance analysis showed that reactive nitrogen input in the aquaculture ecosystem increased from 9.43 Tg N yr-1 in 1978 to 18.54 Tg N yr-1 in 2015, while aquaculture production increased from 0.034 to 1.33 Tg N yr-1 during the same period. The environmental fate analysis showed that nitrogen emissions, accumulation, sediment deposition, and export into the oceans increased by 9.05-fold, 0.24-fold, 9.04-fold, and 2.56-fold, respectively. Finally, we investigated four scenarios representing different consumption levels of aquatic products and provided policy recommendations (larger aquaculture size, standardized aquaculture production model, nutritional element management and balanced dietary structure, etc.) on improved management practices in aquaculture ecosystems.