This study investigates the environmental impact of nitrogen (N) management in intensive agricultural systems in China, focusing on two major double-cropping systems: waterlogged rice/upland wheat in the Taihu region and irrigated wheat/rainfed maize on the North China Plain. Excessive N fertilization has led to significant environmental problems, including nitrogen enrichment in the atmosphere, soil, and water. The study compares knowledge-based optimum N fertilization with current practices, finding that current methods do not significantly increase crop yields but result in twice as much N loss to the environment. The higher N loss rates and lower N retention rates indicate that the rice/wheat system is less efficient in utilizing residual N compared to the wheat/maize system. Periodic waterlogging in the Taihu region causes large N losses through denitrification, while calcareous soils and concentrated summer rainfall lead to ammonia volatilization and nitrate leaching in the wheat/maize system. Atmospheric deposition and irrigation water N have increased significantly, becoming important N sources for agricultural ecosystems. Adopting optimum N fertilization techniques, controlling primary N loss pathways, and improving agricultural extension services can achieve a better N balance without sacrificing crop yields and significantly reducing environmental risk. The study highlights the need for improved N management in intensive agriculture to reduce environmental degradation. Over-fertilization has led to severe environmental issues, including eutrophication, nitrate pollution, acid rain, and greenhouse gas emissions. The research shows that more efficient N use can reduce current N application rates by 30–60%, maintaining crop yields and N balance while reducing environmental risks. The study also emphasizes the importance of considering regional differences in N behavior and management practices to further reduce N losses. Sustainable agricultural systems require balancing yield and environmental consequences, with integrated management packages that include efficient recycling of manures and crop residues, legume crops in rotations, and reduced reliance on synthetic N fertilizers. The findings suggest that reducing fertilizer N inputs is essential for restoring and protecting degraded environments. The study calls for adopting and enforcing relevant agricultural regulations, improving local extension services, and educating farmers on environmental awareness to achieve these goals.This study investigates the environmental impact of nitrogen (N) management in intensive agricultural systems in China, focusing on two major double-cropping systems: waterlogged rice/upland wheat in the Taihu region and irrigated wheat/rainfed maize on the North China Plain. Excessive N fertilization has led to significant environmental problems, including nitrogen enrichment in the atmosphere, soil, and water. The study compares knowledge-based optimum N fertilization with current practices, finding that current methods do not significantly increase crop yields but result in twice as much N loss to the environment. The higher N loss rates and lower N retention rates indicate that the rice/wheat system is less efficient in utilizing residual N compared to the wheat/maize system. Periodic waterlogging in the Taihu region causes large N losses through denitrification, while calcareous soils and concentrated summer rainfall lead to ammonia volatilization and nitrate leaching in the wheat/maize system. Atmospheric deposition and irrigation water N have increased significantly, becoming important N sources for agricultural ecosystems. Adopting optimum N fertilization techniques, controlling primary N loss pathways, and improving agricultural extension services can achieve a better N balance without sacrificing crop yields and significantly reducing environmental risk. The study highlights the need for improved N management in intensive agriculture to reduce environmental degradation. Over-fertilization has led to severe environmental issues, including eutrophication, nitrate pollution, acid rain, and greenhouse gas emissions. The research shows that more efficient N use can reduce current N application rates by 30–60%, maintaining crop yields and N balance while reducing environmental risks. The study also emphasizes the importance of considering regional differences in N behavior and management practices to further reduce N losses. Sustainable agricultural systems require balancing yield and environmental consequences, with integrated management packages that include efficient recycling of manures and crop residues, legume crops in rotations, and reduced reliance on synthetic N fertilizers. The findings suggest that reducing fertilizer N inputs is essential for restoring and protecting degraded environments. The study calls for adopting and enforcing relevant agricultural regulations, improving local extension services, and educating farmers on environmental awareness to achieve these goals.