Abstract: In a paddy rice field experiment with different crop rotation systems and nitrogen application rates, surface water nitrogen content, nitrogen lose via runoff, soil fertility and rice yield were determined. Based on the experiment, chemical nitrogen fertilizer application during rice season in alfalfa-rice or rye-rice rotation systems can be reduced, and not in wheat-rice rotation system in Yixing, Jiangsu Province. Alfalfa-rice and rye-rice rotation systems enhanced soil nitrogen content, promoted rice nitrogen absorption and significantly improved rice yield. Because there was no nitrogen fertilization in winter, nitrogen loss via field water runoff into natural water bodies dropped during this period. The increase of organic fertilizer ratio under the same nitrogen application did also dropped total nitrogen in surface water. The green manure, especially alfalfa, was not only low cost but also effectively replaced chemical nitrogen fertilizers, which resulted in lowered cost of rice production. Replacing traditional wheat-rice with alfalfa-rice rotation system and reducing 120 kg·hm?2 of nitrogen application during rice season resulted in economic benefits and yield increase and environmental sustainability in Yixing, Jiangsu Province.