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Although the traditional rice–fish co-culture system (RF) efficiently uses water and land resources, provides food security, and does not harm the local environment, it requires improvement because of its small scale and low fish yield. We therefore determined whether fish yield in RF can be increased without increasing nitrogen (N) loss into the environment (i.e., the risk of N pollution) by management of N inputs. In an experiment comparing traditional RF (with fertilization, with very low fish feed) with fish monoculture (FM; without fertilization, with very low fish feed), and rice monoculture (RM; with fertilization, without fish feed), rice yields were equivalent in traditional RF and RM, fish yields were relatively low in both FM and RF, and traditional RF released less N into the environment than RM but more N than FM. In a second experiment, an increase in fish stocking density and associated increase in fish feed in RF did not decrease rice yield, but increased fish yield and increased the release of N into the environment. A third experiment indicated that adjusting the ratio of N added as fertilizer vs. N added as feed to 37% fertilizer-N and 63% fish feed-N increased fish yield without reducing rice yield or N use efficiency and without increasing the release of N into the environment. Our results indicate that fish yield can be increased in the traditional RF system without increasing N pollution by managing the relative quantities of N added as fertilizer vs. feed