Context: Water and nitrogen fertilizers have great impacts on rice production. Studies on the effects of waternitrogen coupling on bioactive substances in colored rice have rarely been reported. Objective: Identifying the effects of water and nitrogen coupling on the grain yield and bioactive substance content of colored rice helps to develop rational water and nitrogen management strategies, reduce resource inputs and achieve high yields and quality of colored rice. Methods: A three -factor field experiment including two colored rice genotypes (Youxianghongdao and Suixiangheinuo), three water management practices (rainfed, alternating wet and dry irrigation, and flood irrigation), and four nitrogen application levels (0, 50, 100, and 150 kg ha - 1 ) was conducted to evaluate the effects of different water and nitrogen management practices on the grain yield and bioactive substance content of colored rice. Results: Results showed that the coupling between water and nitrogen management had significant effects on grain yield, anthocyanin content, flavonoid content, phytic acid content, and total antioxidant capacity of colored rice. Increasing irrigation tended to increase the grain yield of colored rice but was detrimental to the accumulation of bioactive substances. Increased nitrogen fertilizer application tended to increase the yield of colored rice and the accumulation of beneficial bioactive substances such as anthocyanin, flavonoid, total phenolic, and antioxidant substances, but decreased the accumulation of phytic acid. The comprehensive evaluation value of the colored rice grains decreased with increasing irrigation water content and increased with increasing nitrogen application rate. Among all the treatments, the rainfed with a nitrogen application of 150 kg ha - 1 treatment had the highest comprehensive evaluation value. Conclusions: There is a trade-off between grain yield and bioactive content of colored rice under various water and nitrogen coupled conditions. Results suggested that rainfed with a nitrogen application of 150 kg ha - 1 treatment had the best balance between grain yield and bioactive substance content. Significance: We conclude that the optimal combination of water and nitrogen management for colored rice production in areas with 380 - 510 mm of rainfall during the rice growth period is rainfed with a nitrogen application of 150 kg ha -1 .