Rice paddy fields are a major source of methane (CH₄) gas. Anaerobic environment is developed in soil by flooding so that CH₄ is generated due to the activity of methane producer (anaerobes bacteria). Previous study showed that intermittent irrigation was of effective to mitigate CH₄ emission in a rice paddy field. However, the various saturation of soil made by intermittent irrigation may emit more carbon dioxide (CO₂) and nitrous oxide (N₂O) than does saturated soil made by flooding irrigation. Further, rice yield was reported as either increased or decreased by intermittent irrigation. In the past two years, we cultivated a Japonica rice , variety called Kinuhikari. We found that water management combining intermittent irrigation, midseason drainage, and flood irrigation was effective both to maintain rice yield and to reduce greenhouse gas emission. In addition, the concentrations of nitrate (NO₃^-) in soil solution increased by intermittent irrigation probably due to the nitrifications of NH₄⁺. According to previous reports by various researchers, Japonica type rice prefers NH₄⁺ to NO₃^-, Indica type rice prefers NO₃^- to NH₄⁺. Therefore, increases in the yield of Indica type rice is expected by intermittent irrigation. The effect of water management of paddy fields on the yield of Indica type rice and greenhouse gas emissions will be discussed.