The effects of water management in rice paddies on the levels of cadmium (Cd) and arsenic (As) in Japanese rice grains were tested. In order to reduce the Cd concentration in rice grains, flooding for 3 weeks before and after heading was most effective, but this treatment increased As concentration considerably. Aerobic treatment was effective in reducing As concentration in rice grains, but increased Cd concentration markedly. In the pot experiment, flooding treatment after heading was more effective than flooding treatment before heading in reducing both Cd and As concentrations in rice grains. The concentration of dimethylarsinic acid (DMA) in rice grains was very low under aerobic conditions, but increased in the continuous-flooding treatment. In the field experiment, the grain As concentration in the case of flooding for 3 weeks before and after heading was higher than that in the case of intermittent irrigation. The ratios of DMA to the total As concentration were 3-52% in the pot experiment and 7-13% in the field experiment.