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Atmospheric CO 2 concentrations and water management practices both affect greenhouse gas (GHG) emissions from rice paddies, but interactive effects between these two factors are still unknown. Here, we show the first study to compare the impact of elevated atmospheric CO 2 (eCO 2) on GHG emissions under continuously flooded irrigation (CF) and under intermittently flooded (IF) conditions. Elevated CO 2 stimulated CH 4 emissions under CF by 50% in a field experiment and by 46% in a pot experiment, but it had no effect under IF in both experiments. Elevated CO 2 had no effect on N 2 O emissions in either the field or pot experiment. Rice root biomass, aboveground biomass and grain yield increased with eCO 2 , but were not affected by water management. Elevated CO 2 only stimulated the abundance of methanogens under CF, suggesting that increased soil O 2 availability with IF limited methanogenic activity under eCO 2. Our findings suggest that estimates of CH 4 emissions from global rice agriculture with eCO 2 need to account for recent changes in water management. • The first study to compare the effect of elevated CO 2 on GHG emissions under CF and IF. • Elevated CO 2 stimulated CH 4 emissions under CF, but had no effect under IF. • Elevated CO 2 did not affect N 2 O emissions under CF and IF. • Elevated CO 2 increased the abundance of methanogens under CF only. • Current estimates of CO 2 effects on CH 4 emissions from rice paddies may be too high. [ABSTRACT FROM AUTHOR]