Atmospheric CO2 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 CO2 (eCO2) on GHG emissions under continuously flooded irrigation (CF) and under intermittently flooded (IF) conditions. Elevated CO2 stimulated CH4 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 CO2 had no effect on N2O emissions in either the field or pot experiment. Rice root biomass, aboveground biomass and grain yield increased with eCO2, but were not affected by water management. Elevated CO2 only stimulated the abundance of methanogens under CF, suggesting that increased soil O2 availability with IF limited methanogenic activity under eCO2. Our findings suggest that estimates of CH4 emissions from global rice agriculture with eCO2 need to account for recent changes in water management.