Water management impacts both methane (CH4) and nitrous oxide (N2O) emissions from rice paddy fields. Although controlled irrigation is one of the most important tools for reducing CH4emission in rice production systems it can also increase N2O emissions and reduce crop yields. Over three years, CH4 and N2O emissions were measured in a rice field in Uruguay under two different irrigation management systems, using static closed chambers:conventional water management (continuous flooding after 30 days of emergence, CF30); and an alternative system (controlled deficit irrigation allowing for wetting and drying, AWDI). AWDI showed mean cumulative CH4 emission values of 98.4 kg CH4 ha−1, 55 % lower compared to CF30, while no differences in nitrous oxide emissions were observed between treatments ( p > 0.05). No yield differences between irrigation systems were observed in two of the rice seasons ( p > 0.05) while AWDI promoted yield reduction in one of the seasons ( p