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Alternate wetting and drying (AWD) system is a water management practice of rice cultivation that has been recommended and promoted to replace continuous flooding (CF). AWD could reduce greenhouse gas (GHG) emissions and save water use without compromising rice yields. However, its effects depend on how water level is effectively controlled. This study aims to evaluate GHG emissions, water use and yield of rice cultivation as affected by the implementation of incomplete AWD and complete AWD. Rice (Oryza sativa L.) was transplanted in the experimental field at Ratchaburi province, Thailand under CF and AWD water management. Water management for AWD in wet season was not complete due to the interference of rainfall in the tillering stage, while it was complete in the dry season. Relative to CF, the incomplete AWD reduced CH4 emission by 10.62% but increased N2O emission by 5.94%. The complete AWD reduced CH4 emission by 23.10% but increased N2O emission by 14.79%. Although both AWD systems increased N2O emission, however, their total global warming potentials (GWP) were still lower than CF by 5.32% under incomplete AWD and 10.83% under incomplete AWD. The incomplete AWD and complete AWD used 11.88% and 3.79% less water (irrigation + rainfall) when compared to CF. In terms of rice yield, it was enhanced only under complete AWD by 2.42% through increased number of tillers and panicles. The yield was reduced under incomplete AWD by 9.12%. Complete AWD and incomplete AWD reduced the irrigation water by 4.52% and 16.72%. The water productivity and water scarcity footprint have been reduced in both AWD systems while the carbon footprint was reduced by 13.95% under complete AWD but increased by 3.44% under incomplete AWD. The results showed that, during dry season, complete AWD is a good water management practice to replace CF as it can help mitigate GHG emissions, save water and increase yield. It was noted that in a case where incomplete AWD happened, although less water was used than the complete AWD but high emissions and yield reduction may occur. Therefore, to avoid incomplete AWD, it is recommended to implement AWD in the area or season with no frequent rainfall. (C) 2019 Elsevier Ltd. All rights reserved.