Abstract With the widespread use of combine harvesters in South and Southeast Asia, rice straw remain largely on the field after harvest and are incorporated into the soil during land preparation. The eddy covariance method was employed for the first time to monitor its environmental impacts on the seasonal variations of methane (CH 4 ) and carbon dioxide (CO 2 ) emissions from irrigated lowland rice ecosystems over the entire cropping period (encompassing land preparation, growing, and fallow) during the dry (DS) and wet (WS) seasons in 2013 and 2014. The continuous incorporation of rice straw increased both the average and cumulative CH 4 fluxes during land preparation and vegetative growth stage through successive cropping seasons. The cumulative seasonal gross primary production (GPP) and ecosystem respiration ( Re ) as well as the seasonal Re /GPP ratio also increased through time, which shows that the amount of CO 2 emissions became higher relative to the CO 2 taken up by the rice plants. This clearly indicates the cumulative effect of residual rice straw from its continuous incorporation in the soil. Results further showed that the annual net ecosystem carbon budget (NECB) for 2013 (984 kg C ha −1 ) and 2014 (740 kg C ha −1 ) were both positive, indicating that the irrigated lowland rice ecosystem was a net C sink for both cropping periods. However, it should be noted that the NECB values decreased from 2013 to 2014 due to a decrease in the annual net ecosystem production (NEP) brought about by higher CO 2 emissions and an increase in the annual CH 4 emissions. The annual net greenhouse gas budget (NGHGB) decreased from 348 kg CO 2 eq. ha −1 in 2013 to −2052 kg CO 2 eq. ha −1 in 2014, indicating that the irrigated lowland rice ecosystem has shifted from being a net GHG sink to a net GHG source due to the increase in annual CH 4 emissions. It should be noted that CH 4 has 25 times higher global warming potential than CO 2 (for a 100-year time horizon). The increasing rate of CH 4 and CO 2 emissions due to continuous rice straw application, such as from combine harvesters, could transform the irrigated lowland rice ecosystem into a net GHG source as well as a net C source. This study, however, showed that leaving rice straw on the surface of the fields after harvest to undergo partial decomposition under aerobic conditions before soil submergence and incorporation during land preparation could provide a management strategy for reducing CH 4 emissions while managing rice straw residues from combine harvesters.