Tropical low land rice ecosystem is a net carbon sink

•Tropical flooded rice ecosystem behaved as net C sink on annual basis.•Low land rice ecology revealed C storage potential in wet and dry seasons.•Annual cumulative net ecosystem CO2 exchange was negative.•Integrated annual net ecosystem CH4 exchange was positive.•Annual gross primary production was greater than ecosystem respiration. A yearlong field study was undertaken to investigate the carbon dioxide (CO2) and methane (CH4) exchange in relation to ecosystem carbon (C) balance in tropical low land rice by employing open path eddy covariance (OPEC) system. The study was conducted on annual basis, included both wet and dry seasons crop. This is the first report from India on net ecosystem CH4 exchange (NEME) from low land flooded rice ecology through eddy covariance techniques. On annual basis the cumulative net ecosystem CO2 exchange (NEE) was −457gCm−2 and NEME was +262.62kgCH4ha−1, respectively. On the other hand, the annual gross primary production (GPP) was +1340gCm−2 and ecosystem respiration (RE) was +883gCm−2. On seasonal basis the rate of NEE was in the range of −3.29 and −2.74gCm−2 day−1, respectively and NEME was +2.80 and +4.34mgm−2h−1 in wet and dry cropping seasons, respectively. As a whole, the integrated NEE in dry and wet seasons was −355 and −341gCm−2, whereas, the integrated NEME in the two seasons was +84 and +129kgha−1, respectively. Considering the net ecosystem production (NEP or −NEE: +695gCm−2), rhizodeposition, algal biomass, root, stubble and compost added as ecosystem C input and NEME (+213kgha−1), C removal through harvest and dissolved organic C as ecosystem C output, the tropical rice acts as net C sink both seasonally and annually. Although CH4 is a source of C loss from low land flooded rice ecosystem, considering all the components of C balance on system basis, this ecology has a good potential to store considerable amount of C.