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Not AvailableLowland tropical rice-rice system has a unique micrometrological characteristic that affects both energy component and net ecosystem energy. Periodic and seasonal variations of methane (CH4), carbon dioxide (CO2), and energy exchange from irrigated lowland rice-rice ecosystem were studied using open-path eddy covariance (EC) system during the dry (DS) and wet (WS) seasons in2015. Concurrently, the manual chamber method was employed in nitrous oxide (N2O) measurement efflux. Cumulative net ecosystem carbon exchange (NEE) was observed highest (− 232.55 g C m−2) during theWS and lowest (− 14.81 g C m−2) during wet fallow (WF). Similarly, the cumulative net ecosystem methane exchange (NEME) was found highest (13,456.5 mg CH4 m−2) during the WS and lowest (2014.3 mg CH4 m−2) during the WF. Surface energy fluxes, i.e., sensible (Hs) and latent heat (LE) fluxes, showed a similar trend. With the advancement of time, the ratio of ecosystem respiration (Re) and gross primary production (GPP) increased. The cumulative global warming potential (GWP) for the two cropping seasons including two fallows was 13,224.1 kg CO2 equivalent ha−1. The GWP and NEME showed a similar trend as soil enzymes and labile carbon pools in both seasons (except GWP at the harvesting stage in the wet season). The mean NEE exhibited a more negative value with decrease in labile pools from panicle initiation to harvesting stage in the WS. Soil labile C and soil enzymes can be used as an indicator of NEE, NEME, and GWP in lowland rice ecology.Not Availabl