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The Ob River floodplain is the second largest floodplain in the world. Despite its vast area, estimates of carbon (C) emissions from the Ob River floodplain are largely absent. Here we present seasonal C emission and water area extent from the main channel and the floodplain along a ~4 km reach in the boreal zone of the Ob River. We found strong seasonality in water area extent of the Ob main channel (~1.8 km2) and floodplain (~3 km2) with water covering 34% of land during flood and subsequently declining to ~16% and ~14% during summer and autumn baseflow, respectively. The C emissions also varied seasonally over the open water period, ranging from −0.1 to 0.6 g C m−2 d−1 for the Ob main channel and from 0 to 9 g C m−2 d−1 for the floodplain. The dissolved organic carbon positively affected CO2 concentrations and fluxes in the floodplain during all seasons, whereas pH and oxygen concentration negatively impacted CO2 concentrations and fluxes. Some nutrients (ammonia and phosphate) positively correlated with CO2 and CH4 concentrations in summer. The total C emission from the study reach (1.8 km2 main channel, 3 km2 floodplain) during moderate flooding was 236 ± 51 tons C yr−1 (>99% CO2, <1% CH4) with the floodplain accounting for ~65%. The contribution of the floodplain to the net river C evasion may be even greater during years of high flooding and in northern regions of the Ob River basin, where floodplain soils are more C-rich and are underlain by permafrost, and in years with more extensive flooding.