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Carbon emission from Arctic rivers constitutes a positive feedback between the climate warming and C cycle. However, in case of rivers with extensive floodplains, the impacts of temporary water bodies and secondary channels on CO₂ exchange with atmosphere, compared to the main stem and tributaries, remain strongly understudied. In order to quantify the relative role of various water bodies of the Arctic river basin in the C cycle, the hydrochemical variables and greenhouse gases GHG concentrations and fluxes were measured within the floodplain of the largest Arctic River, Ob, in its low reaches located in the permafrost zone. These included the main stem, secondary channels, tributaries and floodplain lakes sampled over a 900 km north-south transect (25,736 km² of the main stem and adjacent floodplain area; 7893 km² water surface) during peak of spring flood (May 2023). In addition to main stem and tributaries, providing less than a half of overall C flux, floodplain lakes and secondary channels acted as important factor of C emission from the floodplain water surfaces. Multi-parametric statistical treatment of the data suggested two main processes of C emission from the Ob River floodplain waters: terrestrial organic matter-rich flooded wetlands (fens) provided elevated pCO₂, whereas the sites of possible groundwater discharge in the secondary channels decreased the CO₂ fluxes due to more alkaline environments, rich in labile metals and anionic elements. Based on available high-resolution Landsat-8 images, which matched the period of field work, it was found that the total water coverage of the floodplain during spring 2023 was 30 % of overall territory, compared to 18 % during the baseflow. Based on chamber-measured CO₂ fluxes (1.56 ± 0.47 g C-CO2 m−2 d−1), overall CO₂ emissions during 2 months of the spring flood from the entire Lower Ob River floodplain water surfaces including the main stem amounted to 0.73 ± 0.25 Tg C. Diffuse CH4 flux represented <1 % of total C flux. The main stem of the Ob River accounted for 34 % and 18 % of CO₂ and CH₄ emissions, respectively, whereas the floodplain lakes provided 59 % and 50 % of CO₂ and CH₄ emission, respectively. Considering that the low reaches of the Ob River represent >70 % of total river basin floodplain, and that during some years, the entire floodplain can be covered by water, emissions from the river – if assessed solely from summer (July–August) measurements – can be at least 3 times underestimated. It is therefore important to account for extended water surface during high water levels on Arctic rivers when assessing global riverine C emissions.