Water from the Ambolikha river was sampled in triplicate during the Freshet spring thaw in June and the Summer period in August to understand microbial community dynamics.

Sources and sinks of greenhouse gases (GHGs) in Arctic rivers, and their synergy with the land, are largely unknown. Yet they are projected to change with climate warming. Here, we report high-temporal resolution aquatic CO2, CH4 and O2 fluxes from Ambolikha river in Northeast-Siberian from June to August 2019. River flow conditions controlled the water-atmosphere gas exchange, the in-stream biogeochemistry and quality and quantity of organic substances in the river. The large river CO2 and CH4 emissions reached between 7% and 18% of the floodplain carbon fluxes. During spring, negligible abundances of methanogens and the organic carbon characteristics suggest that high river gas concentrations are mostly floodplain derived. During summer, reversed flow conditions favored river gas emissions adding a new component to the active pipe hypothesis by further limiting carbon export to the ocean.