Arctic rivers are intricate water networks that chemically and biologically process carbon before releasing it as carbon dioxide (CO2) into the atmosphere or carrying it to the ocean. Primary producers use inorganic carbon to build biomass at the basis of the trophic chain. Little is known about how Arctic rivers adapt to climate warming, changes in hydrology and biogeochemical properties. To quantify net and gross biological productivity we measured the dissolved oxygen-to-argon (O2/Ar) ratios and O2 triple isotopologue composition in the river Kolyma and in its tributary Ambolikha during late freshet (June) and base-flow conditions (August) in 2019. We found that hydrological factors restricted river productivity. The river system released CO2 into the atmosphere in June and August, however August emissions were only 6 % of late freshet emissions. Also, the Ambolikha tributary emitted twice as much CO2 per area than the main Kolyma channel in June. Due to higher river flow and turbidity in June, river production was reduced, while lower flows in August permitted more light penetration and a phytoplankton bloom at the confluence of tributary and main Kolyma channel. Total CO2 emissions per area during June and August amounted to (5±11) % of the gross carbon uptake estimated at the bloom site. Thus, in-stream metabolism can exceed riverine CO2 emissions under specific flow and light conditions. Arctic climate change may promote biological productivity in particular locations and increase its contribution to carbon budgets in Arctic rivers as flow slows during longer open water periods.