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The daily and seasonal evolution of O2 and CO2 saturation, water-atmosphere fluxes and budgets were measured in two fluvial reaches of the Mincio River (Italy). The northern reach is free flowing and is dominated by macrophytes while the southern reach is dammed, hypertrophic and phytoplankton dominated. We hypothesized short term regulation of gas saturation and fluxes by primary producers and the reversal of CO2 off-gassing in the southern reach. Results indicated that both reaches were always CO2 supersaturated. Higher CO2 evasion rates in the northern compared to the southern reach depended on reaeration coefficient, in turn depending on water velocity. In the northern reach dissolved inorganic carbon (DIC) production was one order of magnitude higher than oxygen consumption, likely due to a combination of anoxic heterotrophic activity in the hyporheic zone and carbonate dissolution. The activity of macrophytes influenced CO2 saturation on short time scales. A net summer abatement of DIC occurred in the southern reach, probably due to fixation by phytoplankton, which attenuated supersaturation but not reversed CO2 efflux. This study demonstrates how in small rivers CO2 evasion can undergo rapid and significant changes due to eutrophication, altered hydrology and shift in primary producer communities.