1. Eutrophication increases primary productivity and favours the predominance of floating vegetation in wetlands. Carbon (C) fluxes in wetlands are strongly driven by primary productivity and can differ by vegetation type. However, to the best of our knowledge, the role of eutrophication in C fluxes has rarely been assessed. 2. Consequently, we aimed to measure the seasonal variation in carbon dioxide (CO2) and methane (CH4) fluxes at six aquatic sites in four temperate wetlands, ranging along a gradient of sediment total phosphorus content, and determine whether C fluxes correlate with above-ground net primary productivity (ANPP) and plant community composition along this eutrophication gradient. 3. Daytime CO2 emissions were significantly and negatively correlated with wetland net primary productivity as a result of the greater C fixation by photosynthesis during the peak of production. Conversely, CH4 emissions were significantly and positively correlated with wetland ANPP, possibly due to higher litter production and anaerobic decomposition. 4. The highest CH4 emissions were observed above floating vegetation, which favoured hypoxic conditions in the water column. CH4 emissions including ebullition were higher above macroalgal belts than above vascular plants with floating leaves. CH4 emissions without ebullition (i.e. resulting from plant transport and diffusion) better correlated with the abundance of macroalgae than with the abundance of vascular plants with floating leaves. 5. Our results suggest that eutrophication may greatly modify CO2 and CH4 emissions from wetlands through changes in vegetation type and productivity.