Floating-leaved rhizophytes can significantly alter net carbon dioxide (CO2) and methane (CH4) exchanges with the atmosphere in freshwater shallow environments. In particular, CH4 efflux can be enhanced by the aerenchyma-mediated mass flow, while CO2 release from supersaturated waters can be reversed by the plant uptake. Additionally, the floating leaves bed can hamper light penetration and oxygen (O2) diffusion from the atmosphere, thus altering the dissolved gas dynamics in the water column. In this study, net fluxes of CO2 and CH4 were measured seasonally across vegetated [Nuphar lutea (L.) Sm.] and free water surfaces in the Busatello wetland (Northern Italy). Concomitantly, dissolved gas concentrations were monitored in the water column and N. lutea leaf production was estimated by means of biomass harvesting. During the vegetative period (May-August), the yellow waterlily stand resulted a net sink for atmospheric carbon (from 97.5 to 110.6 g C-CO2 m-2), while the free water surface was a net carbon source (166.3 g C-CO2 m-2). Both vegetated and plant-free areas acted as CH4 sources, with an overall carbon release comprised between 71.6 and 113.3 g C-CH4 m-2. On the whole, water column chemistry was not affected by the presence of the floating leaves; moreover, no significant differences in CH4 efflux were evidenced between the vegetated and plant-free areas. In general, this study indicates that the colonization of shallow aquatic ecosystems by N. lutea might not have the same drastic effect reported for free-floating macrophytes.