Isoetid macrophytes such as Lobelia dortmanna and Littorella uniflora are engineering species with an extensive root system and high radial oxygen loss (ROL). Despite several studies on these macrophytes, the effect of their oxygenation on methane dynamics has never been investigated. In this study, we hypothesize that isoetids promote dissolved inorganic carbon (DIC) fixation and methane (CH4) oxidation in sandy sediments. Our whole-ecosystem approach study lasted two years (2013-2014) on two oligo-mesotrophic shallow lakes. Benthic chamber incubations confirmed that, as a result of primary production and methanotrophy, isoetid lawns had consistently lower benthic carbon fluxes than bare sediments. On a daily basis, vegetated areas acted as a carbon sink (-0.7 ± 0.4 g C m-2d-1, as DIC + CH4) whereas bare sediments acted as a net source (0.6 ± 0.5 g C m-2d-1, as DIC + CH4). Photosynthetic quotients of < 1 indicated that photosynthetically-produced oxygen was not released into the water column, but accumulated in leaf lacunae or was transferred to the rhizosphere, that contributing to the alteration of net benthic fluxes at the sediment-water interface. This preliminary study highlights the necessity of further investigating the role that isoetids play in mitigating greenhouse gas emissions from temperate shallow lakes.