Plants (macrophytes) growing in lake and wetland sediments are known mediators of greenhouse gases (GHG), specifically methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O). Current studies have emphasized the potential risk of underestimation regarding emissions of plant-mediated GHGs from terrestrial systems including lakes, streams and other freshwater bodies. In order to differentiate the possible sources and sinks of atmospheric carbon and nitrogen in aquatic environments, this study aims to investigate the spatial variability of GHG fluxes in stands of common wetland macrophytes. Field samplings were carried out in the summer of 2012 where 24-hour diel measurements were conducted with the static chamber method in a boreal lake in south western Sweden. Two macrophyte communities were studied; one mixed-species stand and one species-specific stand of water horsetail (Equisetum fluviatile). Spatial variability was confirmed at several stages, both between and within stands. The species-specific stand emitted more CH4 than the mixed stand, from 0.17 to 8.99 mmol m-2 h-1, compared to 0.63 – 1.95 mmol m-2 h-1 maximum measured. Within stand variability was confirmed as variable CH4 flux per strand of E. fluviatile was established. No significant differences were observed regarding CO2 and N2O, other than weak correlation in diel patterns, e.g. daytime uptake and night time respiration/emission for both gases.