Temporal trends of N2O fluxes across the soil–atmosphere interface were determined using continuous flux chamber measurements over an entire growing season of a subsurface aerating macrophyte (Phalaris arundinacea) in a nonmanaged Danish wetland. Observed N2O fluxes were linked to changes in subsurface N2O and O2 concentrations, water level (WL), light intensity as well as mineral-N availability. Weekly concentration profiles showed that seasonal variations in N2O concentrations were directly linked to the position of the WL and O2 availability at the capillary fringe above the WL. N2O flux measurements showed surprisingly high temporal variability with marked changes in fluxes and shifts in flux directions from net source to net sink within hours associated with changing light conditions. Systematic diurnal shifts between net N2O emission during day time and deposition during night time were observed when max subsurface N2O concentrations were located below the root zone. Correlation (P < 0.001) between diurnal variations in O2 concentrations and incoming photosynthetically active radiation highlighted the importance of plant-driven subsoil aeration of the root zone and the associated controls on coupled nitrification/denitrification. Therefore, P. arundinacea played an important role in facilitating N2O transport from the root zone to the atmosphere, and exclusion of the aboveground biomass in flux chamber measurements may lead to significant underestimations on net ecosystem N2O emissions. Complex interactions between seasonal changes in O2 and mineral-N availability following near-surface WL fluctuations in combination with plant-mediated gas transport by P. arundinacea controlled the subsurface N2O concentrations and gas transport mechanisms responsible for N2O fluxes across the soil–atmosphere interface. Results demonstrate the necessity for addressing this high temporal variability and potential plant transport of N2O in future studies of net N2O exchange across the soil–atmosphere interface.