Peatland ecosystems are unsurpassed in their carbon-storing capacity. However, they can be hotspots for emissions of greenhouse gases (GHGs) depending on soil water saturation and oxygen status. Using automated floating chambers, we investigated the spatiotemporal variability of CH4 and CO2 fluxes and their environmental drivers from inundated areas in a temperate, rich fen. We distinguished between two areas: one with continuous inundation, caused by upwelling groundwater and a lower-lying area with periodic inundation by flooding from an adjacent stream. Using hourly measurements, we found mean effluxes of CH4 and CO2 to be 0.16 and 1.23 g C m-2 d-1 between October and May with more than a 10-fold variation between observations. For CO2, efflux were higher in the periodically inundated area compared to the continuously inundated area. In contrast, CH4 fluxes were higher, and dominated by ebullition, at the area with continuous inundation. Both fluxes increased with soil temperature and wind speed. Advective and diffusive fluxes of CH4 and CO2 associated to groundwater upwelling and upwards diffusion of dissolved gases from shallow groundwater (0.5-0.8 meters below ground level) contributed negligibly to the measured fluxes, suggesting that the emitted GHGs were produced close to the terrain. Our data highlight the large spatiotemporal variation of CO2 and CH4 emissions from fens due to variations in hydrology and topography affecting GHG production near the soil surface. Particularly, the temporary dynamics of soil inundation played a major role in controlling the contribution by CO2 and CH4 to wetland GHG release.