This dataset includes measurements of methane fluxes from two lowland floodplain fen sites in East Anglia, UK under conservation management (Sutton and Strumpshaw Fens). The data were collected on seven monthly to bimonthly visits during 2013 and comprise methane ebullition fluxes measured using inverted funnels, and methane fluxes measured using static chambers. The tall, static chambers captured methane transported by diffusion, plant-mediated transport and steady ebullition, whereas the inverted funnels captured methane transported by steady and episodic ebullition. The dataset also includes measurements of water level and meteorological variables (net radiation, soil temperature, air pressure) along with an allometric measure of plant biomass (Vascular Green Area).