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Peatlands store large amounts of organic carbon, but the carbon stock is sensitive to changes in precipitation or water table manipulations. Restoration of drained peatlands by drain blocking and flooding is a common measure to conserve and augment the carbon stock of peatland soils. Here, we report to what extent flooding affected the contribution of heterotrophic and rhizosphere respiration to soil CO₂ efflux in a grass-dominated mountain fen in Germany. Soil CO₂ efflux was measured in three un-manipulated control plots and three flooded plots in two consecutive years. Flooding was achieved by permanent irrigation during the growing seasons. Radiocarbon signatures of CO₂ from different sources including soil CO₂ efflux, incubated peat cores and live grass roots were repeatedly analyzed for partitioning of soil CO₂ efflux. Additionally, heterotrophic respiration and its radiocarbon signature were determined by eliminating rhizosphere respiration in trenched subplots (only control). In the control plots, rhizosphere respiration determined by ¹⁴C signatures contributed between 47 and 61% during the growing season, but was small (4 ± 8%) immediately before budding. Trenching revealed a smaller rhizosphere contribution of 33 ± 8% (2009) and 22 ± 9% (2010) during growing seasons. <br><br> Flooding reduced annual soil CO₂ efflux of the fen by 42% in 2009 and by 30% in 2010. The reduction was smaller in 2010 mainly through naturally elevated water level in the control plots. A one-week interruption of irrigation caused a strong short-lived increase in soil CO₂ efflux, demonstrating the sensitivity of the fen to water table drawdown near the peat surface. The reduction in soil CO₂ efflux in the flooded plots diminished the relative proportion of rhizosphere respiration from 56 to 46%, suggesting that rhizosphere respiration was slightly more sensitive to flooding than heterotrophic respiration.