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The agricultural use of peatlands usually requires drainage, thereby transforming these organic soils from a net carbon sink into a net source. The Seeland region of Switzerland is characterised by fens that have been intensively used for agriculture for 150 years. Our site is a degraded fen with a remaining peat layer of 60 cm that had been used as cropland until 2009. In connection to a nature protection project it has been managed as extensive permanent grassland since then. The net ecosystem carbon balance (NECB) was determined for two years (2015-2016). For this purpose, the net ecosystem exchange of CO2 (NEE) and CH4 fluxes were measured by eddy covariance, and the carbon removed by harvest was quantified. Our degraded fen site was found to be a net carbon source of 477±73g C m-2 yr -1 and 434±51 g C m 2 yr-1 in 2015 and 2016, respectively. Annual CH4 emissions were marginal in both years with 0.4 ± 0.8 g CH4-C m-2 yr -1 (2015) and 0.7 ± 0.7 g CH4-C m-2 yr -1 (2016). In contrast to NECB, the NEE was considerably higher in 2015 than in 2016 (308±71 g C m-2 yr -1 vs 117±39 g C m-2 yr -1). The year 2015 was characterised by partial flooding of the grassland, followed by a dry and hot summer leading to lower CO2 uptake due to reduced growth, which was reflected in lower harvest compared to 2016. Thus, the short-term plant-induced carbon fluxes were altered, whereas total soil carbon loss remained rather constant. This was verified by an intra site comparison between the flooded and non-flooded part in 2015. Our results indicate that the soil carbon loss of this highly degraded peatland with a shallow peat layer is relatively moderate and hardly influenced by interannual weather variations.