The focus of this study is the relationship between water table depth (WTD) and water vapor [evapotranspiration (ET)] and carbon dioxide [CO2; net ecosystem exchange (NEE)] fluxes in a fen in western Canada. We analyzed hydrological and eddy covariance measurements from four snow-free periods (2003–2006) with contrasting meteorological conditions to establish the link between daily WTD and ET and gross ecosystem CO2 exchange (GEE) and ecosystem respiration (Reco; NEE=Reco−GEE), respectively: 2003 was warm and dry, 2004 was cool and wet, and 2005 and 2006 were both wet. In 2003, the water table (WT) was below the ground surface. In 2004, the WT rose above the ground surface, and in 2005 and 2006, the WT stayed well above the ground surface. There were no significant differences in total ET (∼316 mm period−1), but total NEE was significantly different (2003: 8 g C m−2 period−1; 2004: −139 g C m−2 period−1; 2005: −163 g C m−2 period−1; 2006: −195 g C m−2 period−1), mostly due to differences in total GEE (2003: 327 g C m−2 period−1; 2004: 513 g C m−2 period−1; 2005: 411 g C m−2 period−1; 2006: 556 g C m−2 period−1). Variation in ET is mostly explained by radiation (67%), and the contribution of WTD is only minor (33%). WTD controls the compensating contributions of different land surface components, resulting in similar total ET regardless of the hydrological conditions. WTD and temperature each contribute about half to the explained variation in GEE up to a threshold ponding depth, below which temperature alone is the key explanatory variable. WTD is only of minor importance for the variation in Reco, which is mainly controlled by temperature. Our study implies that future peatland modeling efforts explicitly consider topographic and hydrogeological influences on WTD.