Continuous half-hourly net CO2 exchange measurements were made using nine automatic chambers in a treed fen in northern Alberta, Canada from June–October in 2005 and from May–October in 2006. The 2006 growing season was warmer and drier than in 2005. The average chamber respiration rates normalized to 10 °C were much higher in 2006 than in 2005, while calculations of the temperature sensitivity (Q10) values were similar in the two years. Daytime average respiration values were lower than the corresponding, temperature-corrected respiration rates calculated from night-time chamber measurements. From June to September, the season-integrated estimates of chamber photosynthesis and respiration were 384 and 590 g C m−2, respectively in 2006, an increase of 100 and 203 g C m−2 over the corresponding values in 2005. The season-integrated photosynthesis and respiration rates obtained using the eddy covariance technique, which included trees and a tall shrub not present in the chambers, were 720 and 513 g C m−2, respectively, in 2006, an increase of 50 and 125 g C m−2 over the corresponding values in 2005. While both photosynthesis and respiration rates were higher in the warmer and drier conditions of 2006, the increase in respiration was more than twice the increase in photosynthesis.