The ecosys model was applied to examine the effects of peatland hydrology on soil respiration and ecosystem respiration at Mer Bleue peatland, Ontario, Canada. It was hypothesized that a decrease in near-surface microbial respiration in peat hummocks resulting from water table (WT) drawdown and subsequent desiccation of the uppermost peat would offset an increase of soil respiration at depth with improved aeration (respiration offsetting mechanism). In contrast, shallower water table in hollows would not allow near-surface desiccation to offset increased soil respiration at depth during drying. However, increased hollow soil respiration with WT drawdown would be offset by decreased aboveground moss respiration with near-surface desiccation in hummocks. Model results for microbial respiration were tested against independent laboratory experiments and ecosystem respiration against hourly eddy-covariance measurements of bog CO2 exchange from 2000 to 2004. The respiration offsetting mechanism modeled in hummocks resulted in CO2 production of 0.85 μmol CO2 m−2 s−1 with both low (67 cm) and intermediate (38 cm) water tables in the summers of 2001 and 2004, and of 0.81 μmol CO2 m−2 s−1 and 0.95 μmol CO2 m−2 s−1 with high (31 cm) and intermediate (41 cm) water tables in the summers of 2000 and 2001. Ecosystem respiration was 2.01 μmol CO2 m−2 s−1 and 2.23 μmol CO2 m−2 s−1, and 2.62 μmol CO2 m−2 s−1 and 2.58 μmol CO2 m−2 s−1, respectively, during these periods. Our results suggest that ecosystem respiration at Mer Bleue varied little with water table, but this behavior may not be typical for other peatlands.