Two ombrotrophic bogs in Canada's Hudson Bay Lowlands (HBL), an area storing an estimated 33 Gt of soil carbon, are contrasted with the Mer Bleue temperate ombrotrophic bog approximately 1000 km to the southeast to assess the net carbon dioxide (CO₂) exchange between these ecosystems and the atmosphere. Peatlands in the HBL region may be impacted by not only climate change but also resource extraction practices that may cause drying of surrounding areas. Two years of eddy covariance CO₂ flux measurements show the two HBL bogs to be annual sinks for CO₂. Given random error and gap-filling uncertainties of 6 to 13 g C m^-2 yr^-1, the annual budgets of 45 to 55 g C m^-2 yr^-1 for the HBL bogs did not differ significantly from the temperate bog's budget of 55 g C m^-2 yr^-1 (in the first year) despite differences in climate and vegetation composition and abundance. The temperate bog did have significantly greater net uptake of CO₂ (78 g C m^-2 yr^-1) in the second study year. Component fluxes of photosynthesis and respiration were much smaller at the HBL bogs and speculated to be a result of less vascular vegetation. Less growing season CO₂ uptake at the HBL bogs was offset by less winter loss when compared to the temperate bog. The influence of mid-summer drying and lowered water tables was similar among all three bogs. Decreasing mid-summer net ecosystem productivity (NEP) appeared to be a result of reduced photosynthetic uptake rather than increased respiration. In the short-term, drying of the HBL peatlands might result in a decrease of their C sink strength.