Ponds on peatlands of the Hudson Bay lowlands (HBLs) are complex ecosystems in which the fluxes to the atmosphere of CH4 and CO2 were controlled by interacting physical and biological factors. This resulted in strong diel variations of both dissolved gas concentrations and gas fluxes to the atmosphere, necessitating frequent sampling on a 24-hour schedule to enable accurate estimates of daily fluxes. Ponds at three sites on the HBL were constant net sources of CH4 and CO2 to the atmosphere at mean rates of 110--180 mg CH4 m-2d-1 and 3700--11,000 mg CO2 m-2 d-1. Rates peaked in August and September. For CH4 the pond fluxes were 3--30 times higher than adjacent vegetated surfaces. For CO2 the net pond fluxes were similar in magnitude to the vegetated fluxes but the direction of the flux was opposite, toward atmosphere. Even though ponds cover only 8--12% of the HBL area, they accounted for 30% of its total CH4 flux to the atmosphere. There is some circumstantial evidence that the ponds are being formed by decomposition of the underlying peat and that this decomposition is being stimulated by the activity of N2 fixing cyanobacteria that grow in mats at the peat-water interface. The fact that the gas fluxes from the ponds were so different from the surrounding vegetated surfaces means that any change in the ratio of pond to vegetated area, as may occur in response to climate change, would affect the total HBL fluxes.