Between Nov. 1 2007 and Jan. 31 2008, we calculated the air-sea flux of CO2, sensible heat, and water vapor in an Arctic polynya system (Amundsen Gulf, Canada) using eddy covariance equipment deployed on the research icebreaker CCGS Amundsen. During this time period, Amundsen Gulf was a dynamic sea ice environment composed primarily of first year ice with open water coverage varying between 1–14%. In all cases where measurements were influenced by open water we measured CO2 fluxes that were 1–2 orders of magnitude higher than those expected under similar conditions in the open ocean. Fluxes were typically directed toward the water surface with a mean flux of −4.88 μmol m−2 s−1 and a maximum of −27.95 μmol m−2 s−1. One case of rapid outgassing (mean value +2.10 μmol m−2 s−1) was also observed. The consistent patten of enhanced gas exchange over open water allows us to hypothesize that high water-side turbulence is the main cause of these events. Modification of the physical and chemical properties of the surface seawater by cooling and brine rejection may also play a role. A rough calculation using an estimate of open water coverage suggests that the contribution of these events to the annual regional air-sea CO2 exchange budget may make the winter months as important as the open water months. Although high, the uptake of CO2 fits within mixed layer dissolved inorganic carbon budgets derived for the region by other investigators.