From 23 October 2007 to 1 August 2008, we made continuous measurements of sea surface partial pressure of CO2 (pCO2sw) in three regions of the southeastern Beaufort Sea (Canada): the Amundsen Gulf, the Banks Island Shelf, and the Mackenzie Shelf. All three regions are seasonally ice covered, with mobile winter ice and an early spring opening that defines them as polynya regions. Amundsen Gulf was characterized by undersaturated pCO2sw (with respect to the atmosphere) in the late fall, followed by an under-ice increase to near saturation in winter, a return to undersaturation during the spring, and an increase to near saturation in summer. The Banks Island Shelf acted similarly, while the Mackenzie Shelf experienced high supersaturation in the fall, followed by a spring undersaturation and a complex, spatially heterogeneous summer season. None of these patterns are similar to the annual cycle described or proposed for other Arctic polynya regions. We hypothesize that the discrepancy reflects the influence of several previously unconsidered processes including fall phytoplankton blooms, upwelling, winter air-sea gas exchange, the continental shelf pump, spring nutrient limitation, summer surface warming, horizontal advection, and riverine input. In order to properly predict current and future rates of air-sea CO2 exchange in such regions, these processes must be considered on a location-by-location basis.