Nares Strait, situated between northwest Greenland and Ellesmere Island is a major sea ice export path from the Arctic Ocean. One of the narrowest parts of the strait --- Kennedy Channel --- is host to several islands. These obstacles' impact on the ice flow along the Strait has yet to be investigated. Here we show that during autumn, these islands can interrupt the relatively homogenous sea ice flow through Kennedy Channel, carried by wind and water currents, and shield downstream regions from becoming ice-covered, resulting in the formation of hitherto unknown transient polynyas, whose size and extent were correlated with the wind's strength and direction along Kennedy Channel. These polynyas likely impact the regional meteorology and oceanography through enhanced air-sea fluxes of heat, moisture, momentum, and carbon dioxide. The presence of open water may also impact the complex and productive regional ecosystem.