In subarctic waters winter may be the period during which seabirds face the greatest environmental and physiological pressures, yet seabird distribution during this time is poorly understood. Using at-sea surveys conducted in Prince William Sound, Alaska on research ‘ships of opportunity’ from November 2007 to March 2009, we investigated how seabird abundance and distribution vary within and between winters for three common seabird species with extensive ranges: common murre (Uria aalge), marbled murrelet (Brachyramphus marmoratus), and black-legged kittiwake (Rissa tridactyla). Due to a large proportion of zeros in the survey data, hurdle models were performed using generalized additive mixed models. Across the two winters, consistent temporal patterns in density and distribution were observed for all species. Common murre and marbled murrelet both increased in number in midwinter, while black-legged kittiwake decreased to very low numbers. Habitat association models revealed that common murre favored relatively protected waters while marbled murrelet favored inside bays and passages (which make up 45% of semi-protected waters) and areas of higher sea surface temperatures. Our results suggest that winter storms influenced seabird distribution, particularly in midwinter when temperatures were lowest and storms more frequent. This influence was greater than variables providing proxies for foraging opportunities, which were absent from selected models. Our study highlights the importance of considering species-specific temporal patterns throughout the non-breeding season to guide marine spatial planning that will fully address seabird conservation issues.