Despite the importance of understanding marine bird response to prey fish, few studies have examined this relationship during winter. Over a 5‐year period, we conducted synoptic marine bird and hydroacoustic forage fish surveys during early (November) and late (March) winter to characterize the factors influencing marine bird and forage fish dynamics at two spatial scales (fish school and bay) within subarctic bays of coastal Alaska, USA. Over 40% of observed marine birds were associated with a fish school (within 150 m of a fish school), although only 20% of fish schools were associated with birds. Seasonally, we recorded significantly more schools during early winter. The marine bird community also shifted from being comprised primarily of marbled murrelets (Brachyramphus marmoratus) and large gulls (Larus spp.) in early winter to common murres (Uria aalge) in late winter. At the school level, marine birds were more likely to be associated with shallow fish schools within 500 m of shore and in smaller prey patches. At the bay level, gull abundance was positively associated with the total number of fish schools recorded, while diving birds were more abundant when fish schools were higher in the water column, in shallower bottom depths, and in areas with more eel grass habitat. Our results indicate the importance of temporal, habitat, and fish school variables as drivers of marine bird presence and abundance, underscoring the complexity of predator–prey dynamics in the marine environment during winter.