Wide-ranging marine birds rely on multiple habitats for wintering, breeding, and migrating, and their conservation may be dependent on protecting networks of key areas. Urbanized estuaries are critical wintering and stopover areas for many declining sea ducks in North America; however, conservation measures within estuaries are difficult to establish given lack of knowledge about habitat use by these species and the variety of competing human interests. We applied hierarchical modeling to evaluate resource selection of sea ducks (surf scoters, Melanitta perspicillata) wintering in San Francisco Bay, California, USA, a large and highly urbanized estuary. We also examined their distribution, home range, and movements with respect to key habitat features and regions within the estuary. Herring roe was the strongest predictor of bird locations; however, eelgrass, water depth and salinity were also highly-ranked, with sea ducks using deeper areas of higher salinity associated with herring roe and eelgrass presence during mid-winter. Sea ducks were also strongly associated with ferry routes, suggesting these areas may contain resources that are too important to avoid and emphasizing the need to better understand water traffic effects. Movements and home range size differed between males and females in early winter but became more similar in late winter. Birds traveled farther and used several sub-bays in early winter compared to mid-winter when herring roe availability peaked in the Central Bay. Our findings identified key environmental variables, highlighted core use areas, and documented critical periods for consideration when developing conservation plans for sea ducks in urbanized estuaries.