Southeast Alaska provides non-breeding habitat for >300,000 sea ducks, however little is known about habitat features that may influence their distribution within this area. We used an autologistic regression model to examine relationships between 10 species of sea ducks that winter in southeast Alaska [harlequin duck (Histrionicus histrionicus), red breasted merganser (Mergus serrator), common merganser (Mergus merganser), bufflehead (Bucephala albeola), Barrow’s goldeneye (Bucephala islandica), common goldeneye (Bucephala clangula), long-tailed duck (Clangula hyemalis), white winged scoter (Melanitta fusca), surf scoter (Melanitta perspicillata), and black scoter (Melanitta nigra)] and nearshore habitat features. Habitat features that explained sea duck occurrence included shoreline exposure, distance to streams, number of islets, percentage of rocky substrate and intertidal width. Our results suggest certain features that managers could identify during attempts to mitigate the environmental impacts of new development projects or to protect as important habitats.