Long‐distance migration presents complex conservation challenges, and migratory species often experience shortfalls in conservation due to the difficulty of identifying important locations and resources throughout the annual cycle. In order to prioritize habitats for conservation of migratory wildlife, it is necessary to understand how habitat needs change throughout the annual cycle, as well as to identify key habitat sites and features that concentrate large numbers of individuals and species. Among long‐distance migrants, sea ducks have particularly complex migratory patterns, which often include distinct post‐breeding molt sites as well as breeding, staging and wintering locations. Using a large set of individual tracking data (n = 476 individuals) from five species of sea ducks in eastern North America, we evaluated multi‐species habitat suitability and partitioning across the breeding, post‐breeding migration and molt, wintering and pre‐breeding migration seasons. During breeding, species generally occupied distinct habitat areas, with the highest levels of multi‐species overlap occurring in the Barrenlands west of Hudson Bay. Species generally preferred flatter areas closer to lakes with lower maximum temperatures relative to average conditions, but varied in distance to shore, elevation and precipitation. During non‐breeding, species overlapped extensively during winter but diverged during migration. All species preferred shallow‐water, nearshore habitats with high productivity, but varied in their relationships to salinity, temperature and bottom slope. Sea ducks selected most strongly for preferred habitats during post‐breeding migration, with high partitioning among species; however, both selection and partitioning were weaker during pre‐breeding migration. The addition of tidal current velocity, aquatic vegetation presence and bottom substrate improved non‐breeding habitat models where available. Our results highlight the utility of multi‐species, annual‐cycle habitat assessments in identifying key habitat features and periods of vulnerability in order to optimize conservation strategies for migratory wildlife.