The double‐crested cormorant (Phalacrocorax auritus) has undergone population expansion throughout much of its historical range since the 1970s, resulting in increased pressure on foraging habitats including real and perceived competition with commercial and sport fisheries and impacts on the aquaculture industry. The specific objectives of this study were to determine the stable isotope ratios of birds wintering at aquaculture facilities and natural freshwater and marine habitats, and to determine what percent of birds at distinct breeding colonies wintered in each of these habitats. We exploited natural variation in isotopic ratios of carbon, nitrogen, and sulfur (from feathers) to determine the winter habitat use (i.e., aquaculture, natural freshwater, or marine) of birds collected on their summer breeding grounds in the eastern United States (from Minnesota to Vermont). The distribution of winter habitat use varied significantly across breeding colonies and between male and female cormorants. More specifically, use of aquaculture winter habitat was most prevalent in birds breeding in Lake Huron and Lake Erie. Overall, aquaculture habitats were used more by males, and marine habitats were used more by females. The stable isotope approach used in this study provided dietary confirmation of previously observed migratory patterns in the double‐crested cormorant. Because aquaculture was primarily used by males, and these males migrated to a broad range of breeding colonies, we suggest that targeting breeding birds to reduce aquaculture depredation is a less efficient strategy than managing birds at depredation sites on the wintering grounds. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.