The Great Lakes form the largest freshwater island system in the world and provide breeding habitat for a large proportion of the continental population of double-crested cormorants (Phalacrocorax auritus). Here, cormorants have a high profile due to conflicts with humans; by 2007, most active (64%) breeding sites in U.S. waters were managed. This study used data from the U.S. Great Lakes Colonial Waterbird Database and The Nature Conservancy's Great Lakes Island GIS database to identify important features of breeding sites in the U.S. Great Lakes and broaden understanding of cormorant presence at the island-landscape scale. Islands 0.5–10 ha were used more frequently than expected, and most sites had remoteness values of ≤3km. Colony size was positively correlated with years occupied and large colonies (>1000 pairs) developed primarily (95%) on island sites >1.0 ha. Sites supporting large colonies were more remote than those supporting smaller colonies. Presence of other colonial waterbird species, especially Herring Gulls (Larus argentatus), also characterized cormorant sites. Islands used by cormorants comprised a small proportion (n = 90, 3%) of the U.S. Great Lakes island resource, and <1% of the total island area. Certain characteristics of breeding sites (e.g., small islands, proximity to mainland) may increase negative attitudes about cormorants. To understand cormorant impacts to island resources (e.g., vegetation; other colonial waterbird species), we suggest cormorant presence in the Great Lakes be considered in the broader context of island science, conservation and known threats, and at a landscape scale.