Canadian and US federal wildlife agencies completed three surveys (1976–1980, 1989–1991, and 1997–2000) to census colonial waterbirds breeding on the Great Lakes. We here summarize and comment on nest numbers and colony site distribution of common terns (Sterna hirundo) and Caspian terns (Hydroprogne caspia). Common terns are in serious trouble on the Great Lakes. Numbers declined with substantial losses in nests (-19.1%) and colony sites (-23.2%) between the first and third censuses. An increase in numbers at US sites ( 26.6%) did not compensate for losses (-33.1%) at Canadian sites. Caspian terns increased in nest numbers ( 65.9%) and colony sites ( 50.0%) over the same period. The increase at US sites (136.5%) was greater than at Canadian sites (11.5%). Most (70.7%, n = 186) common tern sites had nests during only one census; 17 sites (6.5%) had nests during all censuses. In contrast, 9 of 33 (27.2%) Caspian tern sites had nests during all censuses and contained a majority of nests (50–82%) in each census. Pairs of both species nested on natural substrates across the Great Lakes. Common terns nested mostly on artificial (human-constructed) substrates on the lower Great Lakes. We identify site characteristics that may have contributed to long-term (three census) occupancy by common terns (small size, artificial substrates, absence of ring-billed gulls) and Caspian terns (natural substrates on large, remote islands). We suggest an urgent need for protection and conservation of common tern colonies and identify specific priority sites for implementation of management protocols.