The Gulf of Panama is a highly productive marine ecosystem at the southern edge of North America. Although the Gulf’s aquatic bird populations have been remarked upon by ornithologists for over 50 years, nesting populations have been neither systematically studied nor completely characterized. In 2005 and 2006, the entire Gulf of Panama was inventoried to document the nesting status of seabirds and other colonial waterbirds. Over 50,000 birds of 20 species nesting at 57 sites were documented. Seabirds nested during the dry season, the period of oceanographic upwelling. Coastal colonial waterbirds nested at the end of the dry season and in the early wet season, when inland feeding habitats were optimal. Brown Pelicans (Pelecanus occidentalis) were the most numerous seabird with over 4,800 nests and 10,000 individuals counted. Over 3,600 Neotropic Cormorant (Phalacrocorax brasilianus) nests and over 2,200 Magnificent Frigatebird (Fregata magnificens) nests were documented. Cattle Egrets (Bubulcus ibis) were the most abundant colonial wading birds, followed by Great Egrets (Ardea alba). Great Egrets were the first wading birds to nest, Cattle Egrets the last. Seven sites contained over 1,000 nests. Colony locations and numbers differed markedly from the historic literature. Some historic information is erroneous, but other differences reflect changes in distribution. More nesting Brown Pelicans and Sooty Terns (Sterna fuscata) and fewer Neotropic Cormorants were found than expected from the literature. New sites documented included some of global or regional conservation importance. This paper presents the first breeding records for Panama of Little Blue Heron (Egretta caerulea), Glossy Ibis (Plegadis falcinellus), and Bridled Tern (Sterna anaethetus), and third record for Cocoi Heron (Ardea cocoi). There is no evidence for long-term declines of seabirds or colonial wading birds in the Gulf of Panama. Populations reaching conservation thresholds globally or biogeographically include Brown Pelican, Bare-throated Tiger-Heron (Tigrisoma mexicanum), White Ibis (Eudocimus albus), Glossy Ibis, and Bridled Tern. The Black-crowned Night-Heron (Nycticorax nycticorax) exceeded conservation thresholds for Central America. Six new sites of global importance for bird conservation were identified and the continued importance of another site confirmed. The continued health of the waterbird populations of Panama will depend on environmental education and protection of important colony sites from disturbance and development.