The distribution and abundance of Yellow-billed Terns (Sternula superciliaris), Large-billed Terns (Phaetusa simplex) and Black Skimmers (Rynchops niger) were estimated, and the effects of habitat features on site occupancy by colonies of these three species nesting in the Anavilhanas Archipelago, Amazonas, Brazil, were examined. Individuals were recorded on beaches during the 2008 and 2009 breeding seasons, with 26 (2008) and 30 (2009) potential nesting beaches (sites) surveyed. In both years, one site included 28% of all the Yellow-billed Terns, while two sites included 65% of all the Large-billed Terns. Site occupancy, the probability that a site is occupied (range ψ;), was moderate to low for all three species, but higher for Yellow-billed Terns (0.58–0.63) than for Large-billed Terns (0.40–0.50) and Black Skimmers (0.23–0.54). Yellow-billed and Large-billed terns and Black Skimmers generally nested on larger beaches on islands that had little vegetative cover and that were exposed to open water, remote from river margins, distant from other islands and closer to large colonies of the same species. Abundance estimates (individuals per breeding season in the archipelago ± SE) in 2009 varied considerably among species (Yellow-billed Terns: 192 individuals ± 1; Large-billed Terns: 80 ± 1; Black Skimmer: 31 ± 1). These results suggest that habitat features that influence breeding site use by Yellow-billed and Large-billed terns and Black Skimmers include physical and vegetation characteristics as well as social attraction. While the probability of site occupancy increased with measures related to beach size and geographical isolation, closeness to large colonies indicates the relevance of social interactions for these species and, as such, the importance of large areas for the occurrence of their colonies.