Globally, seabirds are vulnerable to anthropogenic threats both at sea and on land. Seabirds typically nest colonially and show strong site fidelity; therefore, conservation strategies could benefit from an understanding of the population dynamics and vulnerability of breeding colonies to climate change. More than 350 atolls exist across the Pacific Ocean; while they provide nesting habitat for many seabirds, they are also vulnerable to sea-level rise. We used French Frigate Shoals, the largest atoll in the Hawaiian Archipelago, as a case study to explore seabird colony dynamics and the potential consequences of sea-level rise. We compiled a unique combination of data sets: historical observations of islands and seabirds, a 30-year time series of population abundance, LiDAR- (light detection and ranging) derived elevations, and satellite imagery. To model population dynamics for ten species at Tern Island from 1980 to 2009, we used the Gompertz model with parameters for the population growth rate, density dependence, process variation, and observation error. We used a Bayesian approach to estimate the parameters. All species increased in a pattern that provided evidence of density dependence. Density dependence may exacerbate the consequences of sea-level rise on seabirds because species that are already near the carrying capacity of the nesting habitat will be limited more than species that still have space for population growth. Laysan Albatross (Phoebastria immutabilis), Great Frigatebird (Fregata minor), Red-tailed Tropicbird (Phaethon rubricauda), Masked Booby (Sula dactylatra), Gray-backed Tern (Onychoprion lunatus), and White Tern (Gygis alba) are likely already at carrying capacity at Tern Island and therefore are most likely to be negatively impacted by sea-level rise. We project 12% of French Frigate Shoals (excluding La Perouse Pinnacle) will be inundated with +1.0 m sea-level rise or 32% with +2.0 m. Gray-backed Terns that nest along the coastal perimeters of islands and shrub-nesting species that are habitat limited are especially vulnerable to sea-level rise. However, at Tern Island, seawalls and habitat creation may mitigate projected seabird population declines due to habitat loss. We predict substantial losses in seabird nesting habitat across the low-lying Hawaiian Islands by 2100 and emphasize the need to restore higher elevation seabird colonies.