Sea level rise from anthropogenic climate change threatens waterbird species worldwide. In New Jersey, USA, one such waterbird, the Black Skimmer (Rynchops niger), uses both salt marsh islands and beaches for nesting colony sites. Both habitats vary in flood risk, with salt marsh islands typically being more vulnerable especially in the face of sea level rise. Given that sea level has increased in the mid-Atlantic region over the past four decades, we hypothesized that Black Skimmers have shifted their colonies from salt marshes to beaches, and that this change has led to an increase in coexistence with Least Terns (Sternula antillarum). We analyzed 44 years of seabird population census data from New Jersey and found that the probability that a Black Skimmer colony was located on a salt marsh island, as opposed to a beach, significantly declined over the survey period. Additionally, the probability of coexistence with Least Terns significantly increased. Such climate change driven population shifts of endangered species may have significant consequences for their conservation in human modified systems where habitat is already limiting.