Foraging habitat use by colonial waterbirds breeding in New York Harbor was examined to identify resources that were particularly important for the provisioning of young. Stable isotope values of carbon, nitrogen, and sulfur were measured in nestling waterbird feathers to determine the habitat type (ranging from marine to freshwater and anthropogenic) in which adults primarily foraged. Six species were investigated: Black-crowned Night-Herons (Nycticorax nycticorax), Great Egrets (Ardea alba), Glossy Ibises (Plegadis falcinellus), Double-crested Cormorants (Phalacrocorax auritus), Great Black-backed Gulls (Larus marinus), and Herring Gulls (L. argentatus). Waterbird populations exhibited both inter- and intra-specific variation in stable isotope values (P < 0.001), indicating variation in foraging habitat use among focal species across the estuary. Therefore, depending on the species-and region-specific conservation goal, management strategies would potentially need to target very different foraging habitats for protection and remediation. For instance, habitat use by Double-crested Cormorants closely reflected available habitat near nesting colonies, while Glossy Ibises used primarily freshwater resources at one colony and marine resources at another, despite the fact that both colonies were located in marine environments. Great Egrets and Double-crested Cormorants both showed significant regional variation in isotopic niche size, and both species of gulls (considered to be generalist scavengers) were found to have isotopic niche sizes reflecting a specialist diet. Stable isotope analysis of nestling feathers provided novel information about the foraging resources that were most important to waterbirds in regions across the harbor.