Colonially nesting waterbirds transfer large quantities of aquatically derived nutrients into terrestrial systems, potentially altering community and ecosystem structure. Over the past three decades, the Double-crested Cormorant (Phalacrocorax auritus) has undergone rapid population expansion throughout much of its historic range in North America, recolonizing habitats that had not supported colonial waterbirds for decades. Mounting evidence suggests that these populations are degrading the habitats they colonize primarily through the destruction of vegetation and the alteration of soil conditions. The study examined the effects of cormorants and cooccurring long-legged wading bird species including Black-crowned Night-Herons (Nycticorax nycticorax). Great Egrets (Ardea alba) and Snowy Egrets (Egretta thula) on their nesting habitats by observing plant and arthropod community structure as well as soil and leaf litter characteristics at colonized and non-colonized sites on two islands in New York Harbor. Understory plant species richness and total plant cover were reduced, and the arthropod community shifted from primarily plant feeders to primarily carrion and dung feeders beneath cormorant nests in comparison to adjacent non-colonized habitats. On the island where cormorants have been established longer, the colony tended to be denser and larger and was associated with larger ecological impacts on plants, arthropods and soils. Long-legged wading bird colonies and more recently established cormorant colonies were smaller, less dense, and were generally associated with fewer ecological impacts.