The mission of the Florida Coastal Islands Sanctuaries is the protection of the great colonial waterbird populations of the Florida coast, and the natural systems that support them.

The first Audubon Sanctuary in Tampa Bay was established in 1934 to stop the shooting and harvest of nesting herons and ibis at Green Key in Hillsborough Bay. As human population growth and development in the Tampa Bay area have expanded, the wildlife conservation concerns of the Sanctuaries staff have also broadened from the more direct goal of the protection of nesting colonies themselves, to reflect an ecosystem approach. Today, the scope and area of the Florida Coastal Islands Sanctuaries' activities are still increasing to meet the conservation needs of the state's colonial waterbirds.

Colonial waterbirds are birds that nest in groups or colonies, typically on coastal islands. In all, 23 species nest in colonies, with another six species which often nest in or near bird colonies but are not colonial themselves. Twelve of these 29 species are listed by the Wildlife Commission as "endangered", "threatened", or "species of special concern". Three species are targeted by Partners in Flight as WatchList species, in need of conservation.

The Tampa Bay area is home to a population of colonial waterbirds totaling up to 50,000 breeding pairs at nearly 30 sites. Up to half breed in Hillsborough Bay. Some of the rarer species have currently stable or increasing populations locally (Reddish Egret, Roseate Spoonbill, American Oystercatcher), but more common species including those that rely on freshwater foraging areas are declining (Snowy Egret, Little Blue Heron, Tricolored Heron, White Ibis, possibly others).