The refuge is made up of approximately 17 islands consisting of densely forested red and black mangroves with little uplands habitat. Whoopee, Benedict and Patricio islands are the only islands within Pine Island Refuge able to support upland vegetation. This is due to higher elevated upland sand ridges or shell mounds. Several of the islands are important nesting and roosting areas for colonial birds, particularly the brown pelican. Lack of human disturbance increases the importance of these reserved areas for these species.
Racoons are the primary mammal found on the islands, and dolphins can be seen in the area waters.
Small colonies of gopher tortoises may be found on some of the larger islands. Refuge Objectives To protect and provide suitable habitat for endangered and threatened species including the West Indian manatee, wood stork, eastern indigo snake, American crocodile and bald eagle. To implement sound wildlife management techniques to provide feeding, nesting and roosting habitat for a wide diversity of shore birds, wading birds, waterfowl, raptors and neo-tropical migratory species. To provide wildlife-oriented recreation compatible with the purposes for which the refuge was established. Management Tools Law enforcement.