Many habitat and land use maps, created even in the 1990s, depict the entire coastal fringe of southwest Collier County as solid areas of mangroves. While it is true that mangroves are the predominant wetland in and around the Reserve and the Ten Thousand Islands, the communities of Rookery Bay National Estuarine Research Reserve and its watersheds are a rich and varied mosaic of saltwater, freshwater, and upland ecosystems. There are over 500 plant, 22 mammal, 90 bird, 210 fish, 60 crustacean, and 40 reptile and amphibian species documented in the Reserve.

The plant communities of southwest Florida have been categorized several different ways. Five of these are presented in Davis (1943). Florida Natural Areas Inventory (FNAI) and the contributors to Ecosystems of Florida (Myers and Ewel 1990) have suggested more recent classifications for all of Florida. A classification scheme that is appropriate for a specific reserve, however, needs to meet criteria determined by management issues, scale of management or research, and site-specific structure and function.

This section presents 22 classifications based on pertinent management practices, primarily fire and inundation requirements, and in some instances, susceptibility to exotic plant colonization. The descriptions provided are based on vegetation because this is the easiest recognizable feature. More detailed species lists, for both flora and fauna, are provided, but gaps in completeness exist. These descriptions have been tailored to specific findings in the RBNERR communities representative of each class where available.