The park consists of four primary ecosystems:
- A fringe of mangrove forest along the mainland shoreline
- The southern expanse of Biscayne Bay
- The northernmost Florida keys
- A portion of the third largest coral reef in the world
Each ecosystem includes a variety of smaller communities; seagrass meadows, hardbottom areas and hardwood hammocks. Geological influences include changing sea levels, currents, hurricanes and reef building organisms like corals. The subtropical climate of South Florida includes forests that are more typical of the Caribbean than of North America. Click on the topics at the top of the page to learn more about some of the natural features of the park.