The ecology of Coral Reefs is very unique from other ecosystems. The lagoon and the reef act very much like a field and a forest edge with different animal in each one. The food web of the coral reef is very complex and is still being discovered. Until recently it was thought that the classic pyramid shape food web was inverted in coral reefs do to the lack of producers (plants).

This was clarified by the discovery of zooxanthellae in the live coral itself as well as in the dead coral skeleton. These algae also grows in the sand and in the shingles of the reef edge. While the zooxanthellae provide most of the nutrition necessary for the coral polyps to live, coral polyps also feed at night on zooplankton. Coral reefs are very dependent on this constant flow of nutrients from the circulation of zooplankton from the "open ocean". It is this flow of nutrients in the form of plankton that is the blood stream or coral reefs.

The constant flow of zooplankton into the coral reefs keeps the corals alive and growing, which keeps the fish alive, which keeps the predators alive. The rest of the ocean is also dependent of the reefs. The dead coral erodes in to calcium carbonate which in turn helps to keep the pH of the water salty, which keeps the marine animals alive. Now we begin to explore the vast interdependence between coral reefs and the surrounding environments. A common myth is that coral reefs are very stable environment, the truth is that coral reefs (much like the other ecosystems in the Everglades) are very fragile.

The sand around a coral reef beaches and coral islands is very unstable and needs to be renewed and replaced constantly. The source of this sand is the broken or chewed skeletons from reef organism that have calcareous skeletons like coral, crabs and coralline algae.

The entire coral reef ecosystem can collapses if the zooxanthellae leave there symbiotic coral polyps. When this happens the coral turns white, often referred to as coral bleaching, because the zooxanthellae give the coral its viverante colors. As mentioned before the symbiotic zooxanthellae provide up to 85% of the nutrients for some coral species, so when the zooxanthellae leave the coral polyps die. When the coral polyps die the fish lose there protective homes and there source of food. This goes on down the food chain effecting every organism in the coral reef.

The coral reef ecosystem in the Florida Keys is also dependent in the health of the Everglades. Many of the fish and crustaceans use the protective branches of mangrove forests to spawn there young. Most of these fish grow up and return to the coral reef to feed on coral and algae. These fish are preyed upon by larger fish, which are preyed upon by the top predators like sharks and eels.