Legends hold that sea monsters inhabit the Blue Hole. To date, no sea monsters have been discovered, but many forms are known to inhabit the area. The Blue Hole is home to many marine creatures, including sharks, tuna, barracuda, rays, sand sharks, and remora. The fish of the Blue Hole prefer depths above 250 feet, and below this level are basically nonexistent. Sponges, coral, and sea fans encircle the Blue Hole, covering the upper 10-12 feet of the vertical wall near the surface, with the exception of 65-foot gaps on the North and East sides. They also thrive in the shallow areas surrounding the Blue Hole.

The coral reef environment surpasses all others in terms of diversity and fragility. The complex interrelationships among the different species mandate that the utmost caution be observed when implementing any changes in the areas within and around it.

When discussing coral reef health, one of the vital concerns is prevention and containment of epizootics, epidemics in animal populations. Examples of these are the band diseases. The presence of any of these diseases is a harbinger of death to the coral, and then to the inhabitants, resulting in calamity for the reef system as a whole. Bacteria, fungi, and cyanobacteria cause some diseases in coral, but the causes of many diseases remain a mystery. The exact causes of the band diseases and coral bleaching are unknown, but it is known that human pollution is a major factor.

Ships and land-based pollution are the main threats to reefs. Ships with iron hulls and improperly disposed ballast water are two common sources of eutrophication, or nutrient pollution. Nutrient pollution is beneficial to sponges and algae, but detrimental to coral acclimated to a "nutrient desert" environment. As one man's loss is another's gain so too is this growth of algae. The algae blocks sunlight from the surface, causing lowered immune systems in coral. Land based pollution encompasses many harmful activities, the most dangerous being sedimentation.

Coral's optimal environmental temperature is 26-28 degrees Celcius, but as most corals exist near the upper end of this scale, care must be taken not to generate much thermal pollution. Phosphates pose a similar danger to coral, shutting down calcification and henc growth.

While some research has been made into ways to treat coral diseases, they have so far been restricted to the laboratory. The antibiotic chloramphenical has successfully treated some captive corals at Waikiki Aquarium, but its applicability to the reef at large is doubtful.

As for diseases that humans can contract as a result of their interaction with the reef, there is ciguatera, a fish poison, which turns up in the larger reef fish such as amberjack, mackerel, sea bass, snapper, and grouper, which then turn up on dinner tables.

Quiet water areas around reeds are mantled with soft sediment, and turtle grass often surrounds patch reefs in the Caribbean.

Reefs have extremely complex food chains. For example, corals obtain energy from photosynthesis and plankton. Fish graze on coral, converting it into sand. Big fish eats little fish that eats tiny fish, and the chain goes on.

Reef animals are sensitive to noise and light. There is a distinct change between the night and day activities, as most of the species can be divided into nocturnal or day-creatures.

Reefs are built by the secretion of calcium carbonate, building up over many years to reflect changes in surroundings, organisms, climate, and more, becoming nature's history tome (think tree rings). There are five main categories of reef organisms, constructors, binders, bafflers, destroyers, and dwellers.