The coral reefs form the physical and biological basis of the area with over 150 species of hard and soft corals. The park contains over 500 species of reef fish, the Reserve more than double this number. As a result of this biodiversity, the Park is probably one of the best small Parks in the world for sheer variety of fish, whilst the Reserve is regarded by experts as one of the top world diving areas, with whale sharks, manta rays, marlin and sailfish among some of the larger species encountered. Watamu is also a vital turtle breeding area, with an active turtle watch group. Whereas Green and Hawksbill turtles are the primary species, Olive Ridleys, Loggerheads and Leatherback turtles have been occasionally encountered.
Boat tours are readily available in the park, and guided tours are also available.