North Keeling Island is entirely surrounded by a broken, irregular fringing reef, except at the north-west corner. The reef is narrower on the sheltered sides of the island (north and west), and broader on the exposed sides (south and east). On the east coast it is continuous across the mouth of the lagoon, and forms a wide bar which effectively blocks the entrance. Much of the reef is partly exposed at low tide. Along the western side of the island is a wide coral terrace which drops into deep water. The marine reserve extends 1.5km offshore from the park.
There are three major marine habitat types represented: outer reef slope (subtidal); reef flats including sandy and rocky shores (predominantly intertidal); and lagoon (predominantly subtidal).
The Cocos (Keeling) atolls represent the western limit for many species of the Western Pacific biogeographic province. Biogeographic and ecological interest in the marine biota also stems from the extreme isolation and relatively small size of the atolls, from which there are some unusual absences including benthic skates and rays. Those species established on the islands must be pelagic as adults or have long-lived pelagic larvae. In recent times periodical large-scale natural disturbances including outbreaks of Crown of Thorns starfish (Acanthaster planci), cyclones and deoxygenation of lagoon waters tentatively linked to El Niño events have also reduced the abundance of corals.
Reef-building corals of the southern atoll have received considerable attention, partly because the atoll was the only one ever visited by Darwin (in 1836), and partly because of the intrinsic interest in the atoll's geographic isolation. The primary interest in Cocos (Keeling) corals relates to the atoll's isolation. It is 880 km and 1,830 km from the reefs of Java and Western Australia respectively, with Christmas Island being the only 'stepping stone' for westerly movement of propagules (Berry 1989). Many common and widespread Indo-Pacific taxa have not been recorded from Cocos (Keeling) and are almost certainly absent. Ninety-nine species of reef corals are recorded from the Cocos (Keeling) Islands. Of these, all but twelve are known from Western Australia. Nine species are not recorded elsewhere in the eastern Indian Ocean and two (one being taxonomically doubtful) are possibly endemic (Veron 1990).
About 528 species of fish have been recorded from the islands (Berry 1989). Compared with other oceanic atolls, the fish fauna is impoverished (Allen 1989). Most fish found at Cocos (Keeling) have distributions that cover large areas of the Indo-Pacific region (Allen 1989). There is no endemism in the Cocos (Keeling) fish fauna, although one angelfish (Centropyge joculator) is known only from Cocos (Keeling) and Christmas Island and an undescribed goby of the genus Trimma may have the same distribution (Allen and Smith-Vaniz 1994).
There are no known cetaceans that are restricted to Pulu Keeling National Park, but two species of dolphin are regularly seen in the park. They are the Common dolphin (Delphinus delphis) and the Bottlenose dolphin (Tursiops truncatus). A dugong has been sighted by residents a number of times over a few years in the lagoon of the southern atoll but it is unlikely that there is a resident population.
Nesting green turtles (Chelonia mydas) nest on the island and hawksbill turtles (Eretmochelys imbricata) inhabit the waters of the park. The only species of sea snake recorded from the southern atoll is the yellow-bellied sea-snake (Pelamis platurus).
610 species of molluscs are known from the Cocos (Keeling) Islands. There are 496 gastropods, 109 bivalves, one chiton and four cephalopods.
A total of 198 species of decapod crustaceans and three species of rock lobster have been recorded. A total of 13 species of barnacles in 11 genera have also been recorded from the area.
89 species of echinoderms have been recorded, most being widespread Indo-West Pacific species. The Cocos (Keeling) Islands have a fairly rich fauna of holothurians, including most of the species also known as trepang (Beche-de-mer).