Apo Reef two lagoon systems, the north and south lagoons which are bounded by narrow reef platforms. It is a almost triangular northern and southern atoll-like reefs separated by a deep channel that is open to the west. The channel runs east to west from deep with a fine white sand bottom, numerous mounds and patches of branching corals under the deep blue water. The north lagoon is an enclosed triangular coral reef platform partly exposed during low tide. It is relatively shallow with depths of about . While the south lagoon is an inverted triangular coral platform enclosed on two sides
Coral Sea whitetip reef shark ("Triaenodon obesus", 21%), silvertip shark ("Carcharhinus albimarginatus", 10%), tiger shark ("Galeocerdo cuvier", <1%) and great hammerhead ("Sphyrna mokarran", <1%). The interaction rate (free diving) at the Coral Sea reefs ranged from a few to 26 sharks per hour. The rare "Etmopterus dislineatus" shark species is endemic to the central part of the Coral Sea. It has been observed at depths of 590–700 m on or near the continental slope. The coastal areas of the Coral Sea were populated at least 40,000 years ago by prehistoric people descending through the northern islands. Those Aboriginal tribes have been dispersed