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 reef sea grass and use the reefs for protection or breeding. Reefs are home to a variety of animals, including fish, seabirds, sponges, cnidarians (which includes some types of corals and jellyfish), worms, crustaceans (including shrimp, cleaner shrimp, spiny lobsters and crabs), mollusks (including cephalopods), echinoderms (including starfish, sea urchins and sea cucumbers), sea squirts, sea turtles and sea snakes. Aside from humans, mammals are rare on coral reefs, with visiting cetaceans such as dolphins the main exception. A few species feed directly on corals, while others graze on algae on the reef. Reef biomass is positively related to species diversity.