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 then smother the coral by decreasing the oxygen supply available to the reef. Decreased oxygen levels can slow down calcification rates, weakening the coral and leaving it more susceptible to disease and degradation. Algae inhabit a large percentage of surveyed coral locations. The algal population consists of turf algae, coralline algae and macro algae. Some sea urchins (such as "Diadema antillarum") eat these algae and could thus decrease the risk of algal encroachment. Sponges are essential for the functioning of the coral reef that system. Algae and corals in coral reefs produce organic material. This is filtered through sponges which