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 been observed to be high temperature-tolerant, and has a higher rate of survival than clades B and C during modern bleaching events. Reefs grow as polyps and other organisms deposit calcium carbonate, the basis of coral, as a skeletal structure beneath and around themselves, pushing the coral head's top upwards and outwards. Waves, grazing fish (such as parrotfish), sea urchins, sponges and other forces and organisms act as bioeroders, breaking down coral skeletons into fragments that settle into spaces in the reef structure or form sandy bottoms in associated reef lagoons. Typical shapes for coral species are named by their