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 protection experienced quick-moving currents that efficiently flushed away sediment, protecting the reef, while the other was subjected to currents and wave conditions that allowed sediment to be continuously re-suspended in the water, starving the reef of light. The vast biodiversity of coral reefs consequently create an abundant fishing area for locals. This leads to overfishing of reef herbivore organisms which makes the coral reefs more vulnerable and unable to recover from large environmental disturbances. Unfortunately, most marine ecologists expect future oceans to be more overfished than now. It is difficult to create a substantial plan for the protection of coral reefs