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 fish regions, the richest by far in terms of reef fish diversity is the Indo-Pacific where there are an estimated 4,000–5,000 species of fishes associated with coral reef habitats. Another 500–700 species can be found in the greater Caribbean region. Most reef fishes have body shapes that are different from open water fishes. Open water fish are usually built for speed in the open sea, streamlined like torpedoes to minimise friction as they move through the water. Reef fish are operating in the relatively confined spaces and complex underwater landscapes of coral reefs. For this manoeuvrability is more important than straight