Reefs almost completely surround southern Guam. They are cut by numerous bays at the mouths of the large permanent streams that drain volcanic uplands. Reefs in southern Guam are extremely diverse environments and consist of many distinct habitats.

Reef flats are relatively flat platforms that extend from the shoreline to the wave-washed reef margin. They can be from just a few meters to over a kilometer wide. Some reef flats are intertidal and nearly completely exposed during low tides. Others have deeper areas known as "moats", which retain water at all times. The reef flat zone can be covered by algal pavement, sea grass beds, staghorn (Acropora) thickets, Porites microatolls, fields of sand and rubble, and macroalgae.

Reef margin is the edge of a fringing reef, where the waves crash against the reef. They are almost always washed with surf and support encrusting algae and other tough organisms that can resist constant wave action.

The area extending seaward from the reef margin is known as the reef front. Coral communities in this zone are directly related to the level and frequency of wave action. Areas protected from severe waves usually have gentle slopes with tabular or branching corals. Areas with more wave action are steeper and dominated by lower, stout branched corals. The most typical feature of this zone are alternative ridges and vertical sides channels known as "spur and grooove" formations.

Slopes descending from the reef to deep water belong to the outer reef zones. They support various coral communities that remain rich and diverse to depths of 40-60 m.