Geologically, coral reefs are classified into three main types. Fringing reefs are coral platforms that are more or less continuous with the shore and exposed at low tide. Barrier reefs are separated from the shore by a wide, deep lagoon or surround a lagoon that has a central island. An atoll is a reef surrounding a lagoon that has no central island, with passages through the reef to the sea. It is generally believed that fringing reefs formed as a result of upward and outward growth of corals that became established on rocks near shore; there is disagreement about the nature of barrier reef and atoll formation. Charles Darwin postulated a progression from fringing reef to barrier reef to atoll, as a result of a slow, steady sinking of the seafloor that creates a lagoon and a simultaneous upward and outward growth of coral. Where entire volcanic islands sink, only the reef remains above water, forming an atoll. Not all scientists accept Darwin's proposal, but most current theories involve subsidence of the seafloor, although changes of the ocean level may also be involved.

Sediments accumulate on the lagoon side of atolls and support vegetation; in time the entire lagoon may fill, creating an island. Many such atolls and islands, common in the Pacific and Indian oceans, are inhabited. The Great Barrier Reef of NE Australia is the largest known complex of coral reefs. It is 10 to 90 mi (16–145 km) wide and about 1250 mi (2010 km) long, and is separated from the shore by a lagoon 10 to 150 mi (16–240 km) wide.

Reefs are under numerous environmental pressures, including damage from increased coastal development, water pollution, tourism, runoff containing agricultural chemicals, abrasion by ships' hulls and anchors, and smothering by upstream sedimentation. Coral reefs are sometimes destroyed in fishing when poison or dynamite are used to catch fish and by the harvesting of coral for use in jewelry. During the 1990s, many previously unknown diseases began attacking coral reefs worldwide, causing rapidly spreading damage.