Coral reefs are widespread around all of the main islands. These are mostly fringing reefs, but there is a small barrier reef off St. Croix, and there are a number of offshore patch reefs and bank structures.

Nowhere else in the Caribbean have the combined effects of hurricanes and disease on coral reef population structure been more pronounced than in the US Virgin Islands. In 1976 live coral cover on the fore reef at Buck Island, dominated by Acropora palmata, was 85 percent. Since then, eight hurricanes have caused serious physical damage to these reefs. Hurricane Hugo, in 1989, was undoubtedly the most severe, but in 1995 Hurricanes Luis and Marilyn hit the islands within a ten-day period and caused extensive damage in some areas. Others were less affected, either because of the uneven impacts of the storms themselves or because there was so little coral remaining to be damaged. White band disease has also greatly impacted the region and killed many acroporid corals, with as many as 64 percent of all colonies being affected. Other diseases have also hit less abundant species in the Virgin Islands, such as Agaricia agaricites and Stephanocoenia michelinii. The situation in St. John is similar, with 80 percent of Acropora palmata colonies in Hawksnest Bay being lost in just seven months. Coral cover around St. John was about 30 percent before Hurricane Hugo reduced it to some 8-18 percent. In Lameshur Bay the dominant coral, Montastrea annularis, declined by about 35 percent and there has been no substantial recovery even though coral recruitment is occurring. Despite extensive bleaching in 1998, there was little associated mortality.

Tourism is the islands’ primary economic activity, accounting for more than 70 percent of gross domestic product and 70 percent of employment. Damage to reefs associated with tourism and recreation includes significant harm caused by boat anchors and ship groundings. The Virgin Islands National Park on St. John attracts a million visitors a year, mostly arriving on cruiseships or smaller boats, and an estimated 30 000 anchors are dropped in a single year. In 1989 the cruiseship Windspirit destroyed some 300 square meters of reef with its anchor and chain and there has been little recovery since. This resulted in the successful prosecution of the boat owners by the park authorities, and remains one of the few examples of such action for damages incurred to coral reefs. Direct damage by divers and snorkellers has also been recorded at the most heavily used sites. Mooring buoys were installed following a survey which found that 33 percent of boats anchored in seagrass beds and 14 percent on coral reefs. Unfortunately, there is now little coral left to protect and no limits have been set on the size of vessels allowed in park waters.

Overfishing is widespread throughout the islands, even within protected areas. This is further exacerbated by the widespread loss of fish habitats, including seagrass and mangrove areas, such that fish stocks are highly depleted in most areas.

Other threats to the reefs include sedimentation, land clearance, coastal development and sewage discharge (the eutrophication of some reefs in the Virgin Islands has been attributed to leaching from septic tanks during heavy rain). One of the world’s largest petroleum refineries is at St. Croix, which also represents a significant potential threat to reefs as well as other ecosystems. In 1999 a Marine Conservation District was declared to the southwest of St. Thomas, in cooperation with fishers, divers and local and federal government. Known as Hind Bank, the area is closed to all fishing and anchoring, and represents an important step towards more comprehensive fisheries management.