The main island of Puerto Rico and its five smaller islands are the smallest and easternmost in the Greater Antilles. Puerto Rico has an estimated coastline of 930 km and a land area of 8,950 sq km. Corals grow throughout most of the insular shelf along the northeast, east, and southern coastlines, yet the physical, climatic and oceanographic conditions that affect reef development vary markedly among insular shelf segments.  Fringing coral reefs are by far the most common.  A recent mapping by US NOAA of most waters in the Commonwealth (excluding Monito Island) down to a depth of 65 ft (20 m) identified a coral reef ecosystem of over 5,000 sq km, of which coral reef and colonized hard-bottom habitat comprise about 756 sq km or 15 percent of the total reef ecosystem. Puerto Rican coral reefs are the richest in the US Caribbean,  with 43 hard coral species identified.  Reefs near Descheo Island are probably the best-developed and healthiest in Puerto Rico, with about 70 percent coral cover and very clear water. 
Overall, 93 percent of Puerto Rico’s reefs were rated as threatened in the Reefs at Risk analysis, with 84 percent at high risk and therefore among the most threatened in the Caribbean. The predicted overfishing threatens almost all of Puerto Rico’s coral reefs. Puerto Rican reef catches have plummeted during the last two decades and show the classic signs of overfishing.  Fish landings reported between 1979 and 1990 fell 69 percent.  The decline in the abundance of large fish and the massive region-wide mortality of the long-spined urchin represent a major shift in community structure on Puerto Rican reefs. In addition, spiny lobster is overfished, resulting in increases in coral-eating mollusks and more damage to coral. 
Watershed-based sources threaten about two-thirds of the commonwealth’s reefs. Coastal-development-related pressures threaten more than 50 percent of Puerto Rican coral reefs, compounded by rapid urban and industrial development over the past 40 years.  Both the permanent population and the tourist traffic have grown rapidly,  and nearly 60 percent of the people live within 10 km of the coast. Massive macroalgal cover on the nearshore reefs, first observed in the 1970’s, continues to kill corals. This is indicative of eutrophication from sewage and urban outfalls, and low populations of algal grazing fishes.  High sediment inputs and increased turbidity have degraded water quality around all the reefs off Puerto Rico’s southern coast.  In the west, three rivers deliver excessive sediments and nutrients from agriculture and tuna canneries onto nearshore reefs.  Marine-based threats jeopardize an estimated 30 percent of those reefs.
Military (bombing) activities at Vieques and Culebra Islands are significant threats not included in the analysis.  The US Navy has operated a training facility on Vieques since 1941. Over the years, bombing practice has caused severe destruction of coral reef fisheries and reef frameworks. 
Most common diseases (including white band, black band, yellow-blotch, white plagues I &II, and aspergillosis)  have been observed on the degraded reefs surrounding the main island and have caused considerable damage down to a depth of 30 m.  Branching elkhorn and staghorn corals have declined in most places over the past 25 years as a result of hurricane damage, white band disease, and coral-eating mollusks.  Elevated sea surface temperatures caused massive coral bleaching and mortality in the late 1980’s.  However, a major coral bleaching event in 1998 resulted in very little mortality.  About 30 hurricanes have passed within 40 km of San Juan since 1940.  Physical damage to reefs from hurricanes and tropical storms has been most severe on the eastern coast, primarily affecting the shallow reefs.
Inadequate attention has been paid to protecting and managing the reef resources.  Puerto Rico has designated a series of natural reserves and no-take zones to protect important coastal and marine resources, but they remain essentially paper parks. Natural Reserves are under the jurisdiction of the government, but they bring only a minor degree of protection to coral reefs, and effective management is limited by lack of laws regulating fishing activities and recreation. 
 J.R. Garcia et al., “Puerto Rican Reefs ,” in Latin American Coral Reefs. J. Cort