Cuba is the largest of the Caribbean islands, with a long, complex coastline and considerable chains of offshore islands and coral cays. Coral reefs stretch along virtually the entire border of the Cuban shelf. The majority of these lie offshore in long tracts which resemble barrier reefs, separated from the main island by broad lagoons. The longest runs for some 400 kilometers along the north coast from the Archipiélago de Sabana to the Archipiélago de Camaguey. On the south coast a similar reef tract stretches for over 350 kilometers from Trinidad to Cabo Cruz. Unlike true barrier reefs, the lagoons behind these reef tracts are very shallow. In most cases these wide lagoons, together with the long archipelagos of small coral cays which lie on their outer edges, have protected the reefs from adverse anthropogenic impacts. Hurricanes are more frequent in the south and west where the reef communities are dominated by species resistant to sedimentation and water movement, especially in the Gulf of Batabanó.

Only short stretches of coast have been heavily urbanized or industrialized. For these reasons, pollution tends to be localized: less than 3 percent of reefs in Cuba are believed to be affected by a significant degree of organic pollution. Many of the reefs appear to have shown a general increase in algal cover, probably associated with the Diadema die-off which has affected the rest of the region. Populations of the urchin in Cuba show no signs of recovery, so algal species such as Cladophora catenata, Microdictyon marinum, Lobophora variegata, Dictyota spp., Sargassum spp. and Halimeda spp. achieve biomass figures as high as 3 kilos per square meter. This occurs on reefs which are far from sources of organic pollution and may indicate that the changes are part of the Caribbean-wide impacts of Diadema die-off and loss of Acropora spp. to disease, rather than a result of direct anthropogenic impacts. In terms of reef fish, Cuban populations have higher biomass, species richness and average size than many other countries in the region, but these parameters were declining in the 1980s and 1990s due to overfishing. In 1998, coral bleaching was reported to have been severe on all coasts, although bleaching-related mortality was low.

Levels of sewage, organic and inorganic pollution are high in Havana Bay and this has caused the diversity of scleractinians, sponges and gorgonians to decline severely. These reefs are now dominated by just a few species of scleractinian corals, mainly Siderastrea radians, by the sponges Clathria venosa and Iotrochota birotulata, and by the gorgonians Plexaura homomalla, P. flexuosa or Pseudoplexaura spp.

The Cuban government announced in 1995 that gross domestic product had declined by 35 percent during 1989-93, a decline closely related to the loss of aid from the former USSR and economic sanctions imposed by the USA. Although there has been some economic growth since then, living standards remain at a depressed level compared with 1990. Fluctuations in the price of nickel and sugar have compelled the state to open up areas for tourism development, and this industry now plays a key role in generating foreign currency earnings. However, regulations for the protection of coral reefs directed at both tourists and tour guides are not yet fully implemented. Physical damage and the extraction of stony corals and other organisms are degrading the reefs in some tourist areas, such as the reefs of Rincón de Guanabo and Puerto Escondido to the northeast of Havana Province. The effects of coastal construction are generally unmonitored. At the end of the 1990s the tourist industry largely catered for the European market, but enormous expansion is to be expected if the political situation between Cuba and the USA changes.

Within the southeastern province of Guantánamo there is a large US Naval Base, covering some 114 square kilometers along the sheltered coast of Guantánamo Bay. Although not under US sovereignty, the lease of the base area is held until the US government agrees to relinquish it. The area includes considerable military developments and associated recreational facilities, and much of the bay area has been dredged and degraded. Despite this, there are some coral communities, and recreational diving is practiced by personnel. The beach and waters of Cuzco Beach have been declared a preserve, dredging is prohibited and visitor numbers restricted.