The marine habitat surrounding Vieques Island consists of mangrove wetlands (wetlands dominated by mangrove trees), sea grass beds, and coral reefs.  The mangrove wetlands, which form along the bays and lagoons of the island in areas where wave action is minimal, are present on both the eastern and western portions of the island, including at Kiani Lagoon, Mosquito Bay, Playa Grande Lagoon, and Barracuda Bay. Mangrove wetlands and coastal lagoons provide protected nursery areas for juvenile fishes and crustaceans as well as food for a multitude of marine species. Mosquito Bay is home to one of Vieques' most unique resources, the Bioluminescent Bay. This bay is a Puerto Rico Department of Natural and Environmental Resources (DNER) marine protected area, which is covered under DNER's Bioluminescent Bay Conservation Plan.

During surveys of the benthic habitat of Puerto Rico conducted by NOAA’s Center for Coastal Monitoring and Assessment (NOAA 2001), barrier reefs, patch-type reefs, and scattered coral were documented adjacent to Vieques Island.  Barrier reefs are linear reefs separated from land by a lagoon.  Patch-type reefs are generally circular in shape and present in lagoons or bays.  Scattered coral are isolated coral heads that are present in areas that mostly have a sand or sea grass covered bottom. Sea grass beds are common in the shallow subtidal zone surrounding the island.  The majority of the sea grass beds adjacent to Vieques Island are on the shoreward side of the coral reef structures. The well developed seagrass beds in the waters of northwestern Vieques serve as important refuge and feeding grounds for green turtles and the West Indian manatee.