Vieques harbors both plant and animal species that are designated as threatened and endangered species.

These include the green, hawksbill, leatherback, and loggerhead sea turtles, the Brown Pelican, the Roseate Tern, the Antillean manatee, and four plants (Chamaecrista glandulosa var. mirabilis, Eugenia woodburyana, Goetzea elegans, and Stahlia monosperma).

A number of other species are considered critical or endangered by the Puerto Rico Department of Natural and Environmental Resources.

One of the most important nesting colonies of the endangered Brown Pelican is found on lands in eastern Vieques.

Both subtropical dry forest and subtropical moist forest are found on the island of Vieques. The subtropical dry forest is one of the most endangered habitat types in the tropics and subtropics.

The mangrove lagoons in both western and eastern Vieques provide habitat for waterfowl, including species such as the White-cheeked Pintail.

While most of the forests on the island are secondary in nature, these forests provide excellent habitat for neotropical migratory birds, birds that visit the island during the winter months.

The well developed seagrass beds in the waters of northwestern Vieques provide excellent feeding habitat for both the Antillean manatee and the green sea turtle.