Beaches within the park can be comprised of sand, gravel or coral rubble. The sand on VI beaches is often made up of crushed coral, shells and calcareous algae. The beaches are dynamic and provide habitat for shoreline vegetation, a variety of invertebrates and for nesting endangered sea turtle species.

Mangroves within the park provide important habitat for many species including nursery areas for commercially important fishes and invertebrates and roosting areas for local and migrating birds. Mangrove roots help trap sediments from stormwater runoff and absorb energy from storm waves, thereby protecting our water quality and our shorelines. Mangrove areas are dominated by several species of salt-tolerant trees such as, red mangrove (Rhizophora mangle), black mangrove (Avicennia germinans), white mangrove (Laguncularia racemosa) and buttonwoods (Conocarpus erectus). The most substantial mangrove habitat within the park is located at Great Pond.

Salt ponds are formed when bays are cut off from tidal influence. Salinities within salt ponds can vary greatly depending on the amount of fresh and salt water input they receive. Salt Pond habitats are especially important for a number of local and migrating birds, and have been noted to support several invertebrate and algae species. Like mangrove habitats, salt ponds are important protectors of coastal water quality because they slow down storm water runoff and contain associated sediments before they reach the sea.

The STXEEMP contains extensive seagrass beds. Seagrass areas are dominated by three species of flowering plants (angiosperms): turtle grass (Thalassia testudinum), manatee grass (Syringodium filiforme), and shoal grass (Halodule wrightii). These areas are of great importance as nursery areas and forage grounds for a number of species including herbivorous fish, invertebrates such as conch and sea turtles. Seagrass beds help to stabilize the coastal seafloor and are highly productive habitats.

Coral reefs are the largest structures on earth built entirely by biological processes. The hard structure provided by coral reefs is composed of the compacted calcareous skeletons of reef building coral animals. Coral reefs are diverse habitats and support not only coral species, but algae, invertebrates such as sponges, sea urchins, crabs and lobsters, fish and reptiles. Within the STXEEMP there are a variety of reef types including fringing, patch and barrier reefs. The park’s coral reefs are a source of biological diversity, food, storm protection (through absorption of wave energy), revenue (tourism-related activities) and recreation.