Home > Explore Projects > Habitat Mapping of Fish Bay, Coral Bay, and the St. Thomas East End Reserve in the U.S. Virgin Islands
NCCOS Project

Habitat Mapping of Fish Bay, Coral Bay, and the St. Thomas East End Reserve in the U.S. Virgin Islands

This project began in May 2012 and was completed in November 2013

We developed benthic habitat maps for shallow-water (< 40 meters) areas in and around Fish Bay, Coral Bay, and the St. Thomas East End Reserve in the U.S. Virgin Islands. These maps will help local managers and stakeholders develop place-based action strategies, providing road maps to address key threats to coral reefs in these areas. This effort marks the first time that high resolution depth imagery and digital maps describing over 85 percent of the seafloor are available to local managers.

Why We Care
Land- and marine-based sources of pollution, fishing, habitat loss, marine debris, invasive species, and climate change all threaten the health of coral reef ecosystems in the U.S. Virgin Islands. Fish Bay, Coral Bay, and the St. Thomas East End Reserve (STEER) are no exceptions and were chosen by local managers as priority sites during 2010 scoping meetings hosted by NOAA’s Coral Reef Conservation Program. These sites were chosen because they scored highest (among the 16 sites considered) based on their:

  • high biological value (i.e., irreplaceability, uniqueness, and abundance of organisms),
  • the high degree of risk and threats that they face, and
  • the lack of or low effectiveness of current management activities and stakeholder support.

Fish and Coral Bays are both inlets located on the southern coast of St. John, portions of which are managed by the U.S. National Park Service. The STEER is a marine protected area located on the eastern side of St. Thomas, jointly managed by the Virgin Islands Department of Planning and Natural Resources and the Nature Conservancy.

These three areas encompass a mosaic of seagrass, algal, mangrove, and coral reef habitats, providing sources of food and refuge for a diversity of marine organisms. They also provide valuable ecosystem services to the local community, including shoreline protection, fisheries replenishment, recreation, and tourism.

Managers need a baseline understanding of the benthic habitats and communities in these areas to develop local action strategies to combat threats to these areas and protect their valuable natural resources.

What We Did
We developed benthic habitat maps for over 85 percent of Fish Bay, Coral Bay, and the STEER using a combination of visual interpretation and computer-based classification techniques. We used two different imagery sources to map habitats, including:

  • Aerial photographs collected by the U.S. Army Corp of Engineers, and
  • Light detection and ranging (LiDAR) depth and reflectivity imagery collected by NOAA’s Office of Coast Survey.

The accuracy of these habitat maps was similar to the accuracy of other NOAA benthic habitat maps, ranging from 74.5 to 93.0 percent. These maps were also reviewed by local experts, including staff from the National Park Service, the USVI Department of Planning and Natural Resources, the Nature Conservancy, the University of the Virgin Islands, and the Coral Bay Community Council, before being finalized. Our final products include the benthic habitat maps, source imagery, and georeferenced underwater videos and photos. The LiDAR data collection was funded by NOAA’s Office of Coast Survey, and the habitat mapping effort was funded by NOAA’s Coral Reef Conservation Program.

What We Found
Sand and mud dominated these three areas (i.e., comprising 87.1 percent of Fish Bay, 65.2 percent of Coral Bay, and 74.3 percent of the STEER). Sand colonized by seagrass and balls of coralline algae (called rhodoliths) were the most common habitats inside and outside (respectively) of Fish Bay, Coral Bay, and the STEER’s boundary. Live coral cover rarely exceeded 10 percent in any of these locations, constituting only 1.8 percent of Fish Bay, 8 percent of Coral Bay, and 4.8 percent of the STEER. However, ten locations were mapped as having >50% live coral cover in Coral Bay and the STEER. Live coral cover is one metric (of many) used by managers to help understand the general health of the ecosystem that they manage.

Next Steps
Cartographers used the LiDAR depth data to update nautical charts in the area. Local managers will use the habitat maps to develop and update local action strategies for these areas. These maps may also be used in the future to:

  • Design and plan research projects to monitor the health of the ecosystems in these locations.
  • Evaluate the efficacy of management actions taken within these marine protected areas, including actions related to watershed restoration and enforcement activities.
  • Map ecosystem services and estimate the economic value of goods and services across the seascape.
  • Understand seascape requirements for species, and identify the most productive and diverse seascape types.
  • Predict habitat suitability for priority species to help target monitoring efforts and prioritize action strategies.

Additional Resources

Click to expand resource list(s).

Explore Similar Projects
No posts found.


NCCOS delivers ecosystem science solutions for stewardship of the nation’s ocean and coastal resources to sustain thriving coastal communities and economies.

Stay Connected

Sign up for our quarterly newsletter or view our archives.

Follow us on Social

Listen to our Podcast

Check our our new podcast "Coastal Conversations"