Home > Explore Projects > Shallow-water Benthic Habitat Mapping of Northeast Puerto Rico and Culebra Island
NCCOS Project

Shallow-water Benthic Habitat Mapping of Northeast Puerto Rico and Culebra Island

This project began in March 2013 and was completed in September 2015

We developed benthic habitat maps for shallow coral reef areas (< 35 m) around Northeast Puerto Rico and Culebra Island. These maps are helping scientists and local managers develop place-based strategies to address and remedy specific threats to coral reefs in and around the Northeast Reserves (Northeast Ecological Corridor Nature Reserves).

Why We Care
The shallow-water coral reef ecosystems in the surrounding waters off northeast Puerto Rico and Culebra Island are unique and valuable natural resources in need of protection. The mosaic of habitats, including hard and soft corals, is home to a diversity of marine organisms that provide important ecosystem services to the local communities, as well as fishing and tourism. However, coral reef ecosystems throughout the U.S. Caribbean are under increasing pressure from environmental and anthropogenic stressors. Mitigating these threats requires that resource managers understand the spatial distribution of these resources, making benthic habitat mapping an integral component of ecosystem-based approaches to management.

What We Did
We developed a map of benthic habitat types, including live coral cover present off northeast Puerto Rico and Culebra Island, a region selected by local managers as a priority area for habitat mapping. The map covers 744 km2 of shallow-water habitats at a high spatial resolution (the smallest habitat features mapped are 10x10 meters) and includes 250 km of shoreline for the region’s 210 islands and rock outcrops. This includes the shallow habitats inside the current boundaries of the Northeast Natural Reserves, as well as surrounding areas. The habitat map, generated using a combination of semi-automated classification and visual interpretation techniques of remote sensing imagery (WV-2 satellite imagery collected 2011-2013, hydrographic data collected 1900-2012 and aerial photos collected 2007-2010) and underwater videos (2013-2014), represents the first digital map that describes nearly 100% of the seafloor in the study area.This work updates previous NOAA maps generated by Kendall et al. (2001), which covered  22% of the mapped region (78% of the study area was not previously mapped). This work was conducted by NOAA’s National Centers for Coastal Ocean Science in collaboration with the Department of Natural and Environmental Resources of Puerto Rico (DRNA) and the University of Puerto Rico (UPR) Mayagüez.

What We Found
Softbottom, mainly consisting of sand and rhodoliths (encrusting marine red algae that form hard nodules), dominated the benthic habitats and covered 75 percent of the mapped area. Hardbottom habitats covered 25 percent and were dominated by pavement and coral reefs. Algae was the dominant biological cover for both hard and softbottom areas (57%) followed by seagrass beds (17%) and mangroves (4%). Habitats dominated by live corals were rare (covering only 0.2 percent of the mapping area) since a majority of the hardbottom areas were dominated by algae cover. However, half of all the hardbottom areas still had live coral cover greater than 10%. The live coral cover varied across the region; reefs with relatively high amounts of live coral cover were found outside of existing marine protected area boundaries east of Culebra Island, and south of the Northeast Reserves in the strait between Puerto Rico and Vieques Island, while reefs with low to very low coral cover were identified along the north coast of Puerto Rico. Live coral cover is one metric (of many) used by managers to help understand the general health of the ecosystem that they manage.

We assessed the thematic accuracy of the map using an independent data set. The overall map accuracies (adjusted for proportional bias) were measured as follows: 90% for major and 64% for detailed geomorphological structure, 82% for percent hardbottom, 83% for biological cover and 76% for live coral cover. The final deliverables for this project included the benthic habitat maps, source imagery, and georeferenced underwater videos and photos (both ground truth data and accuracy assessment data).

Benefits of our Work
These benthic habitat maps will be used by DRNA, UPR, NOAA, and other local partners for planning, research and monitoring activities, and to support the management and conservation of the Northeast Natural Reserves. The maps are already being used for the ongoing NCCOS project, Spatial Characterization to Support Development of an Integrated Management Plan for Puerto Rico’s Northeast Ecological Corridor Nature Reserve. The new map connects with a previous mapping effort of moderate to deep water of the Northeast Natural Reserves by NOAA Ship Nancy Foster in 2012-2013.

What’s Next?
When completed, the maps, remote sensing data and videos will be made available to the public through our online Biomapper Portal, and will also be made available for download from this page, together with the project report. Estimated delivery date for these products are September 2015.

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"