Coral reefs are among the most biologically rich and productive ecosystems on earth. This protocol guides the monitoring within the parks that comprise the National Park Service, South Florida/Caribbean Network (SFCN). The benthic marine communities of the SFCN are part of a complex and diverse ecological system that includes algae, corals, and other marine invertebrates. Reef-building corals are the primary architectural organisms and are sensitive to environmental degradation; therefore, they are good indicators of overall health for a park’s reef ecosystem. Coral reefs face a wide and intensifying list of stressors, including disease, bleaching, sedimentation, overfishing, coastal development, eutrophication, storms, marine debris and global climate change. Coral reefs are often proposed as indicator systems for global climate change. For these reasons, coral reef ecosystems were ranked as the number one vital sign for SFCN implementation.

The coral reef monitoring protocol guides the monitoring of this globally imperiled system within five parks of the network: Biscayne National Park (BISC), Dry Tortugas National Park (DRTO), Virgin Islands National Park (VIIS), Buck Island Reef National Monument (BUIS) and Salt River Bay National Historical Park and Ecological Preserve (SARI). As funding becomes available, monitoring will expand to a sixth network park, Virgin Islands Coral Reef National Monument (VICR). Coral reef communities within the network represent some of the best Caribbean and Western Atlantic coral reefs within the National Park Service (NPS). The enabling legislation and/or presidential proclamations for VIIS, BUIS and DRTO specifically mention coral reefs within these park units as significant environmental communities. These reefs support incredible diversity, including corals, hundreds of fish species, conchs, lobsters, and endangered sea turtles. Reefs also play a vital role for humans by supporting fisheries, fish nursery areas, tourism, pharmaceutical bio prospecting and shoreline protection, to name a few. Monitoring coral reefs was identified as a national priority in 1989 through President Clinton's Executive Order 13089 for Coral Reef Protection.

The specific monitoring objectives are: 1) Determine whether percent cover of stony coral as well as other major taxonomic groups (e.g.,algae [turf, calcareous, macroalgae], gorgonians, sponge, and substrate), coral species diversity, coral community structure, and rugosity are changing through time within selected coral reef sites.

2) Determine how the above mentioned response variables vary in space within park reefs and how these variables, which describe coral reef health and composition, are changing through time in parks with different management zones (e.g., DRTO).

3) Track trends in occurrence and severity in reef condition-associated variables such as coral bleaching and coral disease.

4) Track trends in abundance of the regionally important herbivorous sea urchin, Diadema antillarum, within selected coral reef sites.

5) Evaluate effects of unusual events on stony coral cover such as coral bleaching or hurricanes through episodic monitoring, within constraints of program resources.

6) Provide a visual comparison of change through time and allow future analyses of benthic components not identified in this protocol by archiving and maintaining the video and photographic record of transects.

Disease data, coral species list data, the abundance of the long-spined sea urchin, Diadema antillarum, and the number of scleractinian coral colonies (greater than 4 centimeter [1.6 in]) on each transect are collected on field datasheets as covariates of benthic conditions. These data are entered into the SFCN Coral Monitoring web app database on the NPS Integrated Resource Management Applications (IRMA) Portal. Disease photos are linked to their associated data, e.g., transect, sample date, disease type, lesion size, colony number. Additionally, rugosity data (when collected) is entered into this same database.