Coral reef protection activities within the Office of Coastal and Aquatic Managed Areas are primarily conducted through the Coral Reef Conservation Program (CRCP) and Florida Keys National Marine Sanctuary (FKNMS). The CRCP acts as the lead state trustee to help protect the reef tract that runs through Miami-Dade, Broward, Palm Beach and Martin counties. The CRCP co-ordinates with other state, county and federal agencies to enforce the Coral Reef Protection Act (CRPA), a Florida statute brought into law in 2009 that enables resource trustees to pursue damages after impacts to natural reefs, such as ship groundings, cable drags and anchoring incidents. These events can cause significant damage to coral reefs and the surrounding substrate, sometimes to an extent where recovery is unlikely if primary restoration does not occur.

The capacity of elkhorn and staghorn coral to asexually reproduce through fragmentation and their fast growth rates make them good candidates for coral restoration, but any type of coral can be restored. Restoration has been underway in the Florida Keys when local marine life expert Ken Nedimyer started the first offshore coral nursery in 2000. Since then, other nurseries have become established throughout South Florida and elsewhere.

Primary restoration is carried out in an attempt to restore the site to the baseline conditions that were present before the injury, so that recovery can begin. The process involves stabilizing any large pieces of substrate that were dislodged during the impact, backfilling any holes or trenches that were created and removing rubble that may move around during storms preventing species recruitment and recovery. Any coral colonies and fragments that are recovered are reattached to the stabilized substrate and monitored for survival and disease prevalence. Octocorals and sponges can also be recovered and reattached using a variety of methods.

The CRPA also allows the CRCP to recover damages from the responsible party that include, but are not limited to compensation for the cost of replacing, restoring or acquiring the equivalent of the injured coral reef and the value of the lost use and services. The CRCP may also assess civil penalties for anchoring a vessel on coral reef, with the penalty amount being based upon the size of the injury and the number of repeated violations. Damaging the seafloor is prohibited within FKNMS and the responsible party can be fined for damaging the resource, restoration costs and long-term monitoring.

The installation of mooring buoys at popular dive and fishing sites, along with better waterway marking, has helped reduce vessel damage to the coral reef and to seagrass beds. The long-term success of these programs has largely been due to a unique interface of education, outreach, enforcement and research and monitoring activities. Channel marking falls largely under the jurisdiction of the US Coast Guard and in some cases, county government. The sanctuary works with these entities to identify areas in need of marking to protect benthic (bottom) habitats.