Hurricanes and cyclones can cause devastating physical damage to coral reefs, which take years to recover. These natural catastrophic events have caused massive mortalities to corals such as the elkhorn coral (Acropora palmata) biotopes found in Puerto Rican reefs. The large-scale detachment and deposition of coral fragments and the extensive mass mortalities of benthic algae have been reported after the pass of Hurricanes David (1979) and Allen (1980) in Puerto Rico and the U.S. Virgin Islands. After the passing of Hurricane Hugo (1989), reefs off the northwest coast of Vieques Island were reported with massive destruction of elkhorn coral biotopes that were later overgrown by benthic algae and other encrusting biota. There has not been any major storm damage to coral reefs following the passage of Hurricane George (1998); however, several negative impacts such as destruction, burial, fragmentation, and uprooting of corals and sponges were sighted after the passing of Hurricane Dean (2007) within 180 miles of southern Puerto Rico. Exposing the southern coast to 40-kt winds and heavy surf, negative impacts include the destruction, burial and fragmentation of corals in shallow areas and the uprooting of gorgonians and sponges. Particularly affected were colonies of ecologically threatened Acropora species. Although devastating for coral colonies, algae overgrowth was removed allowing for new coral recruitment (For more information, please see CCRI News – Sept 2007).

Anthropogenic activities can also be destructive to coral reefs. For example, during the 90’s, use of fish traps in southwest Puerto Rico has been estimated to damage 116 m2 of reef organisms annually, although this represents less than 0.001% of living habitat.Also in the last 20 years, the most visible damage in the Florida Keys has been from direct human impacts such as boat and ship groundings in coral, seagrasses, or hard bottom areas, anchor damage, destructive fishing practices, and divers and snorkelers standing on coral. In October 1998, the 440-ft cruise ship Windship illegally dropped anchor obliterating 283 m2 of coral reef off the island of St. John.

In Puerto Rico, recent ship groundings have occurred at Mona (Regina in 1985, Fortuna Reefer in 1997) and at Guayanilla, where in 2006 the 748-ft tanker Margara went aground, impacting 8,500 mof reef from both direct collision and from recovery operations. Nine years after the Fortuna Reefer grounding, 10% of the original fragments are still alive and now resemble adult colonies following restoration efforts and continued monitoring of elkhorn coral (Acropora palmata). Emergency Restoration activities, a collaborative agreement between the responsible party and the co-trustees, Puerto Rico DNER and NOAA, were also conducted after extensive damage to a bank type coral reef with significant live cover of corals and gorgonians were made by the tanker Margara.

Tourism development has been reported to be increasing due to the use of personal watercraft, influx of boaters from neighboring islands, and the construction of marinas or docks. Although the Navigation and Aquatic Safety Law protects marine flora and fauna from recreational and other human activities in Puerto Rico, DNER is uniting efforts to become more active in documenting recreational vessel groundings that affect mangroves, coral reefs, or seagrass beds. One of the main concerns regarding the health of coral reefs in Puerto Rico is the unknown recreational carrying capacity of these systems. Due to the dramatic increase in the utilization of coastal resources by local and non-local tourists, there is a critical need to establish the maximum capacity of boats allowed per reef and orientation guidelines for best utilization of reef resources.