Coral reef ecosystems worldwide have been seriously impacted by human activities. The current deteriorated state of coral reef communities is the result of a long history of exploitation. The scientific community has recognized the extent of degradation, its consequences, and how little we have done to avoid further degradation only in the last two decades. Marine reserves are one of the main conservation actions that could help to reduce the impacts of human activities on the ecosystem, particularly those associated with fishing. However, in the Caribbean, full enforcement of protection only occurs in a handful of marine reserves. Positive changes in coral reef communities due to protection have been well documented, but they are mainly restricted to fish assemblages (i.e. increase of fish biomass). Yet, the effects of protection throughout the entire community are little known. In this dissertation I provide a quantitative description of the recent ecological trajectory of coral reef degradation across the Caribbean region. Also, I assess the current conservation status of Caribbean reefs and the recovery of the community within marine reserves.

My results show that the response to protection is variable and depends on local conditions at the time of protection, the degree of enforcement, and the characteristics of the marine reserves (e.g., size). An increase of fish biomass inside reserves was generally associated with increased herbivory and decreased macroalgal abundance. However, corals did not exhibit any clear response to protection. Moreover, my results show that partial protection and/or poor enforcement could be counterproductive and have effects on the reef community that are worse than no protection at all. Fish diversity was related to the gradient of fish biomass in a non-linear way. Maximum fish diversity occurred at 200 g of fish m^-2. However, there was a decline in fish diversity above 300 g m^-2, which indicates an intermediate disturbance due to increased predator abundance.

Most Caribbean reef sites are in a serious state of degradation. My results indicate that the use of large and truly enforced marine reserves ensures the recovery of fish assemblages, but may be insufficient to enhance coral recovery. To enhance community-wide recovery and to increase the resilience of the ecosystem we need further conservation efforts, such as more and larger marine reserves, improved fisheries regulations and pollution control outside the reserves. Only with complementary measures at appropriate scales will we be able to enhance the recovery of the benthic communities to build resilience against global impacts such as climate change.