Global climate change and local anthropogenic pressures are among the primary factors leading to the decline of functional biodiversity and critical habitats in coral reefs. Coral bleaching, the potential decreases in dissolved oxygen concentration (deoxygenation) and pH (acidification) in the ocean scan induce severe changes in coral reef ecosystem biodiversity and functionality. The main objective of this study was to apply four Ecopath with Ecosim models of a Caribbean coral reef system to individually and collectively model the effects of coral bleaching on the trophic web, deoxygenation on fish, and acidification on calcifying organisms.