Many things can effect the ecosystem of the coral reef. The ecosystem is a very delicate system that needs all parts to continue to thrive. When one part disappears, the system is in jeopardy .
One thing that is effecting the coral reef, is coral bleaching. Coral bleaching is cause by climate change in the atmosphere. The coral reefs are in shallow waters near the surface, the weather has been getting warmer due to climate change, so the ocean has become warmer. Thus the very sensitive corals are being affected. Corals depend on their food called zooxanthellae that are deep in their tissues. When the water stays warm for multiple weeks, the zooxanthellae leave the tissues in the coral in thus making them white. Bleached corals are weak and cannot defend themselves from diseases.
Another thing that is effecting coral reefs is ocean acidification. This is also caused by climate change. Most of the carbon dioxide that enters the atmosphere goes into the ocean. Since the carbon dioxide in the ocean is increasing, the ocean pH level becomes more acidic. With acidification, the corals cannot absorb the calcium carbonate that they need to maintain their skeletons. Ocean acidification effects more than just corals. It effects other animals that need calcium carbonate to make their shells, like snails, urchins, and clams.