There are still practices that are hidden from humans that may in danger coral reefs. Pollution, overfishing, destructive fishing practices using dynamite or cyanide, collecting live corals for the aquarium market, mining coral for building materials are some of the ways people damage reefs all around the world every day.
I think in general, if we do not have these kind of problems and factories caused by humans, the waters will be clear and species won’t be affected. It has something to do with greed also.
Greed somehow yes, it is also because no space for disposals.