Reefs have been damaged to varying degrees by pollution from factories, runoff from farms, fertilizers, and pesticides. The net effect of pollution maybe as bad or maybe worse than the effect of global warming. Coral reefs near area where people live have sickly brown spots and are being engulfed by algae that feeds on sewage flowing from the rivers that pass through villages.
Corals can flourish is surprisingly murky waters, as long tides or currents periodically sweep away sediments. Nutrients are what hurt them the most. High levels of nitrogen from sources such as fertilizer provide food for free-living algae which explode in bloom and smother other sea creatures.
Corals deal with stresses like silt and pollution by secreting mucous proteins on their outer tissues, which often attracts viruses, bacteria and fungus that feed on the mucus and sometimes even breed there.
Soil erosion caused my slash and burn farming techniques
Municipal waste and sewage in rivers