Major threats to coral reefs and their habitats include:
- Destructive fishing practices: These include cyanide fishing, blast or dynamite fishing, bottom trawling, and muro-ami (banging on the reef with sticks). Bottom-trawling is one of the greatest threats to cold-water coral reefs.
- Overfishing: This affects the ecological balance of coral reef communities, warping the food chain and causing effects far beyond the directly overfished population.
- Careless tourism: Careless boating, diving, snorkeling, and fishing happens around the world, with people touching reefs, stirring up sediment, collecting coral, and dropping anchors on reefs. Some tourist resorts and infrastructure have been built directly on top of reefs, and some resorts empty their sewage or other wastes directly into water surrounding coral reefs.
- Pollution: Urban and industrial waste, sewage, agrochemicals, and oil pollution are poisoning reefs. These toxins are dumped directly into the ocean or carried by river systems from sources upstream. Some pollutants, such as sewage and runoff from farming, increase the level of nitrogen in seawater, causing an overgrowth of algae, which 'smothers' reefs by cutting off their sunlight.
- Sedimentation: Erosion caused by construction (both along coasts and inland), mining, logging, and farming is leading to increased sediment in rivers. This ends up in the ocean, where it can 'smother' corals by depriving them of the light needed to survive. The destruction of mangrove forests, which normally trap large amounts of sediment, is exacerbating the problem.
- Coral mining: Live coral is removed from reefs for use as bricks, road-fill, or cement for new buildings. Corals are also sold as souvenirs to tourists and to exporters who don't know or don't care about the longer term damage done, and harvested for the live rock trade.
- Climate change: Corals cannot survive if the water temperature is too high. Global warming has already led to increased levels of coral bleaching, and this is predicted to increase in frequency and severity in the coming decades. Such bleaching events may be the final nail in the coffin for already stressed coral reefs and reef ecosystems.