Human activities have substantial impact on coral reefs, contributing to their worldwide decline. Damaging activities encompass coral mining, pollution (both organic and non-organic), overfishing, blast fishing, as well as the excavation of canals and access points to islands and bays. Additional threats comprise disease, destructive fishing practices, and the warming of oceans. Furthermore, the ocean's function as a carbon dioxide sink, alterations in the atmosphere, ultraviolet light, ocean acidification, viral infections, the repercussions of dust storms transporting agents to distant reefs, pollutants, and algal blooms represent some of the factors exerting influence on coral reefs. Importantly, the jeopardy faced by coral reefs extends far beyond coastal regions. The ramifications of climate change, notably global warming, induce an elevation in ocean temperatures that triggers coral bleaching—a potentially lethal phenomenon for coral ecosystems.

Scientists estimate that between 2020 and 2040, about 70 to 90% of all coral reefs will disappear, with primary causes being warming ocean waters, ocean acidity, and pollution. Others believe that the mass mortality events over this time frame will give way to the expansion of thermally tolerant mutant populations, but at the cost of coral genetic diversity. In 2008, a worldwide study estimated that 19% of the existing area of coral reefs had already been lost.Wilkinson, Clive (2008) Status of Coral Reefs of the World: Executive Summary . Global Coral Reef Monitoring Network. Less than 20% of the world's reefs could be currently regarded as in good health and about 75% of the world's reefs may be at risk due to destructive, human-related activities. The threat to the health of reefs is particularly strong in Southeast Asia, where 95% of reefs are endangered. By the 2030s, 90% of reefs are expected to be at risk from both human activities and climate change; by 2050, it is predicted that all coral reefs will be in danger.

Issues

Competition In the Caribbean Sea and tropical Pacific Ocean, direct contact between coral and common seaweeds causes bleaching and death of coral tissue via allelopathic competition. The lipid-soluble extracts of seaweeds that harmed coral tissues, also produced rapid bleaching. At these sites, bleaching and mortality was limited to areas of direct contact with seaweed or their extracts. The seaweed then expanded to occupy the dead coral's habitat. However, as of 2009, only 4% of coral reefs worldwide had more than 50% algal coverage which means that there are no recent global trend towards algal dominance over coral reefs.

Competitive seaweed and other algae thrive in nutrient-rich waters in the absence of sufficient herbivorous predators. Herbivores include fish such as parrotfish, the urchin Diadema antillarum, surgeonfishes, tangs and unicornfishes.

Predation

Overfishing, particularly selective overfishing, can unbalance coral ecosystems by encouraging the excessive growth of coral predators. Predators that eat living coral, such as the crown-of-thorns starfish, are called corallivores. Coral reefs are built from stony coral, which evolved with large amounts of the wax cetyl palmitate in their tissues. Most predators find this wax indigestible.Benson AA and Muscatine L (1974) Wax in Coral Mucus: Energy Transfer From Corals to Reef Fishes Limnology and Oceanography, 19 (5) 810–814. Download The crown-of-thorns starfish is a large (up to one meter) starfish protected by long, venomous spines. Its enzyme system dissolves the wax in stony corals, and allows the starfish to feed on the living animal. Starfish face predators of their own, such as the giant triton sea snail. However, the giant triton is valued for its shell and has been over fished. As a result, crown-of-thorns starfish populations can periodically grow unchecked, devastating reefs.Predators and Prey PBS.org. Retrieved 11 December 2009. (PDF)

Fishing practices

Although some marine aquarium fish species can reproduce in aquaria (such as Pomacentridae), most (95%) are collected from coral reefs. Intense harvesting, especially in maritime Southeast Asia (including Indonesia and the Philippines), damages the reefs. This is aggravated by destructive fishing practices, such as cyanide and blast fishing. Most (80–90%) aquarium fish from the Philippines are captured with sodium cyanide. This toxic chemical is dissolved in sea water and released into areas where fish shelter. It narcotizes the fish, which are then easily captured. However, most fish collected with cyanide die a few months later from liver damage. Moreover, many non-marketable specimens die in the process. It is estimated that 4,000 or more Filipino fish collectors have used over of cyanide on Philippine reefs alone, about 150,000 kg per year. A major catalyst of cyanide fishing is poverty within fishing communities. In countries like the Philippines that regularly employ cyanide, more than thirty percent of the population lives below the poverty line.

Dynamite fishing is another destructive method for gathering fish. Sticks of dynamite, grenades, or homemade explosives are detonated in the water. This method of fishing kills the fish within the main blast area, along with many unwanted reef animals. The blast also kills the corals in the area, eliminating the reef's structure, destroying habitat for the remaining fish and other animals important for reef health. Muro-ami is the destructive practice of covering reefs with nets and dropping large stones onto the reef to produce a flight response among the fish. The stones break and kill the coral. Muro-ami was generally outlawed in the 1980s.

Fishing gear damages reefs via direct physical contact with the reef structure and substrate. They are typically made of synthetic materials that do not deteriorate in the ocean, causing a lasting effect on the ecosystem and reefs. Gill nets, fish traps, and anchors break branching coral and cause coral death through entanglement. When fishermen drop lines by coral reefs, the lines entangle the coral. The fisher cuts the line and abandons it, leaving it attached to the reef. The discarded lines abrade coral polyps and upper tissue layers. Corals are able to recover from small lesions, but larger and recurrent damage complicates recovery.

Bottom dragging gear such as beach seines can damage corals by abrasion and fracturing. A beach seine is a long net about with a mesh size of and a weighted line to hold the net down while it is dragged across the substrate and is one of the most destructive types of fishing gear on Kenya's reefs.

Bottom trawling in deep oceans destroys cold-water and deep-sea corals. Historically, industrial fishers avoided coral because their nets would get caught on the reefs. In the 1980s, "rock-hopper" trawls attached large tires and rollers to allow the nets to roll over rough surfaces. Fifty-five percent of Alaskan cold-water coral that was damaged by one pass from a bottom trawl had not recovered a year later. Northeast Atlantic reefs bear scars up to long. In Southern Australia, 90 percent of the surfaces on coral seamounts are now bare rock. Even in the Great Barrier Reef World Heritage Area, seafloor trawling for prawns and scallops is causing localized extinction of some coral species.

Marine pollution

Reefs in close proximity to human populations are subject to poor water quality from land- and marine-based sources. In 2006 studies suggested that approximately 80 percent of ocean pollution originates from activities on land. Pollution arrives from land via runoff, the wind and "injection" (deliberate introduction, e.g., drainpipes). Runoff brings with it sediment from erosion and land-clearing, nutrients and pesticides from agriculture, wastewater, industrial effluent and miscellaneous material such as petroleum residue and trash that storms wash away. Some pollutants consume oxygen and lead to eutrophication, killing coral and other reef inhabitants.

An increasing fraction of the global population lives in coastal areas. Without appropriate precautions, development (e.g., buildings and paved roads) increases the fraction of rainfall and other water sources that enter the ocean as runoff by decreasing the land's ability to absorb it.

Pollution can introduce pathogens. For example, Aspergillus sydowii has been associated with a disease in sea fans, and Serratia marcescens, has been linked to the coral disease white pox.

Reefs near human populations can be faced with local stresses, including poor water quality from land-based sources of pollution. Copper, a common industrial pollutant has been shown to interfere with the life history and development of coral polyps.

In addition to runoff, wind blows material into the ocean. This material may be local or from other regions. For example, dust from the Sahara moves to the Caribbean and Florida. Dust also blows from the Gobi and Taklamakan deserts across Korea, Japan, and the Northern Pacific to the Hawaiian Islands. Since 1970, dust deposits have grown due to drought periods in Africa. Dust transport to the Caribbean and Florida varies from year to yearUsinfo.state.gov.Study Says African Dust Affects Climate in U.S., Caribbean. Retrieved on 10 June 2007. with greater flux during positive phases of the North Atlantic Oscillation. The USGS links dust events to reduced health of coral reefs across the Caribbean and Florida, primarily since the 1970s.United States Geological Survey. Coral Mortality and African Dust. Retrieved on 10 June 2007. Dust from the 1883 eruption of Krakatoa in Indonesia appeared in the annular bands of the reef-building coral Montastraea annularis from the Florida Reeftract.Merman, E.A. 2001. Atmospheric inputs to the tropical ocean—unlocking the record in annually banded corals. Master's thesis. University of South Florida, St. Petersburg.

Sediment smothers corals and interferes with their ability to feed and reproduce. Pesticides can interfere with coral reproduction and growth. There are studies that present evidence that chemicals in sunscreens contribute to coral bleaching by lowering the resistance of zooxanthellae to viruses, though these studies showed significant flaws in methodology and did not attempt to replicate the complex environment found in coral reefs.

Nutrient pollution

Nutrient pollution, particularly nitrogen and phosphorus can cause eutrophication, upsetting the balance of the reef by enhancing algal growth and crowding out corals. This nutrient–rich water can enable blooms of fleshy algae and phytoplankton to thrive off coasts. These blooms can create hypoxic conditions by using all available oxygen. Biologically available nitrogen (nitrate plus ammonia) needs to be below 1.0 micromole per liter (less than 0.014 parts per million of nitrogen), and biologically available phosphorus (orthophosphate plus dissolved organic phosphorus) needs to be below 0.1 micromole per liter (less than 0.003 parts per million of phosphorus). In addition concentrations of chlorophyll (in the microscopic plants called phytoplankton) needs to be below 0.5 parts per billion. Both plants also obscure sunlight, killing both fish and coral. High nitrate levels are specifically toxic to corals, while phosphates slow down skeletal growth.

Excess nutrients can intensify existing disease, including potentially doubling the spread of Aspergillosis, a fungal infection that kills soft corals such as sea fans, and increasing yellow band disease, a bacterial infection that kills reef-building hard corals by fifty percent.

Air pollution