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 over next 20 years, about 70 to 90% of all coral reefs will disappear. With primary causes being warming ocean waters, ocean acidity, and pollution. In 2008, a worldwide study estimated that 19% of the existing area of coral reefs had already been lost. Only 46% of the world's reefs could be currently regarded as in good health and about 60% 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 80% 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.

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.

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. 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.

Although some marine aquarium fish species can reproduce in aquaria (such as Pomacentridae), most (95%) are collected from coral reefs.^{[citation needed]} 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.^{[citation needed]} Moreover, many non-marketable specimens die in the process. It is estimated that 4,000 or more Filipino fish collectors have used over 1,000,000 kilograms (2,200,000 lb) 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.