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The water is blue and warm, the visibility is perfect. There might be no better place in the world to learn to scuba dive than the glassy seas around Key West, at the southernmost tip of the U.S. As I gradually master my buoyancy and hover 15 feet below the surface, I can see schools of small yellow groupers beneath the dive boat giving wide berth to a blade of a barracuda. A spiny lobster shyly crawls across the seafloor. This colorful diversity of life — like swimming through a tropical aquarium — is all thanks to the shallow coral reefs that exist west of Key West. The world's reefs are the bases for sea life — home to a quarter of all the fish on the planet.

But even though this was my first time diving in the Florida Keys, I could tell something was wrong. Most of the fish were small, and there wasn't much evidence of the larger predators whose presence is the mark of a healthy marine environment. Worst of all were the corals themselves — broken bits of white coral littered the ground like bones at a half-finished burial, their lack of color proof that they were dead. "Diving in the Florida Keys was incredibly depressing," says John Hocevar, oceans campaigner for Greenpeace, who just finished a trip to the Keys and the nearby Dry Tortugas. "I could see how rapidly things had declined over the past 20 years."

Florida isn't the only place where coral reefs are in trouble. Everywhere, reefs are under pressure from rising sea temperatures, ocean acidification, coastal pollution and physical damage. There has already been a major coral bleaching event in Indonesia this summer, in which more than 60% of the coral off the coast of Aceh province has been affected. (Bleaching occurs when heat drives out algae living inside coral tissue; it's an indicator of stress that can eventually kill coral populations outright.) Thanks to the El Niño phenomenon, which often leads to higher-than-normal sea temperatures in parts of the world, this could be one of the worst years ever for coral death — and the gradual warming caused by climate change may only make things worse in the future.

"Coral reefs are incredibly important to ocean health," says Stephanie Wear, the Nature Conservancy's coral expert. "But if we don't act, we could lose 70% of reefs worldwide by the middle of the century."

Perhaps the most direct human-caused threat to coral reefs is coastal pollution. That's the case for the troubled coral reefs of the Keys, which are badly weakened by fertilizer runoff from Florida's agricultural sector. Sediment from runoff on land can cover corals or simply turn the water cloudy, cutting them off from the sunlight they need to survive. (There's a reason coral reefs tend to be found in brilliantly clear water.) The nutrients found in fertilizer — phosphates and nitrogen — can also cause algal blooms, which can smother coral, and low-oxygen dead zones, which aren't much better for them. Overfishing can also upset the delicate ecological balance coral reefs depend on to thrive. And increasingly, dense development along coastlines with reefs — particularly in the heavily affected Caribbean or the Coral Triangle of Southeast Asia — is doing still more damage.

But the truly long-term threats to corals are warming oceans and acidification — both of which are at least partly due to climate change. Corals are actually tiny organisms that join together in colonies, and they depend on a symbiotic relationship with certain species of algae to produce energy through photosynthesis. (It's the algae that give coral reefs their brilliant colors.) But when the water warms — maybe about 1°C to 1.5°C (1.8°F to 2.7°F) above the average high temperature — it throws off that symbiotic relationship, and eventually the coral reject the algae. What's left is the white coral — hence the term bleaching. "If the corals don't recover within a month or two, they'll die," says Wear.

One of the worst mass bleaching events in history occurred in 1998 — which, incidentally, was also one of the hottest years on record, and like 2010, an El Niño year. Globally some 16% of coral reefs died in 1998. This year — which is on track to be the warmest year in recorded history — could be just as bad. While much of that heat is due to independent weather phenomena like El Niño, as climate change warms the atmosphere, it will warm the seas as well — until they could become too hot for corals no matter the year. And since the oceans absorb much of the CO2 we put into the atmosphere, they're slowly becoming more acidic — which over time will make it tougher for corals to build reefs. (They will literally dissolve in more acidic oceans.) "Rising CO2 levels just spell really bad news for corals," says Wear.

Consider that one more reason — of many — to work to reduce carbon emissions in the decades ahead. But in the meantime, there is more we can do now to protect coral reefs. Preventing soil and nutrient runoff from farming near coastlines can help, as can managing coastal development, especially in smaller, crowded islands. Reducing overfishing — especially of predators at the top of the aquatic food chain — adds another layer of defense to endangered reefs. But most of all we need to create more protected areas in the oceans. Less than 1% of the oceans are afforded any protection whatsoever, compared with some 10% of land. Unless we stop treating the oceans like a shared sewer, coral reefs won't survive. "Climate change will be tough enough," says Wear. "We need to do whatever we can to reduce stresses right now if corals are going to have a chance." Otherwise, the oceans' most vibrant areas could become underwater graveyards.

• Bryan Walsh