Animal, vegetable and mineral, a pristine tropical coral reef is one of the natural wonders of the world. Bathed in clear, warm water and thick with a psychedelic display of fish, sharks, crustaceans and other sea life, the colourful coral ramparts that rise from the sand are known as the rainforests of the oceans.

And with good reason. Reefs and rainforests have more in common than their beauty and bewildering biodiversity. Both have stood for millions of years, and yet both are poised to disappear.

If you thought you had heard enough bad news on the environment and that the situation could not get any worse, then steel yourself. Coral reefs are doomed. The situation is virtually hopeless. Forget ice caps and rising sea levels: the tropical coral reef looks like it will enter the history books as the first major ecosystem wiped out by our love of cheap energy.

Today, a report from the Australian government agency that looks after the nation's emblematic Great Barrier Reef reported that "the overall outlook for the reef is poor and catastrophic damage to the ecosystem may not be averted". The Great Barrier Reef is in trouble, and it is not the only one.

Within just a few decades, experts are warning, the tropical reefs strung around the middle of our planet like a jewelled corset will reduce to rubble. Giant piles of slime-covered rubbish will litter the sea bed and spell in large distressing letters for the rest of foreseeable time: Humans Were Here.

"The future is horrific," says Charlie Veron, an Australian marine biologist who is widely regarded as the world's foremost expert on coral reefs. "There is no hope of reefs surviving to even mid-century in any form that we now recognise. If, and when, they go, they will take with them about one-third of the world's marine biodiversity. Then there is a domino effect, as reefs fail so will other ecosystems. This is the path of a mass extinction event, when most life, especially tropical marine life, goes extinct."

Alex Rogers, a coral expert with the Zoological Society of London, talks of an "absolute guarantee of their annihilation". And David Obura, another coral heavyweight and head of CORDIO East Africa, a research group in Kenya, is equally pessimistic: "I don't think reefs have much of a chance. And what's happening to reefs is a parable of what is going to happen to everything else."

These are desperate words, stripped of the usual scientific caveats and expressions of uncertainty, and they are a measure of the enormity of what's happening to our reefs.

The problem is a new take on a familiar evil. Of the billions of tonnes of carbon dioxide spewed from cars, power stations, aircraft and factories each year, about half hangs round in the thin layer of atmosphere where it traps heat at the Earth's surface and so drives global warming. What happens to the rest of this steady flood of carbon pollution? Some is absorbed by the world's soils and forests, offering vital respite to our overcooked climate. The remainder dissolves into the world's oceans. And there, it stores up a whole heap of trouble for coral reefs.

Often mistaken for plants, individual corals are animals closely related to sea anemones and jellyfish. They have tiny tentacles and can sting and eat fish and small animals. Corals are found throughout the world's oceans, and holidaymakers taking a swim off the Cornish coast may brush their hands through clouds of the tiny creatures without ever realising.

It is when corals form communities on the sea bed that things get interesting. Especially in the tropics. Yes, Britain has its own rugged coral reefs, but such deep-water constructions are too remote, cold and dark to really fire the imagination. It is in shallow, brightly light waters, that coral reefs really come to life. In the turquoise waters of the Caribbean, Indian Ocean and Pacific, the coral come together with tiny algae to make magic.

The algae do something that the coral cannot. They photosynthesise, and so use the sun's energy to churn out food for the coral. In return, the coral provide the algae with the carbon dioxide they need for photosynthesis, and so complete the circle of symbiotic life.

Freed of the need to wave their tentacles around to hunt for food, the coral can devote more energy to secreting the mineral calcium carbonate, from which they form a stony exoskeleton. A second type of algae, which also produces calcium carbonate, provides cement. Together, the marine menage-a-trois make a very effective building site, with dead corals leaving their calcium skeletons behind as limestone. For all their apparent beauty and fragility, just think of coral reefs as big lumps of rock with a living crust.

A fragile crust too. The natural world is a harsh environment for coral reefs. They are under perpetual attack by legions of fish that graze their fields of algae. Animals bore into their shells to make homes, and storms and crashing waves break them apart. They may appear peaceful paradises, but most coral reefs are manic sites of constant destruction and frantic rebuilding. Crucially though, for millions of years, these processes have been in balance.

Human impact has tipped that balance. Loaded with the agricultural nutrients nitrates and phosphates, rivers now spill their polluted waters into the sea. Sediment and sewage cloud the clear waters, while over-fishing plays havoc with the finely tuned community of fish and sharks that kept the reef nibbling down to sustainable levels. All of this is enough to wreck coral without any help from climate change.

Global warming, predictably, has made the situation worse. Secure in their tropical currents, coral reefs have evolved to operate within a fairly narrow temperature range, yet, in the late 1970s and 1980s, coral scientists got an unpleasant demonstration of what happens when the hot tap is left on too long. "The algae go berserk," said Rogers. Scientists think the algae react to the warmer water and increased sunlight by producing toxic oxygen compounds called superoxides, which can damage the coral. The coral respond by ejecting their algal lodgers, leaving the reefs starved of nutrients and deathly white. Such bleaching was first observed on a large scale in the 1980s, and reached massive levels worldwide during the 1997-98 El Niño weather event.

On top of a human-warmed climate, the 1997-98 El Niño, caused by pulses of warming and cooling in the Pacific, drove water temperatures across the world beyond the coral comfort zone. The mass bleaching event that followed killed a fifth of coral communities worldwide, and though many have recovered slightly since, the global death toll attributed to the 1997-98 mass bleaching stands at 16%. "At the moment the reefs seem to be recovering well but it's only a matter of time before we have another [mass bleaching event]," says Obura.

With its striking images of skeletal reefs stripped of colour and life, coral bleaching offers photogenic evidence of our crumbling biodiversity, and has placed the plight of coral reefs higher on the world's consciousness. Head along to your local swimming pool for diving lessons these days, and chances are that you will be offered a coral conservation course as well.

Katy Bloor, an instructor at Sub-Mission Dive School in Stoke-on-Trent, says many divers are not aware of the problems corals face, particularly as holiday operators tend to visit reefs in better condition. "Most have probably dived on a coral reef that they thought was a bit rubbish, but they haven't considered why," she said.

If anyone knows what they are missing out on, it should be Charlie Veron. So what does it feel like to dive on a pristine reef? "I have not seen many reefs that can be called pristine, and none exist now," he says. "But if I had to take a punt, I was diving on the Chesterfield Reefs, east of New Caledonia [in the southwest Pacific] about 30 years ago and was staggered by the wealth of life, especially big fish which were so thick that I was hardly ever able to photograph coral. That place made even remote parts of the Great Barrier Reef look second rate.

"I can only describe it like walking through a rainforest dripping with orchids, crowded with birds and mammals of bewildering variety and trees growing in extreme profusion."

Can the coral be helped? If planting more trees can regrow a forest, can coral be introduced to bolster failing reefs? There are a handful of groups working on the problem, many of which have reported encouraging results. Off Japan, scientists are farming healthy coral on hundreds of ceramic discs, which they plan to transplant onto the badly-bleached Sekisei Lagoon reef within two years. In 30 years or so, they hope the reef can recover fully.

A similar, if more low-tech, exercise is under way in the Philippine coastal community of Bolinao, where local people have broken off chunks from the healthy section of their local reef and have crudely wedged them into cracks in bleached sections. Others have cultured corals in swimming pools, and researchers in the Maldives are using giant sunken cages, connected to a low level electric current, to help coral form their chalky shells.

But the problem with all these efforts, according to Rogers at the ZSL, is that they cannot address the looming holocaust that reefs face. A new, terrible curse that comes on top of the bleaching, the battering, the poisoning and the pollution.

Remember the carbon dioxide that we left dissolving in the oceans? Billions and billions of tonnes of it over the last 150 years or so since the industrial revolution? While mankind has squabbled, delayed, distracted and dithered over the impact that carbon emissions have on the atmosphere, that dissolved pollution has been steadily turning the oceans more acidic. There is no dispute, no denial, about this one. Chemistry is chemistry, and carbon dioxide plus water has made carbonic acid since the dawn of time.

As a result, the surface waters of the world's oceans have dropped by about 0.1 pH unit – a sentence that proves the hopeless inadequacy of scientific terminology to express certain concepts. It sounds small, but is a truly jaw-dropping change for coral reefs.

For reefs to rebuild their stony skeletons, they rely on the seawater washing over them to be rich in the calcium mineral aragonite. Put simply, the more acid the seawater, the less aragonite it can hold, and the less corals can rebuild their structure. Earlier this year, a paper in the journal Science reported that calcification rates across the Great Barrier Reefs have dropped 14% since 1990. The researchers said more acidic seas were the most likely culprit, and ended their sober write-up of the study with the extraordinary warning that it showed "precipitous changes in the biodiversity and productivity of the world's oceans may be imminent".

Rogers says carbon dioxide levels in the atmosphere are already over the safe limits for coral reefs. And even the most ambitious political targets for carbon cuts, based on limiting temperature rise to 2C, are insufficient. Their only hope, he says, is a long-term carbon concentration much lower than today's. The clock must somehow be wound back and carbon somehow sucked out of the air. If not, then so much more carbon will dissolve in the seas that the reefs will surely crumble to dust. Given the reluctance to reduce emissions so far, the coral community is not holding its breath.

"I just don't see the world having the commitment to sort this one out," says Obura. "We need to use the coral reef lesson to wake us up and not let this happen to a hundred other ecosystems."

Reefs to see before they die

Florida Keys, United States

The only coral reef system in the continental US and the third largest in the world, stretching 221 miles down the Florida coast. The US National Marine Fisheries Service says live coral is down 50-80% in the last decade, mainly due to damage by humans.

Jamaican reefs

Threatened by sewage disposal, inland agricultural run-off and eutrophication, as well as tourist activities such as glass-bottom boat trips. Hurricanes hinder reef recovery and Caribbean coral cover has declined 80% in 25 years.

Scarborough Reef, South China Sea

Ownership disputes between the Philippines, mainland China and Taiwan mean the waters surrounding this reef are heavily overfished, and mangled by the blasts and cyanide used to maximise catch.

Reefs of the windward Southeast Hawaiian Islands, US

Management is improving around the main Hawaiian islands such as Oahu and Maui, but over-fishing and organic sediment from plantations remain major threats.

Seribu Islands, Java Sea, Indonesia

Spanning over 108,000 hectares and 100 small islands, this reef is a significant contributor to the Indonesian tourism economy. Rapid urban development poses threats from domestic and industrial waste, urban run-off and oil and gas exploration. The 1997-1998 El Niño event triggered severe bleaching and killed over 90% of the coral down to 25 metres.

Stable but for how long?

The Great Barrier Reef

The globe's largest coral reef ecosystem, composed of over 2,900 individual reefs and stretching over 3,000km, is the best example of reef management with little damage since 2004. Significant bleaching occurred in 1998, 2002 and 2006.

The Red Sea Riviera, Gulf of Aqaba, Egypt, Israel and Jordan

These reefs continue to remain in good health despite intense tourism. Coral cover remains high to very high, despite localised losses from coral bleaching and crowns-of-thorns starfish, which prey on coral polyps.

Mombasa National Marine Park, Kenya

Adjacent to the most heavily populated beach along the Kenyan coast, damage due to tourism is inevitable. In 1989 the area was pronounced a marine park, leading to an increase in recorded coral cover from 8 to 30%.

Reefs of the Seychelles, Indian Ocean

Lost some 90% of coral cover during the 1998 El Nino event. Slowly recovering due to granitic coral, which is more resistant and supports regrowth.

Surin Islands, Thailand

The reefs located off this group of islands were weakened by the 2004 Indian Ocean tsunami The majority of the damage is localized and low impact, but the coral is now more susceptible to future destruction.

Lauren Smith