I pulled on my mask and dropped off the back of the boat into the warm water above Nursery Bommie, a dive site at Agincourt Reef more than 70km offshore from Port Douglas, in far-north Queensland, Australia. It is widely regarded as one of the most spectacular tourist reefs in the area.

As soon as I could start to make out the immense shadow of the bommie (an outcrop of coral reef) looming before me I could see that all around its flanks and on the summit, covered in just a metre of water in some places, were blemishes of white.

Mass coral bleaching now affecting half of Australia's Great Barrier Reef Read more

The closer I got, and the more I looked, it was clear there were white patches everywhere. The bleached colonies ranged from tiny plates, shaped like an upturned hand, to areas the size of a table top. Even more striking than the snow white corals was that all around them were other corals coloured in gaudy fluorescent hues that I had never before seen on such a scale. It was as if a masterpiece of nature had been repainted with a colour scheme more befitting a pound shop.

What I was seeing beneath me was evidence of an environmental disaster that has been unfolding over the past few months – the largest mass coral bleaching event ever recorded in this region. This bleaching is the result of a huge El Niño that has driven warm water into the western Pacific Ocean, smothering coral with temperatures beyond their tolerance.

I have dived hundreds of times, with different teams of scientists, along the reef. I have seen the aftermath of other mass coral bleaching episodes such as the most recent major event in 2002.

Facebook Twitter Pinterest Bleached corals at Agincourt Reef. Photograph: James Woodford

In my past experiences of bleached corals, the effect is patchy and, while one area is devastated, another will be mysteriously untouched. Yet the scale of this bleaching event has even the most sober and senior coral reef scientists worried. If the rhetoric from marine biologists is to be believed, then the Great Barrier Reef is now in the grip of a “bommie apocalypse”.

As I continued to dive the Nursery Bommie, the fluorescent pinks, blues, purples and greens became more abundant. While these colours might look striking, they signify that the symbiotic relationship between corals and their zooxanthellae, the photosynthetic algae, has broken down.

The fluorescent colours are always there but in healthy coral colonies the colours of the algae overwhelm those of the host coral, giving them their more typical reddish and brown hue. It is true that not all corals fluoresce, but if they have to survive for too long without the algae then bleaching becomes a death sentence.

Put simply, the majority of the corals on this bommie – bleached or fluorescent – were clearly dead or dying. And it was not only the hard corals. All around were soft corals, still swaying like spaghetti in the ebb and flow of the ocean, that were white and ghostly. Most striking was that the bleaching was not just near the surface, where the water is warmest, but at depths of tens of metres where huge colonies of coral were white as well.

I swam towards a wall of reef off the stern of the boat. As I approached I saw that the seafloor was covered in fragile staghorn corals. Such a patch would normally have been the highlight of any dive to this area but now, bleached white, it was merely more evidence that a catastrophe was under way. Dismayed, I swam back to the boat.

On board was an eclectic collection of reef stakeholders including Imogen Zethoven, the director of the Great Barrier Reef campaign for the Australian Marine Conservation Society, who had also made the dive.

“I was shocked,” she said. “I had expected some patches of bleaching surrounded by mainly healthy, colourful corals. I saw the opposite.

“For decades, scientists and conservationists have been warning that climate change is an existential threat to the Great Barrier Reef and all the world’s corals. We know what needs to be done: a rapid transition to 100% renewable energy; an end to fossil fuel subsidies; the phasing out of coal-fired power stations; and keeping coal in the ground.”

While the mass bleaching is caused directly by an El Niño, which pushes warm water to the east Australian coastline, many scientists believe climate change is making the El Niño worse and more frequent, and this is coupled with a general rise in sea temperatures caused by global warming.

Great Barrier Reef: aerial survey reveals extent of coral bleaching Read more

Also on board the dive boat was the chief executive of the Queensland Tourism Industry Council, Daniel Gschwind. The reaction of his organisation to the current bleaching requires a balancing act – on one hand, highlighting the need to protect the enormous value of the reef to the Australian economy, worth a conservative AU$6bn (about £3.25bn) a year, while on the other, making sure that tourists are not scared off by alarming news. “The Great Barrier Reef is Australia’s most important tourism asset,” he said.

We dived at a second site at Agincourt Reef that day, at Castle Rock. Again, the underwater seascape was devastated by bleaching, and the scale of the devastation was beginning to sink in.

Scientists report that the same scenes are being replicated along a 1,000km section of the reef, more than a third of its total expanse. Of 500 reefs between Cairns and Papua New Guinea surveyed during this current episode, 95% have experienced significant coral bleaching – only four reefs showed no impact.

Prof David Booth, head of the Australian Coral Reef Society, the world’s oldest coral reef society, and representing some of the nation’s most respected marine biologists, said he had never seen scientists so worried.

“The visual is shocking but so is the disconnect between the severity of the bleaching and the decisions by governments to approve coalmines and coal infrastructure,” he said. “Australia is like a drug dealer for climate change – selling all this coal, but all the while knowing the harm we are doing.”

This particular bleaching event will end once the waters begin to cool. What scientists don’t know yet is how many of the corals will die, quickly being covered in a brown algae that tourists will not want to pay to see.

But there is still room for optimism. These areas can and will recover as long as the scale and frequency of bleaching does not increase. And some other areas that have been devastated in the past decade by destructive threats – such as cyclones and crown-of-thorns starfish – are now recovering well. The reef is always a mosaic of damaged, recovering and stable areas that are constantly changing with environmental conditions.

Coral has evolved to deal with attacks from nature. The question is: can it survive all the cumulative assaults from humans?

James Woodford is the author of The Great Barrier Reef (Pan Macmillan). His trip was funded as part of a partnership between the Australian Marine Conservation Society and Oris