The Mesoamerican Barrier Reef is the largest barrier reef in the western hemisphere – an underwater wilderness stretching over 700 miles along the coasts of Mexico, Belize, Guatemala and Honduras.

One of the most biodiverse ecosystems in the Americas, the reef is home to a dazzling variety of coral and more than 500 species of fish, and provides a livelihood for more than a million people. But now, a combination of mass tourism and poor waste management has left the reef increasingly vulnerable to climate change, placing this natural wonder in serious trouble.

“Throughout the Caribbean, we have seen a massive decrease in coral coverage,” says Michael Webster, executive director of the Coral Reef Alliance, a nonprofit organisation that works on reef conservation in Honduras. “Whereas we might have had 60-70% coral coverage in the past, now it’s down to 5-10% in places.”

Now, the rapidly changing climate could make the damage even worse. “We’re seeing these huge variations in rainfall, temperature, weather,” says Amanda Acosta, executive director of the Belize Audubon Society, a nonprofit responsible for managing reefs off the coast of Belize. “In 2012, we had massive rainfall,” she says. “Last year, we had no rain at all. And in the summer, the sea was as warm as a bath pan.”

The impacts of these rapid weather changes are already being witnessed across the reef system. Jesús Arias-González, a researcher at the National Polytechnic Institute in Mexico, conducted a study of the entire region last year and found 22% of the coral colonies presented signs of bleaching from elevated sea temperatures. The bleaching could soon get worse: in September the US’s National Oceanic and Atmospheric Administration began issuing coral bleaching alerts all along the Mesoamerican Reef. While cooler winter waters have since decreased alert levels, such warming events will likely increase as global weather patterns change.

Facebook Twitter Pinterest Corals reefs along the southern region were hit the hardest with up to 80% of corals showing signs of bleaching in Roatan and Utila. Photograph: Courtesy of Bleach Watch Roatan

But although this level of damage is concerning, for many scientists who spoke to the Guardian the more pressing threat is mass tourism. “Climate change happens long term,” Arias-González says. “The massive development happening right now is much more dangerous.”

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“The bleaching is certainly getting worse every year,” says Vanessa Francisco, a field officer with Resiliencia, a collaboration between the United Nations Development Program and the Mexican government to strengthen natural protected areas against the effects of climate change. “But the biggest problem we have is pollution.”

The growth of mass tourism as well as farming has resulted in an increase of untreated waste and agricultural runoff on to the reef; a 2010 study found traces of raw sewage, pesticides and illicit drugs in the underground river system of Mexico’s Yucatán peninsula, groundwater that would “eventually discharge into Caribbean coastal ecosystems”. A 2013 study concluded that “domestic waste management and final disposal in Belize, Guatemala and Honduras is a critical problem that needs to be addressed urgently”.

Facebook Twitter Pinterest On Yucatán peninsula in Mexico, the government is planning to create a marine reserve that would extend 200 miles out from the coast. Photograph: Klaus Thymann

The increase in waste acts as a fertiliser to macroalgae, a kind of fleshy algae that can compete with and eventually smother or kill the corals. According to the Healthy Reef Initiative (HRI), an alliance of more than 30 organisations that monitors the Mesoamerican Reef, macroalgae cover has nearly doubled in the last 10 years across the region. This poses a serious problem because, as Francisco explains, a reef which is in a poor condition due to algae blooms is much less likely to withstand the effects of climate change: “It’s like getting a cold if you have HIV,” she says. “It reduces the reef’s resilience.”

According to Webster, from the Coral Reef Alliance, these underwater ecosystems are highly adaptable under normal circumstances, constantly subjected to the eroding forces of storms and ocean currents. “Reefs are in a perpetual state of recovery,” he says. “A healthy reef is one that’s growing faster than it’s eroding.” A reef that is ravaged by macroalgae, however, will have a harder time bouncing back from an unseasonably warm current or a severe storm.

Mary Peter, 35, is a diving instructor in the tiny town of Xcalak, on the border between Mexico and Belize. Last year, Xcalak was hit by tropical storm Earl, the deadliest Atlantic hurricane to hit Mexico in 10 years. “It left a lot of devastation,” says Peter. “It destroyed a lot of the top reef structure. Everything was broken off; we were swimming through debris.” Six months on, however, Peter says “the reef is recovering nicely. Those chunks of coral that broke off are integrating back into the ecosystem.”

The increase in waste acts as a ​​fertiliser to macroalgae, a fleshy algae ​​that competes with and kills the corals

This kind of destruction and recovery is part of the reef’s natural ebb and flow: However, with hurricanes and storms likely to increase in frequency and severity because of climate change, the recovery process will become more difficult. When you add overfishing and pollution, the result could be devastating. “The future is going to be warmer, more disturbed, more acidic,” says Webster. “Corals are going to have to adapt. But what if they can’t? If you’re protecting the forest and you lose all the trees, it’s not a forest anymore.”

To stave off damage, scientists and nonprofit groups across the region are working with local communities to reduce overfishing, minimise pollution and strengthen the reef. “Climate change is a world issue,” says Webster. “We’re working to solve problems at a community level so we can give the reef a better chance to adapt to those global problems.”

Facebook Twitter Pinterest A coral reef at Banco Chinchorro Photograph: Alamy

Miguel Jarillo is a fisherman in Mexico’s Banco Chinchorro, the largest atoll in the northern hemisphere and a Unesco biosphere reserve. Ten years ago, he was trained by the World Wildlife Foundation to monitor the reef, something he has been doing ever since, providing data on the reef’s health for a number of different NGOs and conservation groups, as well as maintaining a more sustainable fishing practice. “It’s become a vice,” he says. “Going out into the sea and looking after my own resource. Because if I don’t look after it, no one else will.”

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In Belize, too, there is an increasing awareness of the reef as a vital economic resource, generating 15% of the country’s GDP. When the government began seismic tests for offshore oil near the reef last year, the outcry from the community in the tourist town of San Pedro was such that authorities shut the operation down after one day. “Without this reef, we’re just like any other Central American country,” says Elis Mei, 34, a tour operator in San Pedro. “This reef keeps our economy going. Without it, we’re done.”

Facebook Twitter Pinterest Nurse sharks at the Hol Chan marine reserve off Ambergris Caye, Belize. Photograph: Alamy Stock Photo

There are signs that conservation efforts are paying off, albeit extremely slowly. According to HRI’s latest survey, coral cover has increased from 10% to 17.5% over the last 10 years. Herbivorous fish, which can help reduce macroalgae cover, have also increased. Five new Marine Protected Areas have been designated since 2011, meaning that the four countries now protect 20% of their territorial sea. Last year the Mexican president, Enrique Peña Nieto, designated the Mexican Caribbean biosphere reserve, a 5.75m-hectare reserve off the Yucatán peninsula.

But designating marine-protected zones only achieves so much. “Up to now, the decree is just on paper,” says HRI’s Marisol Rueda Flores, pointing out that the Mexican government has simultaneously cut funding from the body that oversees marine parks. “Mexico has some of the best laws for protecting coastal areas – the problem is no one follows them. The government has barely begun to realise the urgency of this situation.”

• Reporting for this story was supported by the Fund for Environmental Journalism