YUCATÁN PENINSULA, Mexico — Researchers and conservationists are sounding the alarm over damage to the cenotes of Mexico's Yucatán Peninsula, which are being affected by pollution, urban development, and the construction of the Tren Maya. Organizations like Sélvame del Tren and Cenotes Urbanos are working on their conservation, mapping, and water monitoring to protect these sacred ecosystems and the biodiversity they harbor.

On a sweltering day in April 2025, a small group of cave researchers, led by veteran diver José “Pepe” Urbina and biologist Roberto Rojo, walked in single file through the dense rainforest of the Yucatán Peninsula, some 24 kilometers from the Caribbean coast. They moved slowly, clearing a path with a machete, in search of their destination: a remote stretch of the flooded Zumpango cave system, which likely had not been visited by anyone for years.

Suddenly, the vegetation grew less dense, revealing the jagged entrance of a limestone tunnel leading into the subsurface. The air cooled as the team descended, carefully navigating around large stalactites. Then, someone shouted, “Whoa!” and everyone saw it: an ancient Mayan vessel resting on a rock ledge.

Such discoveries are not unusual in Yucatán, which contains a vast underground network of limestone caves with rivers running through them. When part of a chamber collapses, it forms a natural sinkhole called a cenote, a term derived from the Mayan word ts’onot.

A Sacred and Vital Resource Under Threat

For the Maya people, cenotes are sacred places inhabited by gods and spirits. They are also geological wonders that can contain historical artifacts and endangered aquatic species, though some have become tourist spots for those wishing to swim in their traditionally crystal-clear waters.

Critically, the cenotes of southern Mexico serve another ancestral purpose: they are part of a deep aquifer that spans 103,000 square kilometers and is the only source of fresh water for millions of people in the region.

“We are all connected through the cenotes,” says Urbina.

For him, Rojo, and a growing group of conservationists, that makes it all the more important to study what is happening inside these enchanting portals.

Cenotes have been threatened by agricultural runoff and residential wastewater leaks for decades. But in recent years, the arrival of the Tren Maya, a railway connecting tourist destinations, has increased the urgency to better understand these fragile ecosystems.

The 1,555-kilometer line, which had an estimated cost of $30 billion dollars and began operations at the end of 2024, was built in part by drilling massive support pillars directly into the same bedrock that underpins the cenotes.

At the same time, Urbina and Rojo fear that the growing development in the shadow of the train could further impact the cenotes.

For years, the duo worked separately to raise the alarm about these spaces. Urbina leads a conservation group called Sélvame del Tren, and Rojo co-founded Cenotes Urbanos. But it wasn't until the Tren Maya was announced that they joined forces and became part of a larger movement.

Now that the railway is fully operational, they are part of a collective of at least 10 groups rushing to catalog the ecosystem's many changes before it is too late.

“I fully trust that there are solutions,” says Rojo, though he worries it could take generations to reverse the ecological damage.

A Subterranean Challenge: Pollution and Destruction

A major challenge is understanding the scope of the network. There are at least 8,000 registered cenotes on the Yucatán Peninsula, but because sinkholes can appear suddenly, there could be many more.

To map the underground system, Urbina and other divers have charted approximately 1,450 kilometers of caverns. Even so, he estimates this is only about 10 percent of the total labyrinth.

One thing is clear: pollution can easily travel through the water flowing from one cenote to another and, eventually, out to sea.

Flor Arcega-Cabrera, an environmental geochemist at the National Autonomous University of Mexico, says the agricultural industry has become the largest source of pollution. Her research shows that animal waste with hormones, fertilizers with heavy metals, and pesticides from crop fields are likely leaching into the aquifer.

This is serious because people use well water and give it to their babies, explains Arcega-Cabrera. For example, nitrate, a common ingredient in fertilizer, can replace iron in the blood. This could result in blue baby syndrome, where babies' systems are no longer able to carry oxygen throughout their bodies.

Many residents without access to wastewater treatment facilities also leach sewage through the soil, a system that causes problems with the porous limestone. (Once, while Rojo was exploring a cave, he heard the faint sound of a toilet and saw feces raining down around him).

Near tourist sites and industrial parks, some cenotes have also become illegal dumpsites.

And then there is the train.

Construction of the Tren Maya began in 2020, despite opposition from many scientists, cave divers, and members of local indigenous communities. Urbina, a cave diver for more than 30 years, joined a lawsuit that reached Mexico's Supreme Court and briefly halted construction in 2023. But the victory was short-lived. The President of Mexico, Andrés Manuel López Obrador, citing national security issues, simply called in the military to finish the job.

In total, the Tren Maya is now anchored by 15,000 pillars, some of which were drilled directly into cenotes.

Researchers worry about the archaeological discoveries that may have been lost along the way. In 2014, a diver encountered the skeleton of a 13,000-year-old girl inside a cenote. Scientists later established that she was genetically related to modern Native Americans, a revelation that has led to a more accurate understanding of how the Americas were first populated.

The caverns also serve as critical habitat for animals like jaguars, tapirs, opossums, foxes, and coatis, which use the cenotes as a water source.

“When you arrive at a healthy cave, you see crickets, blind fish, blind shrimp, bats,” says Rojo. But when a cave is impacted, the original inhabitants are invaded by cockroaches and rats.

Conservation Efforts and the Impact of Awareness

Today, Sélvame del Tren and Cenotes Urbanos remain in regular contact to maximize their research and find ways to inspire greater public awareness.

The expedition to the Zumpango cave, for example, was part of a combined effort to map and track the health of existing caves in the state of Quintana Roo, which includes tourist areas like Cancún and Playa del Carmen, now easily accessible by the train.

While Urbina started Sélvame del Tren to raise awareness about environmental concerns on social media, organize peaceful protests, and monitor pollution, the organization's reach has expanded to track how the train has disrupted the movement of animals in the region.

Since Rojo founded Cenotes Urbanos with his fellow activists Talismán Cruz and Ximena Chávez nearly eight years ago, the group has grown to almost 500 members. They now conduct about twenty annual "re-dignification" expeditions to collect trash and gather water samples, and they organize workshops on mapping and speleology.

Guillermo D. Christy has worked as a water quality consultant for more than 25 years, advising hotels on purification and treatment processes. He is now partnering with Sélvame del Tren and Cenotes Urbanos to measure water quality in eight caves in Quintana Roo that are home to increasingly threatened animals specially adapted to live in the dark caves, such as the blind swamp eel (Ophisternon infernalis) and the Mexican blind brotula (Typhliasina pearsei), a transparent white fish.

He conducts tests to detect things like increased salinity, heavy metals, and bacteria such as E. Coli. So far, the effort has revealed elevated levels of E. Coli in the region, which D. Christy has shared with local communities and government officials to encourage better sanitation practices.

D. Christy has also been analyzing water samples from cenotes penetrated by the Tren Maya's support pillars. The tests show iron oxide in the water, a sign that metal from the piles could be leaching. Large concentrations of these chemical compounds can cause toxic algal blooms, says Arcega-Cabrera, which could affect the development of eggs and larvae of animal species living in the cave.

Earlier this year, Urbina, Rojo, and D. Christy took officials from the Ministry of Environment and Natural Resources (SEMARNAT) and the National Commission of Natural Protected Areas (CONANP) to the Oppenheimer Cave, another cenote about 21 kilometers from Playa del Carmen. As they moved from the first chamber to the second, the turquoise waters and towering stalactites gave way to mud and concrete pillars oozing iron oxide.

In the weeks following their visit, SEMARNAT officials made a public announcement concluding that the construction of the Tren Maya had damaged ecosystems in Yucatán. More than seven million trees were felled, and 125 caves and cenotes were drilled as the pillars were installed.

The agency has committed to a rescue plan, which involves the removal of fences that impede wildlife movement and a ban on the construction of secondary roads to tourist sites.

For his part, Urbina believes that if government officials see the beauty of these places, they will want to protect them. One day this past April, he took Óscar Rébora Aguilera, the Secretary of Ecology and Environment of Quintana Roo, diving in Sac Actún, one of the world's largest flooded cave systems. When they emerged from the water, he says he told Aguilera about plans to build a road above it. Shortly after, the Federal Attorney for Environmental Protection issued a temporary order to suspend construction.

It is a sign that their collective efforts may be bearing fruit.


Discover more from Riviera Maya News & Events

Subscribe to get the latest posts sent to your email.

Discover more from Riviera Maya News & Events

Subscribe now to keep reading and get access to the full archive.

Continue reading