Threats to underwater caves today, and how they are protected

Underwater caves look timeless, but the water in them is part of living landscapes that are changing quickly. This article summarises the main pressures documented in recent, dated sources: pollution, construction, falling spring flows, invasive species and the impact of visitors, along with the tools being used to protect caves. Each situation is described as of the date of its source; conditions may since have changed.

What goes into the water

Pollution is the oldest and most widespread threat. Karst filters water poorly and moves it fast, so contaminants spread far ^[19]. In the Yucatán, a 2011 review identified wastewater as the main groundwater quality problem: with no rivers, most wastewater was injected back into the aquifer or released into cenotes and lakes, and only about a third was treated. It warned that rapid tourism growth on the Riviera Maya, without comprehensive wastewater regulation, was steadily increasing pressure on water supplies and on groundwater-dependent ecosystems, and singled out landfills as critical in such permeable rock ^[1].

In Florida, the Department of Environmental Protection (DEP) names excess nutrients, mainly nitrate, and declining flows as the main threats to springs. It reports nearly $268 million spent specifically on springs restoration over four years, and restoration plans covering all 24 nitrogen-impaired Outstanding Florida Springs ^[9]. Cave divers have helped trace pollution sources: Global Underwater Explorers credits Woodville Karst Plain Project research with showing that water from Tallahassee's sewage treatment facility was reaching the groundwater in the Wakulla cave system, contributing to changes in the city's water management ^[12].

Building on top of caves: the Tren Maya

The largest recent construction project over cave country is the Tren Maya railway around the Yucatán Peninsula. Its Section 5, between Cancún and Tulum, crosses the coastal karst where many of the longest known underwater caves lie.

The sequence of dated reports is as follows. On 2022-04-18 a federal district judge in Yucatán granted a provisional suspension of construction on Section 5 South, between Playa del Carmen and Tulum, on the grounds that it lacked an environmental impact authorisation; the case had been brought by a group of divers. The president said the next day that his government had not been officially notified and described opposition to the project as politically motivated ^[3]. Regional press later reported, citing other outlets, that cement had been poured into several cenotes and caves and that support piles had been driven into caves, and that the project's designation as a national-security work meant court rulings to halt it had no practical effect ^[6]. The federal tourism development agency, Fonatur, said that 75% of the Playa del Carmen to Tulum stretch was being built on an elevated viaduct to protect the karst, cenotes, caves and underground rivers ^[7].

Survey records reflect some of this. In February 2024 the Quintana Roo Speleological Survey (QRSS) reported that Cenote Ni Ha, recently connected to Sistema Ox Bel Ha, was reported to be buried under the right of way of the new Tulum to Bacalar railway, adding that it had no reports on the extent of damage to the cave and that a nearby cenote still gave access to that section ^[2].

In April 2025, under a new federal administration, the head of the environment ministry (SEMARNAT), Alicia Bárcena, acknowledged that the whole route needed integral restoration, including care of caverns and cenotes; a deputy minister said those who built the work should pay for the damage, and that the ministry was analysing a biosphere-reserve-type protection for the Quintana Roo cave system ^[5]. In August 2025 the newspaper El País reported that Section 5 had changed route several times, that about 42 km of its roughly 66 km were raised on viaduct to protect the karst, and that some 10,000 pillars ended up cutting through the very ecosystems the design was meant to protect, without the legally required updates to environmental and construction permits ^[4].

These reports come from courts, government statements and journalism rather than from a published scientific survey of cave damage along the whole route; this article did not find such a survey. What they establish is that infrastructure over karst is now one of the main documented pressures on the Yucatán's caves.

Invasive species

Not all threats come from construction. The QRSS reports that the Mexican tetra, a predatory fish native to open-water cenotes, has moved into cave passages and has decimated populations of blind cave fish and crustaceans in the Carwash, Sac Actun and Naranjal caves ^[8].

Less water in the springs

Florida's DEP links declining spring flows to falling aquifer levels ^[9]. In September 2026 the Florida Springs Institute reported that several springs in High Springs, in the Santa Fe River basin, had stopped flowing during that summer's drought and that some popular spring parks had closed because of stagnant water ^[10]. The institute argued that land conservation is a key protection for springs and stated that the state's Florida Forever programme received no money in the 2026-2027 budget ^[10].

Development next to caves

Development threatens individual sites as well as whole aquifers. In January 2026 the National Speleological Society said that commercial and residential projects planned around its Mill Creek Sink Nature Preserve in Alachua, Florida, risked stormwater and other diffuse pollution draining into the sink, which it described as draining a basin of more than 70 square miles (about 180 km²) and feeding priority springs. The society said it had hired lawyers to review zoning and permit applications ^[11].

Visitors and divers

Popularity brings its own pressure. Florida State Parks warned, when checked in October 2026, that Madison Blue Spring State Park frequently closes on weekends and holidays when it reaches capacity ^[18]. The NSS Cave Diving Section notes that, as diver numbers have grown, diver impact has become one of the biggest conservation concerns for some government owners of dive sites, and that most visible damage, such as broken formations and scarred clay banks, can be avoided with good buoyancy, trim and propulsion technique ^[14]. A study at Bundera Sinkhole in Australia showed that even careful research diving disturbs the layered water of anchialine caves, with open-circuit scuba having a more obvious effect than rebreathers ^[15].

Sea level and climate

Coastal caves sit at the boundary between fresh and salt groundwater, so they are sensitive to sea level. Announcing a 2017 study of the Ox Bel Ha ecosystem, the US Geological Survey quoted biologist Tom Iliffe saying that the work gives a baseline for evaluating how sea-level rise, coastal tourism development and other stressors will affect these food-poor systems ^[13].

How caves are being protected

The tools are varied, and most of them depend on documentation:

Legal protection. The Bahamas declared the South Abaco Blue Holes Conservation Area a Conservation Forest in 2015, according to the Bahamas Caves Research Foundation, which used cave survey and radiolocation to show what lay beneath the land ^[16]. In Australia, the Bundera remipede was listed as endangered under state and federal law by 1999 ^[15].

Land purchase and management. Florida's restoration plans and land acquisition in spring recharge areas ^[9] and the work of caving societies that own sites, such as the NSS, are aimed at protecting both caves and water.

Courts and public process. The 2022 Section 5 case in Mexico was brought by divers ^[3], and the NSS is using legal review to protect Mill Creek Sink ^[11].

Protecting the aquifer as a whole. Researchers writing about Italy's Pozzo del Merro noted that a deep flooded sinkhole is also an access point to the deep aquifer and should be protected against pollution ^[17].

For divers, the most useful contributions are rarely dramatic: keeping impact low, following site rules, supporting the groups that survey and monitor caves, and passing observations of damage or pollution to those groups so that they enter the record.