Why Water Quality Matters for Coral Reefs

Clean water is vital for coral reef health. 

Poor water quality fuels algae blooms, smothers corals, and increases disease, threatening the biodiversity and resilience of these ecosystems. Learn more about why water quality is so important for coral reefs >

Across the MAR, reefs are particularly vulnerable to pollution from untreated sewage, agricultural runoff, and tourism development. Our Regional Water Quality Monitoring Project, which collected data at 90 sites across Belize, Honduras, and Mexico, revealed alarming levels of turbidity, pathogens, nitrogen, and phosphorus—all of which can stress or kill coral reefs.

The good news? Now we know. And we can do something about it.

Collecting Data for Action

At CORAL, we gather solid data for meaningful action.

Our regional water quality work began with a protocol that ensured a coordinated study to pinpoint the major sources of pollution and identify priority areas for intervention. Here’s what we found:

The entire Mesoamerican Reef is impacted by high levels of nutrients, particularly ammonia, and these contaminants are found on the reef. 

Honduras
30 sites revealed high nitrogen and pathogen levels, particularly around tourism hubs in the Bay Islands and sites close to river outflows from the mainland.

Belize
30 sites showed elevated turbidity, phosphorus, and pathogens.

Mexico
30 sites highlighted elevated ammonia and phosphorus.

Pollution sources for the region come from untreated sewage, poor update and management of septic tanks, urban runoff, and unsustainable agricultural practices.

What does this mean for the reef?

When pollution enters the ocean, it can fuel algae growth, smother coral, disrupt the delicate balance of reef ecosystems, and spread harmful pathogens that make corals more vulnerable to disease. Nutrient-rich runoff and untreated sewage can also cloud the water, blocking sunlight that corals need to thrive.

Over time, these impacts can reduce biodiversity, weaken reef resilience to climate change, and harm the communities that depend on healthy reefs for food, tourism, and coastal protection. Learn about other water quality issues plaguing coral reefs today >

What We’re Doing

It’s time for collective action to spark global changes.

Based on these findings, we’re working with local water associations, governments, and partners across the MAR to put real solutions in place. These actions are tailored to the unique challenges of each country and are designed to drive meaningful change.

Here’s what we’re doing to tackle water quality challenges head-on:

Investing in Wastewater Treatment
Advocating for infrastructure and governance investment that leads to improved sewage treatment infrastructure in tourism-heavy areas and urban centers, especially in Cozumel, Belize, and Honduras.

Community-Led Water Management
Strengthening local water associations—like the West End Polo’s Water Association in Honduras— and water and sanitation service providers across the region to manage water and sanitation sustainably.

Integrating Water Quality in Protected Area Management
Ensuring water quality standards are included in marine protected area management plans throughout the MAR.

Expanding Monitoring and Enforcement
Collaborating with local partners to build robust water quality monitoring and compliance systems to track improvements and guide action.

Our Recommendations

These recommendations are rooted in science, community collaboration, and a commitment to solutions that last. They’re designed to guide governments, communities, and private sector partners in taking meaningful action.

Upgrade and Expand Wastewater Infrastructure
Prioritize sewage treatment in high-tourism zones and urban centers in Belize, Honduras, and Mexico.

Strengthen Land-Use and Agricultural Policies
Develop land-use plans that consider water quality and quantity impacts, and promote sustainable agriculture to reduce runoff.

Modernize and Enforce Regulations
Invest in strengthening technical skills, update and enforce regulations to control discharges, and include water quality standards in protected area management plans, aligning with international standards.

Raise Awareness
Support education actions to engage communities and tourists in protecting water quality and reef health.

Secure Funding for Solutions
Advocate for funding from governments, donors, and the private sector to invest in sustainable water quality management.

Together, these actions can drive real progress—reducing pollution at the source, strengthening community resilience, and ensuring coral reefs remain a vibrant, life-sustaining resource for generations to come. By working collaboratively across the MAR, we can build a cleaner, healthier future for reefs and people alike.

Dive Deeper into the Policy Briefs

Want to explore the details? Read our policy briefs for Belize, Honduras, and Mexico.

Download the Belize Policy Brief

Download the Honduras Policy Brief

Download the Mexico Policy Brief

The Power of Partnership

We know lasting change is built on collaboration. 

That’s why our water quality efforts in the MAR region are rooted in partnership, trust, and the power of collective action. By working side by side with communities, governments, scientists, and tourism leaders, we’re transforming data into solutions that protect both coral reefs and the people who depend on them.

This work is more than a project—it’s an alliance. An alliance that unites local knowledge with global expertise and puts communities in the driver’s seat. This makes progress possible. All for the future of coral reefs.

We believe that everyone has a role to play in protecting coral reefs. Whether you’re a policymaker, a scientist, a business owner, or a visitor to these remarkable places, you are part of the solution. Join us in this alliance for clean water and healthy reefs. Together, we can turn the tide for the Mesoamerican Reef—and for our shared future.

Let’s build a cleaner, healthier world—together.

The post Turning the Tide on Water Pollution in the Mesoamerican Reef appeared first on Coral Reef Alliance.

These aren’t distant problems. They’re happening now—and they’re reversible. Here’s how different types of pollution directly impact coral reefs and what we can do to stop the damage.

Nutrient Pollution Overfeeds the Ocean

Imagine dumping fertilizer into a tropical garden nonstop—eventually, things overgrow, choke each other out, and die. That’s what happens when excess nutrients like nitrogen and phosphorus enter coastal waters. These nutrients come from agricultural runoff, leaking septic systems, and untreated sewage. And they don’t just disappear.

Once in the ocean, they act as fuel for algae. The result? Massive blooms that blanket coral reefs, block out sunlight, and outcompete corals for space. When these algae die, they decompose and consume oxygen from the water, creating low-oxygen “dead zones” where coral and fish struggle to survive.

Worse, these conditions invite pathogens. Nutrient pollution has been linked to spikes in coral diseases like white syndrome and black band disease, which can spread rapidly across entire reef systems.

Main sources

• Fertilizers and manure from farms and lawns
• Poorly treated sewage and septic overflow
• Rainwater runoff from cities and roads

Impact on reefs

• Algal overgrowth that smothers coral
• Increases risk of coral disease and mortality
• Lower oxygen levels and light availability

What you can do

Support wastewater upgrades and local clean water initiatives. At home, choose organic or low-phosphorus products and be mindful of what goes down your drain.

Sediment Turns Coral Reefs Into Dustbowls

Healthy coral reefs need clean water—sunlight powers their symbiotic algae, which feed the corals from within. But when land-based sediment washes into the ocean, it clouds the water and settles on reef surfaces like a suffocating blanket.

This sediment usually comes from poorly managed construction sites, deforested areas, and overgrazed pastures. With no vegetation to hold soil in place, rain sweeps mud and debris into rivers that lead straight to the sea.

Once it reaches the reef, sediment does real damage. It blocks light, preventing photosynthesis. It clogs coral mouths, interfering with feeding. And it makes it harder for coral larvae to settle and grow—slowing reef recovery and disrupting the delicate balance of life.

Read about our work in Maui to reduce sedimentation smothering the reef >

Main sources

• Land clearing and construction
• Unregulated agriculture
• Erosion from poorly managed landscapes

Impact on reefs

• Reduces sunlight critical for coral survival
• Smothers coral polyps and disrupts feeding
• Hinders growth and reef regeneration

What you can do

Support smart coastal development and reforestation. When traveling or living near the coast, look for businesses that practice sustainable land management.

Plastic Waste Brings Disease

It’s easy to think of plastic pollution as a surface problem—bottles bobbing in the waves, nets tangled in sea turtles. But look closer beneath the surface, and you’ll find plastic has become a chronic threat to coral reefs. It’s showing up in the most remote places on Earth—reef systems once considered untouched now littered with debris.

Floating plastic doesn’t just ruin the view. As it drifts through the ocean, it collides with coral structures, scraping delicate polyps and creating wounds that leave them vulnerable to infection. Larger debris, like discarded fishing gear or plastic bags, can get snagged on the reef, physically breaking coral branches and blocking sunlight.

But the problem goes deeper—literally. As plastic breaks down, it releases microscopic fragments called microplastics, and these aren’t just inert particles. Scientists have discovered that microplastics act like little rafts for harmful bacteria and pathogens. When these bacteria-laden plastics make contact with coral, they dramatically increase the risk of disease—up to 89% higher, according to some studies.

One particularly insidious effect is how plastic changes the coral microbiome—the collection of beneficial bacteria that help coral stay healthy. Disrupting this microbial balance makes coral more susceptible to stress, disease, and bleaching. And unlike a one-time event like an oil spill, plastic keeps accumulating. It never truly goes away.

Main sources

• Single-use plastics (bags, wrappers, packaging)
• Abandoned or lost fishing gear
• Microfibers from clothing, cleaning cloths, and hygiene products

Impact on reefs

• Cuts, abrasions, and physical damage to coral
• Reduced sunlight exposure
• Increased rates of disease and infection
• Disrupted coral microbiome

What you can do

Reducing plastic use might feel small, but it makes a big difference. Choose reusable items over disposables, avoid products with microbeads or glitter made from plastic, and support local and global efforts to reduce marine plastic pollution.

Oil and Chemicals Poison the Reef One Drop at a Time

We often think of oil spills as rare catastrophes—but oil and chemical pollution happen every day in smaller ways. Storm drains flush chemicals from roads, lawns, and factories straight into the sea. Farms spray pesticides that wash into coastal waters. Even tiny spills from boats add up over time.

Oil is especially toxic to coral. It coats their surface, suffocates polyps, and interferes with reproduction. Juvenile corals are particularly vulnerable, with exposure often leading to stunted growth or death. Chemical pollutants like mercury, lead, and pesticides accumulate in reef species, weakening coral and the creatures they shelter.

Unlike physical damage, these toxins often linger—building up in the reef’s food web and altering life on a microscopic level. In high enough concentrations, they can wipe out entire reef sections and make recovery nearly impossible.

Where it comes from

• Oil spills, fuel leaks, and marine transport
• Pesticides, herbicides, and industrial waste
• Household chemicals and automotive runoff

Why it matters

• Interferes with coral reproduction and growth
• Kills coral larvae and juvenile reef species
• Contaminates reef food webs and ecosystems

What you can do

Dispose of chemicals properly and avoid toxic pesticides. Support policies that hold polluters accountable and invest in safer, cleaner alternatives.

Sunscreen Is a Silent Coral Killer

Most people don’t think twice about slathering on sunscreen before diving into the ocean—but what protects our skin can be deadly to coral reefs. Many commercial sunscreens contain chemicals like oxybenzone and octinoxate, which have been shown to cause coral bleaching, deform coral larvae, and damage DNA.

Don’t miss the other 6 harmful ingredients. You can read more in our article Sunscreen 101 >

These effects can happen at incredibly low concentrations—just a single drop in a swimming pool-sized area of water can be enough to disrupt coral development. The chemicals wash off swimmers, rinse down the drain in showers, and end up in the ocean through wastewater systems.

Over time, this chemical cocktail builds up in coastal areas, especially in popular tourist zones. Even reefs that appear healthy can be silently weakened by long-term chemical exposure.

Where it comes from

• Chemical sunscreens used by swimmers and divers
• Wastewater and stormwater runoff

Why it matters

• Causes bleaching and tissue damage
• Disrupts coral hormones and DNA
• Reduces coral resilience and reproductive success

What you can do

Switch to mineral-based sunscreen with non-nano zinc oxide or titanium dioxide. Wear sunshirts and dive skins for sun protection. These alternatives protect your skin without harming the reef.

A Cleaner Ocean Starts With Us

Pollution is a complex problem, but the solutions are within reach. At CORAL, we work with communities to reduce local threats—from upgrading sewage systems to promoting reef-safe tourism and sustainable development. 

And you don’t have to live near a reef to make a difference.

Reefs may be resilient, but they’re not invincible. Every piece of plastic skipped, every cleaner product used, and every advocacy effort adds up. Small changes ripple outward—and those ripples are what coral reefs need most.

The post How Pollution Threatens Coral Reefs and What We Can Do About It appeared first on Coral Reef Alliance.