Sitting along the Pacific Ring of Fire, the Philippines’ volcanic geology features porous rocks that allow water to move easily underground and flow into its ocean.
These hidden flows – called submarine groundwater discharge – are known to maintain balance in the ocean’s chemistry. But with experts noting that only about 30% of the country’s wastewater is being treated, these flows have an insidious impact.
Submarine groundwater discharge (SGD) is a natural process driven by a mix of climatic, hydrogeologic and oceanographic forces, often occurring in coastal areas. It is more pronounced in rocky and volcanic regions.
Rivers are another direct link between land and sea, but they are also visible – their freshwater and pollutants more obviously flow into the ocean. SGD, which combines terrestrial groundwater and recirculated seawater, is often more concentrated with nutrients and pollutants, and hidden below the ground.
Research on SGDs has only occurred in the past decade. Scientists now recognise that the discharge of fresh, brackish and marine groundwater into coastal oceans is just as impactful as that of rivers.
Estimates sourced from the Great Barrier Reef in eastern Australia suggest the total volume of water flowing from the ground into the coastal ocean is greater than river discharge. Moreover, in certain coastal areas, the concentration effects of SGDs result in a nutrient input into the ocean surpassing that of surface water – rivers, lakes and streams. Scientists say this has impacts on the Philippines’ coral reefs, which make up nearly a tenth of the global total.
How SGDs help and hurt reefs
In some contexts, groundwater can support reef systems, delivering the right combination of nutrients at modest levels, or cooling marine heat.
However, rising coastal population densities, changing agricultural practices and ageing wastewater systems impact this balance.
At two small coral islands in the northern South China Sea, researchers found that even a small amount of SGD carries carbon compounds that can degrade the shells or suppress the growth of certain marine animals.
In many coastal areas of the Philippines, harmful algal blooms – commonly known as “red tides” – have become increasingly frequent, with over 44 distinct coastal locations across the archipelago experiencing outbreaks since the first major bloom was recorded in 1983.
“I recall the feeling of the hot viscous layer of water sitting on top of the colder, clear water below, the first time I swam in the Philippines,” says Amelia Wenger, conservation scientist and water pollution programme lead for coral reefs at the Wildlife Conservation Society, describing an algal bloom.
Scientists link red tides to a combination of climate change and eutrophication – where an overconcentration of nutrients stimulates excessive algal growth. SGDs are increasingly recognised sources of these nutrients, which include nitrogen, phosphorus and dissolved silica.
“The science shows very clearly that wastewater is one of the two big killers of coral reefs … in Hawaii and in other places in the world,” Greg Asner, director of the Center for Global Discovery and Conservation Science at Arizona State University, said in a radio interview in January. “The only other one that’s competing with wastewater is climate change. And when the two combine, it is a terrible mix.”
In many island territories, porous volcanic rock or limestone’s high permeability limits the soil’s natural filtration capacity, allowing rapid transport of water and pollutants. Private houses and holiday resorts alike often rely on private cesspools or septic tanks in these territories, where sewage systems are typically insufficient or non-existent. These simple holes, or containers in the ground, collect the wastewater but are often badly sealed. They use some form of chemical treatment but are often outdated, poorly maintained or vulnerable to flooding, allowing contaminants to seep into groundwater with minimal intervention. From there, pollutants travel unseen to coastal waters, with consequences ranging from coral disease to unsafe swimming conditions.
A study on the reefs around Santiago Island in the north-western Philippines found that groundwater emerging beneath reef flats had nutrient concentrations much higher than those of normal seawater. In other sites, such as the resort island of Boracay, researchers found residues of caffeine and painkillers travelling from land to sea via groundwater. These results clearly point to untreated wastewater, especially in busy tourist areas.
“Contaminants can also be agrochemicals and petrochemicals, and science barely knows the impacts of the huge range of those chemicals,” Asner said in an email interview with Dialogue Earth.
Wastewaters threaten the coral triangle
In Metro Manila, the Philippines’ largest metropolitan area, less than 15% of the city’s population is connected to a sewage system. From the majority of households, untreated waste flows directly into rivers or leaks into the ground. From there, they are an easy reach to Manila Bay, a natural harbour on the western border of the region.
The bay is now heavily polluted from household wastewater, with faecal contamination far exceeding safe limits – a hallmark of the faulty human waste system.
Amid mounting water pollution and these high levels of faecal bacteria, in 2025 the Metro Manila Development Authority, alongside the Department of Environment and Natural Resources and the Metropolitan Waterworks and Sewerage System, began drafting a plan to expand sewerage infrastructure. Their target is to service around 80% of the national capital region by 2047. Early progress has been visible: Manila Water, the main concessionaire involved, added over 43,000 new sewer accounts in September 2025 alone.
However, SGD remains largely absent from policy frameworks.
“We know that SGDs play a key role in marine pollution,” Von Hernandez, vice president of the conservation NGO Oceana Philippines, tells Dialogue Earth. “We need governments to add it to their priorities for research and investigation, to make the issue more visible to the public so that appropriate actions could be taken.”
High stakes
Researchers are pushing to change that. “There is not enough attention from policymakers in the region on the phenomenon, and that tells us that there is still much work that needs to be done,” says Fernando Siringan, research professor at the University of the Philippines’ Marine Science Institute.
His team discovered storms and heavy rainfall events can temporarily boost groundwater flow into the ocean for several days after the event. As climate change intensifies storm events in the region, the pulse of pollution could become more dynamic and less predictable, adding another layer of concern.
“Coral reefs are already suffering from climate change consequences. Polluted hidden effluents are increasing the impact,” Siringan tells Dialogue Earth.
For coastal countries reliant on healthy reefs for fisheries, tourism and shoreline protection, the stakes are high. Reef degradation lowers fish stocks, reduces tourism and causes significant income declines for coastal households. For example, the six-month closure of the Philippines’ tourist gem Boracay in 2018, due to environmental degradation, was projected to have affected over 36,000 workers and caused losses of nearly USD 1 billion. Beyond tourism, over 2 million people work directly or indirectly in the country’s fisheries sector.
“An invisible problem is becoming visible,” says the chemical oceanographer Gil Jacinto. A 2024 global meta-analysis of coastal groundwater nutrient concentrations identified SGD as a significant source of nitrogen and phosphorus in the ocean of many coastal areas. Yet it is rarely included in official nutrient budgets. These budgets balance the input, output and storage of such nutrients, making them critical to identifying sources of eutrophication.
“There is good data and evidence that SGD pollution affects coastal environment health in the Philippines. Still, most policy responses here only focus on river discharge, while the contribution of SGD remains largely unaccounted for,” Jacinto tells Dialogue Earth.
From mapping pollution to integrated solutions
As evidence mounts, local communities and scientists in island territories are pushing to integrate SGD monitoring into environmental management at tourist sites – a first step toward recognising groundwater as part of the land-sea pollution continuum.
One example can be found in Hawaii, where researchers from Arizona State University including Asner worked with the ʻĀkoʻakoʻa Reef Restoration Project. The team mapped over 1,000 locations where groundwater contaminated with faecal bacteria enters reef systems on the western coast of the state’s largest island. This data is now informing policymakers when considering new land reformation efforts, wastewater infrastructure upgrades, and community-led efforts to replace cesspools and repair septic systems.
“When I started working on pollution issues, there weren’t that many people who were interested,” Wenger tells Dialogue Earth. “In the last five years, there’s been a real shift. The more we know about it, the more we can raise awareness and adapt solutions for other countries.”
I wish we’d started this 20 years ago, but we didn’t. Here we are now, and we’re thinking about the solutionsAmelia Wenger, water pollution programme lead, Wildlife Conservation Society
Wenger is now developing guidance for the sanitation and production sectors (agriculture, livestock and aquaculture), with plans to expand this to encompass plastic pollution, coastal erosion and urban runoff.
This follows from a previous guide and toolkit she and her colleagues developed to help conservationists and sanitation workers reduce wastewater pollution. Released in 2024, the toolkit includes factsheets to help such professionals diagnose, assess and monitor specific types of pollution within their systems, and to design ad hoc solutions.
“I split my time talking to ocean people and then talking to sanitation people about what they both need to think about pollution. Coastal communities are generally receptive, especially when shown that reducing wastewater pollution directly benefits local reefs, fisheries and public health,” she says. “But often the high costs are a limitation. Working alongside the WASH [water, sanitation and hygiene] sector can help on this front.”
She adds: “I wish we’d started this 20 years ago, but we didn’t. Here we are now, and we’re thinking about the solutions.”
Submarine groundwater flows might be invisible, but their impact is not. As scientific understanding deepens, researchers say governments must widen their scopes beyond rivers and pipes and confront the hidden currents shaping coastal systems.
