EPA warned Vermont was ‘not on track’ to meet its 2036 target
On the last day of August, Jeff van den Noort walked into the water a few steps from his home on North Hero island in Lake Champlain and found thick swirls of neon green film coating the surface. He waded in up to his ankles and dipped a jar for a sample. His parents bought the island house in 1966, and the lake was clear then; van den Noort has watched it deteriorate in the decades since, most sharply after he moved in full time in 2010 to care for his ailing mother. That late-August day was the worst he had seen all summer.
“The worst days ever are really, really bad,” he said. “Just as far as you can see, the whole bay is green.”
Later that week, van den Noort loaded his rusting Saab with a bucket, Mason jars and a smartphone, stopped at four more spots along the shore to gauge the muck, take photos and note the weather, and uploaded his reports to an online database. He is part of a large volunteer effort monitoring a problem that has plagued the lake, which supplies drinking water to about 200,000 people. In recent decades, blooms of potentially toxic cyanobacteria, often called blue-green algae, have killed pets, forced beaches to close and hurt business and property values along the shore.
“I just don’t feel like enough is being done,” van den Noort said. “And I think the state needs to take this seriously.”
The state promised more a decade ago. In 2015, then-Gov. Peter Shumlin stood near the Burlington waterfront and signed Vermont’s Clean Water Act, which promised to tighten pollution limits and fund waterway cleanup in response to pressure from environmentalists and the U.S. Environmental Protection Agency, which had told Vermont officials for years that they needed to take much stronger action. The EPA finalized tougher cleanup targets in 2016 that Vermont must meet by 2036. After 10 years and nearly a billion dollars spent on water quality projects and programs, the state’s most recent estimates put the effort at 35% of the goal. In a 2025 letter to the head of the Vermont Department of Environmental Conservation, the EPA’s regional administrator warned that the state was “not on track” and would need to more than double its annual pace. Eric Perkins, a former EPA official involved in setting the target, said steps taken so far, such as upgrading sewage treatment plants, represent “low-hanging fruit.”
Phosphorus, an element present in all organic matter and an essential building block of life, drives the blooms. Too much of it enters the lake from farm fields saturated with fertilizer and manure, dirty stormwater, and raw sewage from treatment plants overwhelmed by heavy rains, tipping the lake’s ecosystem out of balance and spurring the growth of microorganisms that turn shallow bays and shorelines into no-go zones. Ingesting cyanobacteria-laden water can cause vomiting, diarrhea, dizziness and liver damage, while skin contact can lead to rashes. Researchers have also detected possible links between chronic exposure to cyanobacteria and heightened risk of Parkinson’s disease and ALS, also known as Lou Gehrig’s disease. The blooms can also deprive fish and other aquatic life of oxygen.
Unlike chemicals and heavy metals, which can be removed from lakes and rivers by dredging, phosphorus cannot be feasibly extracted from the lake, so regulators instead limit how much enters each day. The EPA sets a total maximum daily load based on how much phosphorus the lake can absorb and remain healthy, and the state must cut pollution from agriculture, stormwater, roads, forests and wastewater treatment plants to meet it.
Progress is uneven across the lake. Some areas have seen incremental improvements in phosphorus concentrations and blooms, while other parts are getting worse. A Seven Days and ProPublica analysis of lake monitoring data through 2025 shows seven of the lake’s 15 sampling stations have exceeded the EPA’s annual phosphorus limits every year since 2015, and four stations recorded higher average phosphorus levels over the past decade than in the decade before, including in the southern part of the lake and its northeast arm. In September, the Department of Environmental Conservation told the EPA that in two northeastern sections most chronically plagued by phosphorus runoff, Vermont is not nearly on track to meet its targets. The department acknowledged it is not making enough progress on stormwater runoff and that reductions in farm pollution in the Missisquoi River watershed have slowed since 2023.
Vermont shares the 120-mile-long lake with New York and Quebec but is the source of about two-thirds of the phosphorus that flows into it. Agriculture is the largest polluting sector, while stormwater runoff from development, such as urban parking lots and rural roads, contributes the highest amount of phosphorus per acre. State agencies have repeatedly delayed taking more difficult and politically fraught action against pollution from farms, businesses and housing developments, and those policies have encountered resistance from the dairy industry, property owners and lawmakers sympathetic to their interests.
The challenges in cleaning up Lake Champlain also raise a question with stakes well beyond Vermont: if a small, conservation-minded state cannot tackle algae blooms in its own waters, what does that mean for other areas of the United States grappling with the same problem — in the Great Lakes, the Chesapeake Bay and the Gulf of Mexico?
State officials counsel patience. “We are moving apace with the commitments we’ve made, in terms of the projects, but it isn’t manifesting itself nearly as quickly in the lake monitoring data,” said Julie Moore, secretary of the Agency of Natural Resources. “This is a complex ecosystem, and we need to come at this work with a whole lot of humility.”
Laura DiPietro, water quality program director for the Agency of Agriculture, Food and Markets, said the agency spent its first five years building programs, including ones to reduce soil erosion and help farmers upgrade manure storage equipment, but implementing them “doesn’t happen overnight.” She said she expects greater phosphorus reductions from the programs in the coming decade.
The early years of the cleanup went better. The EPA set initial targets for the lake in 2002 and tougher ones in 2016, and Perkins, then the EPA’s Vermont water quality coordinator, felt the state was generally on the right track. State agencies and lawmakers set up the Clean Water Fund with dedicated tax revenue streams, put in place stronger rules for fertilizer use and manure storage, and created permit programs to limit stormwater runoff from roads and municipalities. An EPA report card in 2020 acknowledged that Vermont had checked off all the milestones up to that point. “Overall, I was very impressed with the level of commitment demonstrated by the state,” Perkins wrote. By the time he retired in 2021, Perkins and his colleagues at the EPA had become concerned about signs of lagging commitment on enforcement against farms.
One clear opportunity to speed reductions, Perkins said, is to ensure farms comply with required agricultural practices and avoid spreading manure before anticipated rainstorms, which has caused “major phosphorus runoff events.” Making that a priority “could likely make a big difference,” he wrote. Vermont could also tighten water quality requirements and enforcement for concentrated animal feeding operations — CAFOs, the farms that keep animals confined in barns for long periods — by overhauling its permitting system. In recent years, many small family dairies have closed or consolidated into larger operations that would be considered CAFOs under federal law. Vermont has delayed action on an EPA directive to strengthen its approach to regulating CAFOs; a recent state task force report recommended working to develop the program for another five years. Just across the lake, New York has used such permits for decades to ensure better environmental practices on larger farms.
A second EPA recommendation is to change which agency leads farm regulation. Vermont’s Agency of Agriculture regulates how farms handle waste on site, while the Agency of Natural Resources is responsible if runoff leaves the farm. The split has caused oversight problems, including lapses in following up on reported water quality violations with inspections and enforcement, and environmental advocates have long maintained that the agriculture agency has a conflict because it also has a mandate to promote the state’s farm sector.
The arrangement frustrates farmers, too. In a letter to Gov. Phil Scott earlier this year, owners of one Vermont dairy farm wrote that “the lack of alignment and clear communication between these agencies” places farmers in an uncertain position, adding that “Many in the farming community feel caught in the middle of interagency disagreements, unsure which standards will ultimately govern their operations or how enforcement will proceed.” Officials at both agencies acknowledged the communication problems and said they have taken steps to improve how they share information on potential violations and coordinate inspections.
In 2024, the EPA ordered Vermont to consolidate the regulation of agricultural pollution under the Agency of Natural Resources, the state’s main environmental agency, which the EPA says has sole authority to administer federal Clean Water Act rules. In a letter that year to Moore, EPA Region 1 administrator David Cash wrote that the agency had monitored the situation in Vermont for well over a decade and that, “despite having had ample time and opportunity to cure longstanding program deficiencies,” ANR “has failed to do so.” Cash noted that the state has failed to give ANR “sufficient resources or operational authority” to regulate runoff from farms. Over the back-and-forth hangs the threat that the federal government could take over enforcement of water pollution rules from Vermont.
The divisions between the two agencies surfaced in internal emails obtained under Vermont’s Public Records Act. In a 2025 email, Agency of Natural Resources general counsel Catherine Gjessing reminded her counterpart at the agriculture agency and legislative counsel staff that “there are a significant number of farms that are in fact discharging without a permit,” in violation of the federal Clean Water Act. She added that the agencies had worked under the split arrangement, with the agriculture agency taking the lead, “for decades now and we are still not in compliance.” In an interview, the agriculture agency’s general counsel, Steve Collier, said there was never “a Wild West situation where farms were not being regulated” and that his agency’s rules protect the environment, adding: “Whether or not the Clean Water Act was being administered exactly as it should be is a different issue.”
Outside agriculture, Vermont has also yet to fully implement a third EPA demand, along with the directives of its own Clean Water Act. The 2015 law required the Department of Environmental Conservation to require properties with three or more acres of paved surface, such as parking lots, to install systems to slow and capture stormwater runoff — a permit system known as the “3-acre rule.” Five years later, with the permit system still unfinished, the EPA warned Vermont that it would have to give the state “a failing grade” if it did not finish by Sept. 4, 2020. Vermont met that deadline, but in 2025 the state passed a law pushing the date for obtaining permits to 2028 for properties in the Champlain basin. Those property owners do not have to make the stormwater upgrades until 2033.
Steve Cushing has spent a quarter century working to clean up St. Albans Bay, in the northeast part of the lake near the epicenter of Vermont’s dairy industry. Over that quarter century, he listened as federal and state environmental officials came through town and pledged to act. In 2015, one EPA official told him and his neighbors to “Expect a lot of progress 10 years from now in many segments of the lake.” This summer, Cushing said, the cyanobacteria blooms in the shallow bay were some of the worst he has seen in several years, and the public beach in St. Albans Bay Park has mostly been closed to swimming since June. “Overall, you can’t really see a big improvement in water quality in the bay,” he said.
Public data supports his account: the federally funded Lake Champlain Basin Program, which coordinates research and grantmaking across the watershed and issues a water quality report every three years, found in its 2024 edition “deteriorating” trends in phosphorus and cyanobacteria in the lake’s northeast arm and no progress in Missisquoi Bay, a shallow stretch spanning the U.S.-Canada border that frequently suffers intense blooms.
Scientists and advocates point to two forces compounding the problem: pollution accumulated over decades and a changing climate. What scientists call “legacy phosphorus” has built up in soils and lake sediments after many decades of fertilizer use, manure spreading, deforestation and unregulated septic and wastewater systems. “We are working on a system that’s been impacted by human activities for the past 150-plus years,” said Matthew Vaughan, chief scientist of the basin program. Since 2003, cyanobacteria blooms have appeared earlier in the spring and later in the fall as temperatures rise, and can appear even at lower phosphorus levels. The drought that hit Vermont in 2025 led to a spike in blooms, thanks to a combination of heat and low water levels. Downpours, meanwhile, wash phosphorus-laden sediment through the state’s streams and rivers: in a single week in July 2023, record-shattering floods pumped six months’ worth of phosphorus into the lake. “All of this just makes it more urgent to do our part to address these water quality challenges,” Vaughan said.
Some state officials and researchers contend that phosphorus deposited in the lake bed and soil decades ago might play as significant a role in fueling algae blooms as today’s runoff. Eric Smeltzer, who worked for the Department of Environmental Conservation for 35 years, including as the state limnologist who monitors the health of Vermont’s lakes and ponds, said that while legacy phosphorus remains a challenge, “I think it’d be wrong to just rely on that as the excuse.” “The most important technical question about the Lake Champlain phosphorus cleanup is: Are these practices working? And if not, why not?” Smeltzer said. “How can it be done better? I think you can’t just explain it away based on time lags and legacy phosphorus forever.” Smeltzer said wastewater treatment still garners an outsize share of Vermont’s clean water spending, even though it has been clear for years that it is not a major contributor of phosphorus, while agriculture and stormwater are.
Cushing traces the blooms to the dairy farms that dominate the watershed and to regulators’ failure to “put any teeth behind” restrictions on manure spreading and other water quality rules. A former dairy farmer, he has pushed for policy changes as a volunteer with the St. Albans Area Watershed Association and has led an effort to mechanically remove vegetation that contributes to the phosphorus problem in the bay. At 78, he is searching for someone to take over the weed removal effort. “I’m getting a little burned out,” he admitted.
Three EPA demands have shaped the state’s regulatory choices: consolidating farm-pollution regulation under the Agency of Natural Resources, building a permitting program for the state’s largest dairies, and requiring stormwater controls at properties with three or more acres of paved surface. Vermont has delayed action on the dairy permitting directive, has yet to fully implement the stormwater rule, and pushed the basin permitting deadline to 2028, with required upgrades not due until 2033, against a phosphorus target the state must meet by 2036.
Seven miles to the west, on the island of North Hero, van den Noort questioned this summer whether all the data he gathers is making a difference. “If we really wanted to solve the problem, I think we’d have to make some tough choices,” he said. “I don’t think anybody wants to do that. It’s a head-in-the-sand thing.” Every week he drives up the western edge of Isle La Motte on his monitoring circuit, looking out over a stretch of water that is supposed to be one of the cleanest parts of Lake Champlain. On the worst days, a pea green broth of blooms stubbornly hugs its entire shoreline.