If you were to go looking for a magnificent American body of water worthy of an epic end-to-end swim, Lake Champlain might be it. Carved out of high country by glaciers, fed by Green Mountain brooks and icy Adirondack springs, it stretches 120 miles, forming much of the border between New York and Vermont. It provides drinking water for 145,000 people. But in 2004, when clean-water activist Christopher Swain swam the full length, he was immediately confronted by the truth: Lake Champlain was anything but pristine. “I swam through clouds of manure runoff that were kind of slippery and sticky at the same time,” Swain recalls. “I could smell the fertilizer, when it was pouring down rain. There was this lawn-and-garden chemically smell.” In the northern reaches of the lake, he swam through blue-green algae. In the south, he encountered invasive aquatic weeds that entangled him. At another point, he felt a tingling on his leg, “like a cellphone buzzing in my pocket.” It turned out to be a sea lamprey, an eel-like, parasitic fish, trying to suck his blood.

The stink, the animal feces, the algae blooms, even the lamprey were all “things that didn’t belong here but now had the run of the place,” Swain says. Many could be linked to nutrients that leach from farms upstream and fertilizers flowing from fields and lawns, making their way into streams and eventually the lake. This persistent ooze of waste has been steadily rising over the last century, changing the lake’s ecology and stimulating the growth of blue-green algae, which can prove fatal to dogs and toxic to humans. Beach closures have become an annual summer event in part due to the toxic algae, setting up a conflict between those like Swain who prize Champlain for its recreational opportunities and those who make a living by growing food in the watershed.

But Champlain is just one lake in a much larger struggle. Today the U.S. Environmental Protection Agency rates nearly half of all American rivers and streams as “poor,” with 46 percent of water bodies overloaded with phosphorus and 41 percent with nitrogen, much of which flows off farms in the form of fertilizers, manure and soil. These farm-born pollutants overwhelm the Susquehanna River and the Chesapeake Bay that it feeds; they choke the San Joaquin on down to San Francisco Bay; and they punish the Mississippi River ecosystem all the way south to the Gulf of Mexico, where excess nutrients stimulate the growth of oxygen-sucking algae, which in turn create an annual dead zone bigger than the state of Connecticut. The complex array of problems tied to this pollution not only pits die-hard greens against regulatory-averse farmers, but fishermen against dairy producers, neighbor against neighbor. With the Trump administration in Washington viewing clean water regulations as a symbol of regulatory overreach, these conflicts are poised to rise to a fever pitch.

Legislating Better Water

In today’s political climate, it might be hard to believe that at one time the country was nearly unified in the fight for clean water. In 1972, Congress overrode President Nixon’s veto and passed what is commonly called the Clean Water Act, one of the country’s most significant environmental laws, which continues to shape water quality to this day. Ohio’s Cuyahoga River no longer catches fire from dumped petrochemicals (the 1969 fire became a symbol that helped launch the environmental movement). A corporation can no longer dump oil in the ocean and walk away scot-free. The billions BP paid to settle claims from the 2010 Gulf spill are a direct result of the Clean Water Act’s provisions. That’s because the Clean Water Act subjected polluters that directly discharge waste into America’s waterways to permitting, fines and potential lawsuits if they fail to comply with regulations. These were designated as “point source” polluters, because the sewer pipe, or wastewater plant, could be easily identified as the source.

But the act also defined “nonpoint source” pollution, which arises from diffuse sources, such as irrigation ditches that carry fertilizer into rivers, or dry streambeds that can channel cow manure into rivers after a heavy storm. Significantly, agriculture won an exemption under the Clean Water Act, which meant that nonpoint pollution from agricultural sources could continue unchecked. Attempts to limit or more precisely define this exemption are often framed as an attack on farmers by bureaucratic regulators and environmentalists. So progress in cleaning up water often stalls and conflict persists.

But Vermont, in its typically iconoclastic way, has tried to bridge the opposing camps. Starting a few years before Christopher Swain was stroking across Champlain’s murky surface, state regulators sought common ground to take action and restore the lake. The resulting water-­protection rules have been exemplary. If the Trump administration succeeds at rolling back federal water regulations, Vermont and Lake Champlain may well serve as an example for other states that want to clean up their local waters while keeping farmers solvent.

Upstream on the farm

Guy Choiniere is a third-generation Vermont dairy farmer based in the village of Highgate Center. His operation, which is certified organic, sits on 450 acres of rolling land that today is an incarnation of the well-managed farm. Grasses of a half dozen varieties flutter in the light breezes, 100 healthy cows loll in the fields and rest peacefully in the loafing barns, and a robust buffer of woods and shrubs guides the eye down to the Rock River, which meanders to nearby Lake Champlain. But 15 years ago, Choiniere’s farm was an exposed swath of mud and manure—just the sort of farm that would be a source of nonpoint water pollution and a direct threat to Vermont’s great lake.

The Decline of a Watershed 1609-1750

Samuel de Champlain sights the lake in 1609. More than a century of British-French conflict ensues, but the land and valley remain relatively untouched. Abundant salmon, lake trout, sturgeon and whitefish are noted. An early observer writes that a man standing on a wagon in a tributary with pitchfork in hand could “obtain in a few minutes all the fish needed for consumption.” 1750s-early 1800s

Old-growth forests are felled as settlers clear land for farming. 60% of the basin is logged, releasing millions of tons of sediment containing massive amounts of phosphorus. The entire Northeast loses 99.5% of its old-growth forests. 1800-1930s

The Champlain-Hudson Canal opens the lake to sea lamprey. Silt washed into the lake and tributaries from logging and farming increases lamprey spawning habitat—soon they prey on trout and salmon. New dams on the lake’s tributaries block spawning of salmon, sturgeon and other valuable fish. Causeways built across the lake impede water flow in shallow northern bays, leading to further concentration of nutrients. Thanks to these factors, along with overfishing, salmon and lake trout are extinct in the lake by 1900. 1930-1950

Dairy becomes Vermont’s principal agricultural product. Farmers begin draining wetlands around the lake, further removing buffers to runoff of nutrients and other pollution. By 1980, 35% of Vermont’s wetlands are drained, largely for farmland. 1960-1985Farmers become reliant on corn to feed dairy cows. They supplement exhausted soils with phosphorus-rich industrial fertilizers. Cornfields are often tilled down to streambanks, releasing still more phosphorus. Manure is regularly spread on fields, with much of it running off into water instead of being absorbed into the soil. 1999-present

Blooms of cyanobacteria (blue-green algae) become commonplace in summer. Overflow stormwater runoff leads to increased levels of E. coli. These two factors trigger regular beach closures.

“There wasn’t a blade of grass on those riverbanks,” Choiniere comments as he ambles over clover and vetch. “The cows were destroying it. There were landslides every other year. Conservation is about keeping your soil and your minerals on your own farm. And that’s exactly what I wasn’t doing. I attracted attention long before these rules were mandated”—because of fertilizers and manure he routinely spread on his fields that leached into the Rock River.

Guy Choiniere’s farm shows how agricultural pollution built up not just over years but centuries. Choiniere is of Quebecois heritage and his French pre­decessors were the first white men to colonize the valley after Samuel de Champlain “found” it in 1609. The farm, like the rest of the Champlain Valley, had been covered in forest, which the settlers cleared, starting the first big pulse of pollution into the lake.

Cleared trees and dairy cows, however, weren’t the only source of the lake’s rising levels of nutrient pollution. An even more potent vector arose by the time Choiniere’s father carved out his farm from the family land: “My dad took over in the ’60s and that’s when corn took over,” Choiniere explains. His father followed conventional advice to rely on feed and reduce the time cows spent on pasture eating grass, with the goal of pumping more milk from the cows. “As cows’ genetics improved we were milking heavier so we had to satisfy their energy needs,” Choiniere says. “And corn became a nice energy source. Cows love it.”

But corn—with all the fertilizers and pesticides it takes to produce—is an exceptional burden on waterways. Unlike pasture, which keeps ground covered in grass year-round and the soil intact, corn requires plowing and added nutrients to pump up yields. To supplement soil with nitrogen and phosphorus, farmers spread cow manure, never in short supply on a dairy farm, as well as chemical fertilizer on their plowed fields. Through the winter snow and spring rains, fields are kept bare—meaning that the exposed soil can wash away. Besides adding sediment to the watershed, the soil has phosphorus bound up in it, adding to the nutrient load. Until the early 2000s, most Vermont corn was grown this way. Even though their goal was to fertilize corn, farmers were inadvertently overfertilizing Lake Champlain.

At water level

Phosphorus and nitrogen stimulate plant growth, which is why farmers spread them on their fields. But when rains wash fertilizers and manure into streams and lakes, these nutrients feed microscopic algae. During warm weather, they proliferate at a tremendous rate in “algae blooms.”

They’re an eyesore, turning lakes bright green and portions of ocean, such as the Gulf of Mexico, red. These algae consist of multiple species, some harmful, others benign. They foul shorelines, lakes and rivers. Particularly worrisome is blue-green algae, which is technically a bacteria known as cyanobacteria. These microorganisms can produce toxins that kill fish, mammals and birds. Across the country, dogs have died after swimming in lakes and rivers choked with blue-green algae. People have also been sickened, because under certain conditions, the algae emit toxins that can cause rashes, respiratory symptoms, diarrhea and intestinal pain, and with long-term exposure, may harm the liver and digestive system.



Preliminary research at Dartmouth College has linked cyanobacteria toxins to ALS (Lou Gehrig’s disease). Researchers mapped higher-density clusters of people with ALS across northern New England near lakes with the lowest water quality that are likely to have harmful algae blooms. The researchers suspect that toxic algae blooms may play a causal role in clusters of the neurodegenerative disorder. But they warn against overreacting, saying that swimming in fouled water once won’t cause the disease. If there is a connection between ALS and cyanobacteria it likely involves long-term exposure to cyanobacteria, as well as a genetic predisposition to the disease and other environmental or chemical triggers.

Good Farm, Bad Farm From barn to streamside, these farming practices protect water bodies—or don’t. Bad Practices

1. Cows spend much of their time in a barn with a big roof. Rain runs freely off the roof and water puddles around the barn, mixing with manure before seeping into the ground or running off.

2. A large pit collects manure. Although better than no management, this smells, often leaks and can overflow. It can contaminate soil and groundwater with excess nitrogen.

3. Farmers spread manure on fields to manage it, making it more likely to run off into the water.

4. Cows roam freely including into streams and drainages. This causes erosion and direct water contamination.

5. Fields are planted with corn to feed cows. At the end of the season, fields are tilled and left bare, making them more susceptible to runoff and erosion.

6. Almost no land is in pasture.

7. Row crops and bare ground lead down to the river. Plus a tiled drainage system installed under row crops funnels excess nutrients straight into the water. Good Practices

8. Barns have under­ground catchment systems to slow runoff of dirty water, allowing it to slowly filter through soil. Gutters on the roof direct clean water to separate areas.

9. Manure goes into a methane digester generating energy for the farm. The digester also produces liquid manure, which is injected into the soil as a fertilizer. Manure injection limits runoff.

10. Cows traveling from pasture to pasture are restricted to a few paved pathways, limiting erosion. Bridges over streams protect banks.

11. For farmers with some land in corn, “no-till” or “low-till” practices limit turnover of soil and slow down the release of nutrients. Cover crops like winter rye planted immediately after corn harvest further lock soil in place.

12. Trees and shrubs planted in a 20-foot or wider swath create a streamside buffer strip around the river to reduce erosion and absorb excess nutrients before they can enter the water.

13. More land put back into pasture keeps ground covered year-round, preventing loss of nutrients. Though production per cow is lower, “grass-fed milk” earns a premium over regular organic and conventional milk, incentivizing good practices.



Though this research sounds scary, it is not conclusive at this point, and many other potential factors could have caused the ALS clusters. “We agree that there should be rigorous research into that devastating disease, but this hypothesis about a linkage with a particular amino acid in cyanobacteria is not supported,” says Vermont state toxicologist Sarah Vose, Ph.D.

Although Vermont authorities say there are no records of serious human health effects from blue-green algae on Lake Champlain, beach closures occur every summer, impacting the $300 million in annual recreational revenue from vacationing families, watersports enthusiasts and fishermen. Cyanobacteria isn’t the only culprit: E. coli from livestock, pets and untreated sewage can foul the lake too. By the early 2000s, beach closures were common—between 2012 and 2014, there were more than 60 closures.

Algae—both toxic and nontoxic species—are harmful in other ways too. In warm weather, the blooms shade out more benign aquatic plant life. Once the algae die off in winter, waterborne bacteria gobble them up and multiply, consuming oxygen from the water and choking fish and other species. By springtime, a pond suffering from nonpoint source pollution and algae blooms may be effectively dead. Were this just occurring in Lake Champlain, the concerns would perhaps not travel further than the state legislature. But the blooms occur in nearly every state, peaking in August and September, though no national agency tracks them—or the illnesses they cause.

The Gulf of Mexico’s oxygen-poor “dead zone,” for example, comes like clockwork each summer as nutrients flow from the heartland and out the mouth of the Mississippi River into the Gulf. This feeds the Karenia brevis algae that cause “red tide.” State agencies closely monitor red tide, closing shellfish beds and limiting fishing to ensure contaminated seafood doesn’t make it to consumers. The states surrounding the Chesapeake Bay have tried, for decades, to address nonpoint pollution and algae blooms, but annually receive failing marks on water quality, much to the chagrin of seafood lovers. In the Midwest, favorite summer lake-recreation spots suffer because visitors can’t enjoy waters fouled with blue-green algae.

And then there’s drinking water. In 2014, the city of Toledo shut down its water supply, forcing it to truck in bottled water, because of blue-green algae that engulfed the western end of Lake Erie. (Vermont, New York and Quebec have been mostly successful at treating the 20 million gallons of water that’s drawn from Lake Champlain each day for algae and other pollutants.)

Des Moines, Iowa, faces a related crisis, spending millions of dollars each summer so its water utility can clear drinking water of nitrates, which arise from fertilizer runoff and can be especially harmful to infants and small children. “Look at the culverts discharging [agricultural runoff] into the Raccoon River”—the main source of drinking water for 500,000 people, says Des Moines Water Works utility manager Bill Stowe. “They have the exact same configuration as if they were coming out of a city storm-sewer system. But thanks to our friends at EPA, agriculture has an exemption for stormwater discharge under the Clean Water Act.” The utility sued three northern Iowa counties to block upstream agricultural pollutants, but a federal judge dismissed the closely watched suit in March 2017. The judge said it was up to the Iowa state legislature to act.

Suing to save our waters

Guy Choiniere would never say that the Clean Water Act or any regulation caused him to completely rethink his way of farming. Like most good farmers, he senses, almost preternaturally, what his land needs. As the Clean Water Act’s co-drafter Thomas Jorling notes, “Farmers tend to be much more knowledgeable about natural systems than people who’ve gotten a Ph.D.”

But the aspirations of the Clean Water Act and the failsafe devices baked into the legislation made a radical change economically feasible in a state like Vermont—even when it involved rethinking agriculture. Jorling, then a Senate staffer, and the other drafters of the act recognized that “government agencies have a tendency to become paralyzed by complexity or funding.” So they wrote the Clean Water Act in such a way that there was no legal wiggle room if water quality fell below an acceptable threshold. In other words, if the powers that be are not doing their job to keep the water clean, the act allows them to be sued. The “civil suits” provision in the act gave the people of New England legal recourse when the water in Lake Champlain became unacceptable. Which is exactly what happened.

6 Everyday Choices to Keep Water Clean Go Grass-Fed: Switching cows to grass, instead of grain, leads to less phosphorus pollution—up to 75 percent less for beef and 23 percent for dairy—according to USDA researchers. “The change in land use provides the benefit,” explains Al Rotz, agricultural engineer with the USDA. Converting grain row crops to grass provides stable cover, reducing nutrient runoff. However, grass isn’t necessarily perfect. “A poorly managed grass system could be worse than a well-managed crop system,” adds Rotz. Know Your Fish: Questionable fish-farming practices can pollute water bodies. Oversight of U.S. aquaculture makes domestic farmed fish mostly eco-friendly. Fish farms in other countries are improving, but some continue to discharge anti­biotics, hormones, pesticides and excess waste into surrounding waters. Check seafoodwatch.org to see which farmed fish get the green light from Monterey Bay Aquarium. Better yet, choose oysters, mussels and clams—they naturally filter and improve water quality. Box the Rain: One inch of rain on a 1,200-square-foot roof can create 750 gallons of runoff that flows across your driveway where it picks up debris (like trash, oil and copper dust) and ferries it into waterways. Install a rain barrel to keep water for your plants or lawn. Researchers estimate capturing rainwater can reduce stormwater runoff up to 20 percent. Another option: create your own rain garden to further reduce runoff. Ditch Fertilizers: Home lawn and garden fertilizers contribute one-third or more of the total nitrogen in urban watersheds, University of Minnesota researchers found. That’s more than comes from golf courses, cemeteries, parks and campuses combined. If you must use fertilizer, look for one made with controlled-release or slow-release nitrogen. Skip Mowing (this week): Let grass grow long and set the mower blade to 3 inches or higher to support a deeper root system that requires less water. Deep roots mean grass can grow even during drought, and without bare, brown patches, nutrients stay in place. When you mow, leave clippings behind as a slow-release fertilizer. Check cbf.org (Chesapeake Bay Foundation) for more water-friendly landscaping tips.Scoop the Poop: Dog waste is high in fecal coliform bacteria, which can contaminate watersheds. It’s also a large source of phosphorus and nitrogen in urban waterways, according to University of Minnesota researchers. —Sara Ventiera

In 2002, the state of Vermont proposed phosphorus limits for the lake to comply with the Clean Water Act, setting a “Total Maximum Daily Load” (TMDL) that marks a threshold for the maximum amount of pollutants that a body of water can handle each day. But the evolving science on the matter convinced the nonprofit Conservation Law Foundation that these limits were insufficient to stop the algae blooms and protect the ecology of the lake. So in 2008, the foundation sued the EPA, arguing that the Feds needed to step in, revise Vermont’s limits and fund measures to reduce the flow of nutrients into the lake. The EPA and the state eventually agreed to set a lower TMDL for the lake, which was issued in 2016.

Since the bulk of the lake nutrients arise from farms, the state realized it had to focus on that source. Luckily federal conservation grants are available to farmers, paying for water-protecting measures, such as streamside vegetation buffers. These USDA grants, which increased from 2002 through 2014, can amount to hundreds of thousands of dollars for even small farmers. Funded every five years under the massive Farm Bill, they have a good chance of surviving in the Trump era because of support by Republican lawmakers in Congress. The money, after all, flows to farm-state constituents.

In Vermont, federal programs work in tandem with the state’s water-cleaning Act 64. Passed in 2015, the law requires all farms to start using specific farming techniques to reduce runoff by July 2017. Even farms with fewer than 50 animals must use practices like manure injection, underground catchments for storm­water runoff and extension of streamside forested buffers—all measures that are designed to protect the watershed and can often be funded under federal farm programs.

Hope for the Future

The impact of well-placed farming subsidies and water-quality management laws are now evident on many farms in Vermont. At Lorenzo Whitcomb’s conventional dairy farm just outside of Burlington, he sows winter rye as a cover crop over his harvested cornfield. In just 10 years, cover crops in Vermont have gone from 50 to 25,000 acres. On the southern end of the lake in Orwell, where 24-year-old Rachel Orr has taken over from her father to run their 200-cow dairy farm, the young farmer produces a dictionary-thick “nutrient management plan” that pinpoints her soil types down to the square foot and indicates precisely the amount of fertilizer that needs to be applied. All of these different efforts were co-funded by federal and state matching grants.

But most impressive is Guy Choiniere’s organic farm. When farm inspectors first started snooping around his property in the late 1990s, he admitted it was hard to take. “Someone coming onto your farm and telling you you’ve got problems is very insulting,” Choiniere recalls, echoing a common complaint of farmers. “We had to get over that.” Ten years later, strolling through his pastures, it is clear he is very much over it. Beneath his barn, catchments slow drain water and cause it to percolate slowly through the soil, filtering out nutrients. Up ahead is a cow path that had previously been a mudslide but has been reworked as a tidy, erosion-proof stone lane. And leading down to the river itself is a lush forest planted with the most efficient trees for absorbing nutrients before they can hit the river and fertilize an algae bloom. All this was partially financed by an active federal and state government grant program, including $250,000 from the USDA’s Natural Resources Conservation Service. Choiniere chipped in around half of the bill for the improvements—eager to grow his business and lighten his farm’s footprint.

Eventually Choiniere took a leap of faith and went a step further than the government required. He went organic and planted his cornfields back into native pasture. Since pasture is never tilled, it holds the soil and nutrients better than an annual crop like corn. And there are other benefits. His vet bills have plummeted now that his animals are 100 percent grass-fed. The price he earns from his milk has risen 15 percent and he spends nothing on tilling. “Being sustainable is money in my pocket,” he says, as he looks out over his lush fields. “That’s the name of the game for staying in business. Agribusiness will give you recommendations all day long. How much fertilizer to use. How much grain to feed… Me, I went with my instincts.”

In other words, in a bid for water quality, measures were put in place that ultimately improved farming and, in Choiniere’s case, profitability. But even farmers who have not gone organic or reverted to pasture have taken basic but effective steps. And those successful in controlling their nonpoint pollution have seen profits rise, says Ryan Patch, ag development coordinator for Vermont’s Agency of Agriculture, Food and Markets. He oversaw many of the state’s listening sessions with farmers leading up to Act 64 and recalled a number of “aha” moments when farmers would suddenly exclaim, after a nutrient-management training course, “You just saved me $10,000 in fertilizer!” Savings arose because nutrients were applied more judiciously and kept on the farm instead of washing into Lake Champlain.

Of course not everybody in the agricultural community is on board. Plans to reduce nutrient runoff hit roadblocks last year, when farmers sought more time to implement the kind of measures that Choiniere champions. Across-the-board change, it seems, won’t come easily.

Nor will it come fast. Although some streams running into the lake show marked improvement, others continue to exceed their nutrient limits. And portions of the lake remain far above target levels for phosphorus, meaning a continued pattern of toxic algae blooms, summer beach closures and dead zones for aquatic life. But Patch, for one, takes a long view. “I am optimistic about the road map we’ve laid out,” he says, speaking of the state’s plans. “We’ll do it with the help of the farms.” He also notes that the lake is dealing with centuries of human impacts—all the latent pollution from logging, erosion and residential development—that “won’t be able to be addressed until we shut the faucet off” from all the farms upstream. Patch and other officials estimate that it will take 20 years to close the tap for good, and once that’s done, they can begin to reduce the residual nutrients in the lake.

Will the rest of the country, facing similar water-quality crises, follow suit? In these tumultuous times, with environmental regulations under siege from the White House, the paths that individual states and the federal government take on water quality may diverge. Vermont, as its most famous poet, Robert Frost, once wrote, is taking the road “less traveled by.” Whether other states head down that road, too, will determine how clean our nation’s water will be in the future.