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Fertilizer Washes off Midwest Farm Fields and Taints Communities’ Drinking Water, Poisons Gulf of Mexico

As Rainfall Events Become More Intense and Frequent, Fertilizers Applied to Midwestern Farmland Wash Away, Contaminating Waterways Near and Far

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Above image credit: Excess fertilizer applied on corn crops in Champaign County, Illinois, eventually winds up in the Gulf of Mexico where it feeds a massive, toxic algae bloom referred to as the dead zone.

Located in the heart of America’s breadbasket, Champaign County, Illinois, helps feed the nation’s demand for corn and soybeans while fueling one of the more insidious impacts of climate change – fertilizer runoff. 

Every year, farmers apply tons of nitrogen fertilizer to the vast swaths of crops that blanket Champaign’s flat landscape.

As rain carries unused fertilizer into the nearby Spoon River, it spurs toxic algae growth downstream. 

The excess nutrients flow with the waters from the Spoon into a series of larger rivers until dumping into the Gulf of Mexico, fueling a massive dead zone where no life can survive.

The environmental devastation – increasing blooms and a consistently growing dead zone – has been well documented for decades.

But changes in the way rain falls, as explained in a yearlong USA TODAY investigation, have set the stage for things to get much worse, many scientists now believe. The warming planet is bringing more precipitation overall, and more downpours in particular, to the same U.S. regions that grow a majority of America’s fertilizer-dependent crops.

Excess fertilizer applied on corn crops in Champaign County, Illinois, eventually winds up in the Gulf of Mexico where it feeds a massive, toxic algae bloom referred to as the dead zone.

About This Story

This story is a collaboration between USA TODAY and the Midwest Center for Investigative Reporting. USA TODAY is funding a fellowship at the center for expanded coverage of agribusiness and its impact on communities.

Champaign County, which has one of the nation’s top nitrogen surplus amounts, is ground zero for this impact. 

USA TODAY and Investigate Midwest analyzed spring precipitation data and nitrogen levels between 2014 and 2020 in the Spoon River. The analysis found that the kinds of extreme rainfall events made more common by a warming planet cause three times as much fertilizer runoff than other rain events and contribute to an outsized share of it in the waterways.  

The media outlets chose Champaign County because of its high rates of nitrogen surplus for corn crops – No. 3 in the nation – and because it’s one of relatively few places where the U.S. Geological Survey tracks watershed nitrogen concentration over a multi-year period.

Nitrogen in the Spoon spiked 42 times during those seven springs that the federal government tracked it. Thirty-six of the spikes came after a rainfall, when the fertilizer attaches to the soil particles and slips away from farm fields and into the river.

Sometimes, though, the rains came so fast and heavy that tens of thousands of pounds of nitrogen fertilizer poured into the river and sent levels soaring. 

The three heaviest storms dumped one-third of all the nitrogen during this time period into the Spoon River. 


Flood of Nitrogen


The findings mirror a larger study conducted by several researchers that found heavy rain across the Mississippi River Basin also contributed to one-third of the nitrogen flushed to the Gulf of Mexico. This heavy rain happens in just nine days per year.

Among the most striking consequences of fertilizer runoff, the Gulf’s dead zone spans the coasts of Louisiana and Texas and has rendered uninhabitable some 6,330 square miles of water, according to recent measurements by the National Oceanic and Atmospheric Administration.


This story is part of a larger USA TODAY project focused on climate change and rainfall. You can read the other stories here.


The floating algae bloom has expanded and contracted over the past 35 years but consistently surpasses the target set by the U.S. Environmental Protection Agency’s Hypoxia Task Force. The current five-year average is nearly three times higher than the target.

But it’s not just the Gulf of Mexico. Fertilizer runoff wreaks havoc on rivers and lakes across the country. It contaminates drinking water, harms aquatic life and sickens both people and pets. It has decimated the manatee population in Florida and fouled the Chesapeake Bay in the northeast.

Certain types of algae blooms, like cyanobacterial, cause respiratory infections, gastrointestinal bleeding and vomiting and are responsible for at least 321 emergency room visits in the United States between 2017 and 2019 alone, a Centers for Disease Control and Prevention study found. Worldwide, about 60,000 people annually are poisoned from algae blooms.

The blooms alsoemit methane – a greenhouse gas that exacerbates global warming. The EPA recently found the emissions from blooms could increase 30% to 90% in the next century.

It’s a devastating feedback loop. Algae blooms contribute to global warming, which increases rainfall, which then exacerbates fertilizer runoff.

In Illinois, the number of days with at least 2 inches of rainfall has increased about 40% over the last century, according to the state’s 2021 climate assessment. And spring – when many farmers apply fertilizer – is expected to see some of the largest gains in rainfall by the end of this century, the assessment said.

At the same time, farmers have used increasingly more fertilizer. Between 1960 and 1980 alone, its use on the nation’s top crops tripled – from 7.5 metric tons applied annually to 23.7 million tons. Those levels have hovered around the high point ever since.

Multiply what happens in Champaign County by the hundreds of agricultural communities across the United States – and in the Mississippi River Basin in particular. 

One of the “strongest signals” of climate change is the increase in precipitation intensity, said Trent Ford, Illinois’ state climatologist. And one of its biggest challenges is the increase in fertilizer runoff, he said.

Despite the problems, there is little government regulation of fertilizer application and management. Unlike with pesticides, farmers can use as much fertilizer as they want and face no fines or penalties for exceeding safe amounts.

Regulating the application of chemical fertilizers and manure would be difficult, said Richard Cruse, a professor of agronomy at Iowa State University. “You would have to police virtually every acre that’s farmed,” he said.

Governmental attempts to do just that have been consistently opposed by agriculture groups like the American Farm Bureau Federation.

Meanwhile, voluntary measures to reduce runoff – such as planting cover crops – have been slow to take hold.

In Illinois, farmers planted a total of 1.4 million acres of cover crops in 2019, but it will take an additional 20.7 million acres in conjunction with other management practices to reach the EPA’s long-term goals of nutrient reduction, according to the state’s biennial report.

“They’re not on the order of magnitude that we need to see to actually have a change,” said Catie Gregg, an agriculture specialist at the Illinois nonprofit Prairie Rivers Network. “Then this is further complicated by climate change.”

More Fertilizer, More Problems

In late June, Champaign County farmer Ann Swanson looked on as the gathering rain clouds darkened the sky.

She cursed.

Swanson, who runs a 10-acre organic farm growing tomatoes, peppers and squash, knew the incoming rain spelled disaster for her crops.

The surprise soaker that fell over much of central Illinois that week spawned tornadoes and put an abrupt end to outdoor events. It also drenched the Champaign-Urbana metropolitan area with 5.1 inches of rain

Ann Swanson, manager of Hendrick House Farms in a field that would normally have plants throughout on Tuesday, September 21, 2021. Flooding earlier in the season damaged the crop.
Ann Swanson, manager of Hendrick House Farms in a field that would normally have plants throughout on Tuesday, September 21, 2021. Flooding earlier in the season damaged the crop. (Darrell Hoemann, |Investigate Midwest)

That’s a half-inch above the area’s average rainfall amount for the entire month, according to the Illinois State Water Survey at the University of Illinois at Urbana-Champaign.

The downpour caused most of Swanson’s 2,000 tomatoes to develop bacterial spots, ending the season early.

“You just don’t expect that much rain beyond June,” Swanson said. “It was really disappointing.”

Swanson is not in the Spoon River watershed, so any excess fertilizer from her farm drains instead into the Kaskaskia River. But Swanson employs a host of farming practices to ensure nutrients stay in her soil.

At the beginning of every season, Swanson said, she samples her soil to see how much nutrients it already has and adjusts her fertilizer use accordingly. Instead of dumping it all on at the start of the growing season, she applies it little by little as her crops grow.

If the weather forecast shows heavy precipitation, she will wait until drier conditions so that the crops can take in the most nutrients.

“That’s exactly why ‘side dressing’ is generally more efficient, because you’re spoon-feeding the crop throughout the growing season, as opposed to putting on this huge lump at the start of the season or before the season even starts,” said Kelsey Griesheim, a graduate student researcher in the department of natural sciences and environmental resources at the University of Illinois.

Swanson also uses cover crops. Planted in the off-season when fields are usually bare, cover crops can improve the soil’s structure, making it more like a “sponge,” Gregg said. The sponge soaks up excess water and nutrients and also improves the overall health of the soil.

“With cover cropping,” Swanson said, “I want to make sure I’m putting those nutrients back in the soil so I’m not constantly depleting them of nutrients year after year.”

Health peppers at the Hendrick House Farms on Tuesday, September 21, 2021. Flooding earlier in the season damaged the crop.
Health peppers at the Hendrick House Farms on Tuesday, Sept. 21, 2021. Flooding earlier in the season damaged the crop. (Darrell Hoemann | Investigate Midwest)

But Swanson is an exception.

Many farmers over apply fertilizer as a hedge against heavy rain, said Cruse, the Iowa State University professor. It’s a cheap way to ensure the most from each harvest, he said, but it can exacerbate the runoff problem.

“It’s like an insurance policy,” Cruse said. “Fertilizer costs, but not having enough out there to optimize your yield, costs even more.”

Corn crops in Champaign County alone had an average of 31 million pounds more nitrogen than they needed every year during the decade ending in 2019, according to data compiled by Iowa State University researchers. 

That’s the nation’s third-highest nitrogen surplus amount for corn, which is one of the most fertilizer-dependant of all the crops.

Toxic and Costly

Some 350 miles north of Champaign County, Erika Balza knows firsthand the toxic and costly consequences of unchecked fertilizer runoff. 

When the mother of two moved into her new husband’s house in rural Kewaunee County, Wisconsin, outside Green Bay, nearly a decade ago, she remembers him warning them not to drink the water. 

“You can shower with it, you can do laundry with it, run the dishwasher, but you cannot drink the water here,” she remembers him saying.



The reason: Manure used as fertilizer on nearby farm fields seeps into her family’s well after it rains, Balza said. The water has tested positive for coliform bacteria several times. 

It’s an especially dangerous situation for Balza because of her compromised immune system from stage four metastatic breast cancer. 

But that’s not the only problem.

One day in 2016, Balza said, she started her dishwasher before heading upstairs for bed. As she turned the faucet on to brush her teeth, the water poured out brown and smelled of manure. Testing revealed cow and E. Coli bacteria.

The Wisconsin Department of Natural Resources and a donation from a farmer covered the more than $13,000 cost of installing a new well to run water to her house. But Balza had to purchase a new $700 dishwasher herself after the incident ruined the old one.

These jars contain brown water taken from a tap in Kewaunee County that researchers tied to spreading of manure on a nearby field in 2016. The soil from the field and water from the home shared the same signatures for fecal contaminants.
These jars contain brown water taken from a tap in Kewaunee County that researchers tied to spreading of manure on a nearby field in 2016. The soil from the field and water from the home shared the same signatures for fecal contaminants. (Courtesy | Kewaunee County Land and Water Conservation Department)

Even with the new well, she said, her water still shows evidence of coliform and E. coli bacteria, as well as high levels of nitrates.  

Balza said there’s a lack of oversight for farmers that apply manure.

“He walked away with a slap on the wrist,” she said of the farmer whom she thinks was responsible for the runoff. 

Communities’ water treatment facilities are just as at-risk as individual wells.

Just a half-hour drive east of Champaign in the neighboring county of Vermilion, the Aqua Illinois surface water treatment plant cleans the drinking water from Lake Vermilion that’s served to around 38,000 people.

Nitrates in the supply are a seasonal problem, said the plant’s manager, David Cronk.

In the spring – when some farmers apply fertilizer and a time of the year that’s expected to see one of the greatest increases in rainfall due to climate change – the nitrate concentration can be 12 to 13 milligrams per liter before the water is treated, he said. The federal limit is 10 mg/L.

In the 1990s, when nitrate levels breached the federal limit, residents were given bottled water, Cronk said. So, in 2000, a $4 million ion exchange unit was installed to filter the water.  

Cronk said his plant works with farmers so they employ the best methods to ensure nitrates aren’t getting into water.

“That’s your main defense, honestly. We are the last defense,” Cronk said. “We’re making your water safe to drink here. But what’s it doing for the rest of the Mississippi River Basin? It’s still going there.”

Another problem communities across the country face from runoff is toxic algae blooms in lakes and ponds. 

T.J. McCloud (left) and Chris Hoffman (right), prepare a bentonite clay solution to treat a pond at 3850 N Wilke Rd, Arlington Heights, Illinois, on Tuesday, Oct. 19, 2021.
T.J. McCloud (left) and Chris Hoffman (right), prepare a bentonite clay solution to treat a pond at 3850 N Wilke Rd, Arlington Heights, Illinois, on Tuesday, Oct. 19, 2021. (Ignacio Calderon | Investigate Midwest)

Ava Boswell, the environmental services manager at McCloud Aquatics, a lake management company based in Northern Illinois, said cyanobacteria, a type of toxic algae, has become more frequent in some agricultural areas or areas with a lot of urban development in Illinois.

Although regular green algae was more commonly found by the company than cyanobacteria, green algae can also deprive fish of oxygen if the lake or pond is not treated, she said.

Although the decreased water quality they have seen could be due to an overall increase in algae blooms, Boswell said it could also be attributed to increased testing frequency.

‘Feeble, Unfocused, and Underfunded’

Attempts to regulate fertilizer application and runoff have been met with stiff resistance from the agriculture industry.

That challenge is made even more difficult, ironically, by the 1972 Clean Water Act. Even though agriculture has long been identified as a major source of water pollution, the nation’s landmark law explicitly exempts its discharges from regulation.

As a result, efforts to address it have been “feeble, unfocused, and underfunded,” a Vanderbilt University researcher named J.B. Ruhl wrote in 2000, and intense lobbying from farm groups has kept regulations with teeth from being enacted.

That’s what happened in 2014 when the Obama administration sought to define more broadly what waters were protected by the act in a move that farmers called an overreach. They feared the government would try to regulate their irrigation ditches, ponds and even puddles.

The American Farm Bureau Federation responded by launching a #DitchtheRule campaign that framed the effort as a “land grab.”

State farm bureaus and other groups representing farmers also joined the action, according to the Center for Responsive Politics. In 2015, the American Farm Bureau Federation spent $2.8 million lobbying on issues that included clean water rules.

The EPA fired back with its own campaign called #DitchtheMyth to combat what it called “misinformation.” Other tactics it employed, the Government Accountability Office later found, violated a law against covert propaganda.

In the end, the rule fizzled.

A few years before that battle, in 2011, the EPA had warned that half of U.S. streams had medium-to-high levels of nitrogen and that nitrate drinking water violations had doubled in the previous eight years.

The agency issued this warning in what’s known as the “Stoner memo,” and it proposed that states reduce those levels by focusing on several areas, including agricultural fertilizer use.

But, a decade later, Illinois and its stakeholders are still in the process of implementing a plan to reduce runoff. 

“You’re trying to affect change on about 22 million acres of cropland that’s operated by about 72,000 independent farmers, and that’s a big lift,” said Trevor Sample, who coordinates the Illinois Nutrient Loss Reduction Strategy Implementation for the state’s EPA.

The state EPA is one of several partners in the ongoing effort to reduce runoff. Others include the state Department of Agriculture and the Illinois Farm Bureau.

The groups took the Stoner memo to heart, said Lauren Lurkins, Illinois Farm Bureau’s director of environmental policy. “Now we’re firmly in the middle of implementation of our strategy of a very complex environmental challenge.”

Charles Meier, a Republican lawmaker, said the majority of farmers are already doing their best to leave the environment better for the next generation.

“A farmer doesn’t want to pay for fertilizer that’s gonna end up washing and leaching down into the water either,” he said. “We want to keep fertilizer in the soil.”

Taking Action

There are signs some government programs are gaining traction.

In Illinois, the Fall Covers for Spring Savings program offers a $5 insurance discount for every cover crop acre enrolled. During the 2019-20 growing season, the state had funding for 50,000 acres.

The allotment was filled just one week after opening.

Last season, the allotment was met in 12 hours, with an additional 130,050 acres that had been requested, according to the state’s biennial report. Now, the program will double its acre cap, according to the state’s EPA.

Beyond holding in fertilizer, cover crops may improve how much food a farm produces. Farms that used cover crops for at least five straight years could expect a 3% increase in corn production and about a 5% increase in soybean production, according to Sustainable Agriculture Research and Education, a program supported by the U.S. Department of Agriculture.

Ann Williams, a Democratic state representative in Illinois and chair of the state’s energy and environment committee, said many in the agricultural community are adapting as they see these benefits.

“Notwithstanding the climate impacts, it has benefits to their yields, to their profits,” she said. “That’s when you really are able to make a real strong argument that implementation adoption is not just in the best interests of the community and the globe at large, but in your own, economic best interest.”

But implementing all the necessary management practices in agriculture can be expensive — about $789 million per year to reduce nitrogen and phosphorus in long-term goals, according to the state’s biennial report.

“The reality is that addressing and mitigating the damage from the climate crisis is going to take long-term aggressive sustained action in all levels of government,” Williams said. “I think that it’s going to take a combination of education (and) more resources allocated to the agriculture community.”

The time to act is now, said Prairie Rivers Network’s Gregg, otherwise it will be even more difficult to adapt.

“As we see the weather changing, it’s getting harder to get where we want to go,” she said. “There really isn’t a perfect time to try something new, but this is something that is getting worse.”

Ignacio Calderon is a USA Today Network agricultural data fellow with the Midwest Center for Investigative Reporting.

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