The $369bn Inflation Reduction Act (IRA) was applauded by a chorus of US organizations and activists enthusiastic about the generous funding earmarked for projects designed to mitigate climate change and improve environmental health.

But some researchers and activists are raising concerns that several provisions of the new law will actually worsen a growing environmental disaster in the nation’s heartland by increasing the tide of farm-related pollution washing into waterways and groundwater.

The sweeping new statute, which includes more than $140bn in incentives designed to promote renewable fuels and cleaner electricity generation, could slash greenhouse gas emissions 40% below 2005 levels by the end of the decade. But in its efforts to promote climate-friendly agriculture, it also promotes corn-fed ethanol refineries and manure-based energy production that could unintentionally supercharge fertilizer and fecal contamination.

“It’s going to end up in the water,” Rebecca Ohrtman, a water quality specialist from Iowa, said of the contaminants from crop production and what are commonly called “confined animal feeding operations” (CAFOs). Ohrtman spent much of her career as a water protection coordinator with the state of Iowa. “I can’t believe they’re going to provide all this funding with no strings attached.”

The Great Lakes and midwest regions face nothing short of a water quality emergency, say those on the frontlines. Farming-related contaminants have already fouled thousands of drinking water wells from Minnesota to Missouri, and virtually every waterway in Iowa is degraded with little regulation to rein in the pollutants.

“It’s already a national emergency and a national scandal,” said Emma Schmit, a senior organizer in the Midwest for Food and Water Watch, an environmental advocacy group. “When we test our waterways, the main pollutants are E coli and nitrates and phosphorus from agriculture. These are pathogens and contaminants that can cause serious issues for people. We’re about to give large corporate farms carte blanche to make it worse.”

A threat to clean water

How can legislation billed as an environmental protection statute risk being a primary threat to clean water? The answer is that there could be seemingly unintended consequences of investments to reduce greenhouse gases and replace fossil fuels with cleaner options.

There are two particular farm-related provisions in the IRA that won’t put more food on the table, but will nevertheless impact water quality in the midwest. One will incentivize producing more ethanol, a renewable fuel, from corn. Another will move to limit emissions of methane, a potent greenhouse gas, by processing manure generated by massive livestock and poultry farms. Wastes from these could end up polluting waterways.

The incentive for more corn production is particularly worrisome as farmers typically make heavy use of nitrogen fertilizers when growing corn, said Chris Jones, a research engineer and water quality specialist at the University of Iowa.

“Anytime we incentivize production of a nutrient-hungry crop, you’re going to get nutrient pollution,” Jones said. “Corn loses a lot of nutrients to the environment. We know that for a certainty. We’re incentivizing further production. We’re going to get more pollution. You don’t need to be a genius to know that.”

Corn is the most heavily fertilized row crop in America, accounting for 11bn lb of commercial nitrogen fertilizer applied to farmland annually, with nine of the 11bn lb applied in the midwest, according to the USDA. State and federal research shows that up to 70% of applied nitrogen runs off the land and into streams, rivers and groundwater.

Agricultural nutrient pollution is the primary reason that the Clean Water Act has not come close to meeting its “fishable and swimmable” goal for US surface waters. Because of waivers written into the Clean Water Act, which last year marked its 50th anniversary, nutrient runoff from arable farms and smaller livestock operations are completely unregulated. (Large livestock operators, meanwhile, are given broad discretion by states for managing and spreading manure.)

Boosting corn acreage, to create more ethanol, is one of the Biden administration’s goals. It wants to increase ethanol production from 15bn gallons in 2022 to 21bn gallons this year, and 23bn gallons by 2025, principally to meet the administration’s national energy strategy for ethanol to be a primary feedstock for producing “sustainable” fuel for airlines.

Though the $1.01 a gallon tax credit provided in the new law is a win for corn and ethanol producers, the administration’s plan for ethanol is a big problem for water. Corn farmers already apply more than 4bn lb of nitrogen fertilizer to produce the current national supply of ethanol. Based on this usage rate, refining five billion more gallons of ethanol could lead to 1.5bn more pounds of fertilizer being applied to fields in corn-growing states. That would exacerbate the water quality issues plaguing the region.

“We’re putting more and more pressure on the productivity of agriculture to produce more corn, more livestock for our fuel,” said John Ikerd, professor emeritus of agricultural economics at the University of Missouri. “It’s also producing more pollution. Any other industry that creates this amount of pollution and represented this level of risk to public health would be heavily regulated.”

Congress didn’t add any additional safeguards for water in the Inflation Reduction Act.

Livestock

The law’s effect on large cattle and other livestock feeding operations also is worrisome.

The country’s large livestock operations, primarily centered in the midwest, produce hundreds of billions of gallons of untreated liquid manure and tens of millions of tons of solid manure that are spread over farmland with scant oversight. Manure contains nitrogen, phosphorus, and dangerous pathogens that can also run off and contaminate waters across the region.

In 2016, the U.S. Environmental Protection Agency (EPA) identified phosphorus and nitrogen discharges from US farmland as “the single greatest challenge to our nation’s water quality”.

For millions of Americans in the heartland already contending with dirty water, the new law risks making the country’s most severe surface and groundwater pollution worse, according to water quality experts.

This is because another feature of the IRA is a flurry of tax incentives to generate renewable energy from biodigesters – large tanks where bacteria and heat help convert organic waste to methane.

The American Biogas Council, an industry trade group, counts 2,300 biodigesters in operation in the US. With tax credits in the new climate law, the council estimates 15,000 more could be installed, including nearly 8,600 on large dairy, hog, and poultry farms. The methane produced could be used by electricity producers in rural regions.

But biodigesters don’t reduce the volume of waste. The same amount of liquid and solid manure that goes into biodigesters is returned as “digestate” The liquid waste contains more concentrated forms of phosphorus and nitrogen and is used as fertilizer on farmland close to where it was produced and where it will drain into waters in the Midwest.

The incentives are sure to lead to more biodigesters. The American Biogas Council, an industry trade group, counts 2,300 biodigesters in operation in the US. With tax credits in the new climate law, the council envisions that 15,000 more will be installed, including nearly 8,600 on large dairy, hog and poultry farms.

Even though digesters provide livestock farmers with a new source of revenue, the Biogas Council asserts that the extra cash will not lead to an expansion of intensive animal farming operations and more manure.

“That would mean that farms are buying cows to produce manure to put into the biogas system,” said Patrick Serfass, the council’s executive director. “I guarantee you that no one is doing that.”

But limited real world evidence suggests that biodigesters are a powerful incentive to increase the number of animals – and the amount of manure – at industrialized livestock operations.

Last year, after Iowa enacted a new law that encouraged livestock operations to install biodigesters, five of the nine dairies awarded construction permits said they would also increase the size of their herds. The USDA did not respond to questions raised about the effects of the new statute on water pollution. Corn and livestock industry executives did not respond to interview requests.

‘Conservation’ programs

In approving the Inflation Reduction Act, neither the Biden administration nor Congress wholly ignored the risk to water. The law enables the USDA to fund its $19.5bn climate smart program, a portion of which is devoted to “managing nutrients”.

The law also provides $18bn for decades-old “conservation” programs. “The Inflation Reduction Act provides major incentives for a broad range of different practices and strategies for managing nutrients, guarding water quality and keeping carbon in the soil,” US senator Debbie Stabenow, the Michigan Democrat and chairwoman of the Senate agriculture committee, said. “There are a lot of strategies that work but there are not enough farmers participating because there hasn’t been enough money to fund all the requests.”

Indeed, the climate smart program includes $300 million for organic and sustainable farm practices, the largest investment ever made by the federal government for environmentally sensitive crop and livestock production. But while that $300 million has been allotted to dozens of growers, as well as other research and planning projects, these farms ultimately account for just a few thousand acres of the more than 100 million acres of cropland in the Corn Belt and Great Lakes states.

Most of the USDA “climate smart” and conservation programs support existing voluntary “best management practices” that include not plowing before planting, raising cover crops, and planting buffer strips to soak up excess nutrients. But best management practices, initially designed to control soil erosion, have been largely ineffective at reducing phosphorus in streams in the Great Lakes states.

In fact, installing best management practices to impede discharges from fields can make conditions worse. Two years ago, during the annual meeting of researchers studying Lake Erie’s harmful algal blooms, Deanna Osmond, a crop and soil scientist at North Carolina State University, reported that the most popular best management practices thought to curb runoff actually increased nutrient concentrations that cause harmful blooms.

For instance, buffer strips planted on field edges increased the amount of phosphorus draining into ditches and streams. The same thing occurred with planting cover crops. “Conservation practices have potential tradeoffs,” Osmond said. “We have to acknowledge these tradeoffs.”

These best management practices, moreover, have never been especially popular with corn growers and livestock producers in the nine-state corn belt from the Dakotas to Missouri. Just 2.2m of Iowa’s 30m acres of farmland, for example, were planted with cover crops, according to the most recent analysis by the state agriculture department.

“We’ve got an industrial agriculture system that’s regulated as if it were still scattered, independent, diversified small family farms,” said Ikerd, the agricultural economist. “It’s not. Industrial agriculture focuses on production and profitability. Not public health. Not conservation. Not the environment.”

• This report, co-published with the New Lede and Circle of Blue, was made possible by an investigative reporting fellowship awarded by the Alicia Patterson Foundation