Iowa’s polluted waterways rarely see improvement. Lawmakers still resist efforts to regulate industrial ag

More than four years ago, Terry Skahill bought land along the banks of the Yellow River in Allamakee County a place he had visited for decades to camp and kayak. But the retired electrician said he’s since witnessed the river transform. Its banks have widened due to flooding, and its water quality has declined sometimes to the point where kayaking on the river has become impossible.

“Terrible, terrible. It stunk so bad,” Skahill, 70, told Investigate Midwest last June, referring to a particularly polluted day for his stretch of the river in northeast Iowa. “And obviously, it’s coming out of all the feedlots, into the little streams, and whatever. And of course, they had just put all the fertilizer on the fields, and the fields weren’t yet growing. So there it is, right down the river.”

Pollution from industrial agriculture is one of the main contributors to the impairment of hundreds of river and lake segments across Iowa. As a result, many bodies of water fail to meet federal and state quality standards for drinking, swimming or fishing.

While some water segments have recovered over time, most remain impaired.

Nearly eight out of 10 river segments have been in a continuously impaired status for at least a decade, according to an Investigative Midwest analysis of reports from the Iowa Department of Natural Resources. During the same period, 43 percent of lake segments have experienced a similar condition.

In fact, 65 river segments (15 percent) and six lake segments (11 percent) have fallen short of a key water quality standard for a specific use and impairment for at least 20 years.

While most impaired river and lake segments have failed to recover, state lawmakers have resisted efforts to impose new pollution rules on industrial farms. The legislator behind the Clean Water Act for Iowa has blamed the Republican majority for bowing to agribusiness interests.

“When there are some segments of rivers and some lakes that have been on the impaired water list for decades, that’s telling us that there hasn’t been meaningful improvement in the quality,” said Gregory LeFevre, associate professor of Environmental Engineering and Science at the University of Iowa.

“The whole idea of putting waters on an impaired list is not that they should stay on the impaired list, like it’s some sort of punishment. The idea is to try to figure out ways to generate remedial actions and get them off of the impaired list,” he added.

Over the past decade, the Iowa Department of Natural Resources has reported 694 impaired water segments. The majority — 80 percent — are rivers, followed by 127 lake segments, or 18 percent. Wetlands and reservoirs account for less than 2 percent, according to an Investigate Midwest analysis.

Four segments of the Yellow River — renowned for panoramic views and being Iowa’s longest cold water trout stream — have remained impaired for over a decade, with one segment affected for 20 years. This prolonged impairment has curtailed recreational activities and undermined the river’s role as a vital habitat for aquatic life.

Last month, Driftless Water Defenders, a nonprofit environmental group from northeast Iowa, filed a federal lawsuit against Postville-based Agri Star Meat & Poultry. The suit alleges that the meat plant repeatedly violated the Clean Water Act by dumping pollutants into Hecker Creek and the Yellow River.

According to the complaint, Agri Star has been discharging pollutants — including ammonia nitrogen, total suspended solids, chloride, oil and grease — above legal limits. The lawsuit seeks economic sanctions of up to $68,445 per day per violation plus additional measures to enforce compliance.

Agri Star did not respond to a request for comment.

Regulators pinpoint pollutants and set limits

When a water body is impaired for failing to meet the water quality criteria for a pollutant, regulators first calculate its Total Maximum Daily Load (TMDL) — the maximum amount of that pollutant the water can safely absorb while still meeting quality standards. They then set maximum limits on the identified pollutant based on this calculated capacity.

Noah Poppelreiter, former supervisor of the Iowa DNR’s water monitoring staff, said each impairment faces unique challenges. This team works with other government agencies and external stakeholders to tackle these issues.

“In turn, those stakeholders handle challenges that are outside the scope of the TMDL program, such as practical matters like where precisely to build a bioreactor and how to fund it,” Poppelreiter said.

The Iowa DNR updates the impaired waters list every two years and reviews it with the U.S. Environmental Protection Agency to comply with the federal Clean Water Act. However, the data does not indicate whether one river segment is more impaired than another — it simply identifies which segments fail to meet water quality standards for at least one of the designated uses.

Nearly half the river and lake segments continuously listed as impaired over the past decade are associated with recreational activities involving full-body immersion with prolonged, direct contact with water, such as swimming and water skiing.

A 2019 Iowa State University survey found that 65 percent of residents visit Iowa’s lakes at least once a year, either for a single-day trip or overnight trip, collectively spending over $1 billion annually on outdoor lake recreation.

“People are voting with their dollars when it comes to recreation,” said Mary Skopec, executive director of the Iowa Lakeside Laboratory Regents Resource Center, in an interview. “If a water body doesn’t look or smell good enough, whether or not it’s on the impaired waters list, that has a detrimental impact on Iowa’s recreation economy.”

The decline in water quality in more than half continuously impaired river segments is primarily due to E. coli contamination, the second-leading cause of impairment in lake segments, affecting 16 percent of them.

“E. coli is known as an indicator species. While there is little risk of becoming sick from the E. coli strains present, a high level of the bacteria has been shown to indicate a potential presence of organisms which can make people sick,” said Poppelreiter, who now represents the DNR as an attorney.

Fecal contamination at Iowa’s beaches often originates from human and animal sources, according to the state’s DNR. Improperly constructed or poorly maintained septic systems, malfunctioning sewage treatment plants, manure spills, and runoff from areas contaminated by wildlife and pet droppings all contribute to elevated bacteria levels. Direct contamination from waterfowl, livestock, or even young children in swimming areas adds another layer of risk. In Iowa, runoff significantly worsens this issue.

“E. coli are coming from a mixture of sources in Iowa’s recreational waters, with human waste contributing significantly in urban streams, but also in some rural lakes and streams,” said Claire Hruby, assistant professor of Environmental Science and Sustainability at Drake University. “Nearby and fresh sources of fecal material often contribute more than sources farther upstream.”

Hruby, a water quality researcher, said her studies frequently detect genetic markers identifying raccoons as a source of fecal contamination in Iowa’s waterways following rain events. Swine markers typically do not appear in lakes or streams during midsummer, though markers linked to swine do show up following manure spills and in late-fall samples.

Still, Hruby emphasized that several other studies clearly link higher livestock densities in Iowa to increased nitrate contamination.

Iowa is the top producer of hogs in the United States. In a 2024 report, the Iowa Department of Natural Resources stated animal feeding operations (AFOs) pose ongoing concerns for water quality in the state.

Impaired waters linked to agriculture runoff

Iowa has more than 10,000 active AFOs, each housing 300 or more animal units. Of these operations, at least 160 are open feedlots classified as concentrated animal feeding operations (CAFOs), which operate under active federal discharge permits.

While manure application on agricultural fields remains the predominant method of managing animal waste, smaller AFOs in Iowa are not required to submit manure or nutrient management plans. Although regulations are designed to mitigate pollution, gaps in oversight and enforcement leave some water sources vulnerable to ongoing contamination.

The DNR report also identified agricultural and urban runoff as significant sources of water pollution across Iowa.

Agricultural runoff frequently carries sediment, nutrients and pesticides. For example, in lake segments consistently reported as impaired over the last five monitoring periods, algal blooms — characterized by elevated chlorophyll levels and linked to fertilizer runoff from agricultural fields — account for roughly 25 percent of the pollution.

Urban runoff contributes sediments from construction sites, oil and chemicals from vehicles, nutrients and pesticides from lawns, yard waste, road salts and heavy metals.

Skopec, executive director of the Iowa Lakeside Laboratory Regents Resource Center, believes the list of impaired waters is only the “tip of the iceberg” in a much bigger picture.

The Iowa DNR assesses slightly more than half the state’s designated water bodies. In 2024, 27 percent of these segments were classified as healthy waters, while just over half were categorized as impaired. Meanwhile, a little over one-fifth require further investigation, as they are identified as “potentially impaired.“

“You think about a state, the size of Iowa, to have 60 monitoring stations for the Iowa DNR — 60 for 72,000 miles of stream — like we just aren’t collecting enough information,” said Skopec, who coordinated Iowa’s volunteer water quality monitoring program at DNR from 2005 to 2016.

Waters can only be classified as impaired if a specific standard is unmet. But, according to Skopec, the state does not have standards for nutrients and many pesticides.

Since Iowa has not set nutrient standards for its rivers and lakes, the list likely underrepresents the true extent of water impairment. This means that even though reducing nitrogen and phosphorus levels could have a substantial impact in Iowa, such improvements aren’t reflected in the impaired waters data.

“The only standards we have for, say, nitrogen, would be nitrate; but that’s only in the segments that are classified as drinking water — and very few segments are classified as drinking water,” Skopec said.

Tarah Heinzen, Food & Water Watch legal director, noted that Iowa’s chronic water issues make it unsurprising to see so many lakes and stream segments repeatedly labeled as impaired without proper cleanup efforts.

She noted that a mix of technical issues under the Clean Water Act, along with the complexities of implementing cleanup plans, contributes to the problem.

"The long and short of it, I think, is that really the key polluter in Iowa is industrial agriculture, and it's very difficult to use the Clean Water Act to tackle that pollution if a state doesn't have the political will to do so," she explained.

Heinzen also pointed out that the TMDL process — the Clean Water Act’s tool for establishing pollution budgets — is especially hard to enforce for nonpoint source pollution typical of agriculture, meaning the state is only addressing a fraction of its impaired waterways.

Legislative roadblocks

Efforts to tighten regulations on CAFOs and other agricultural polluters have repeatedly stalled in the Iowa Legislature.

In February, Sen. Art Staed, a Democrat from Cedar Rapids, introduced the Clean Water Act for Iowa — Senate File 183 — which would require CAFOs to obtain National Pollutant Discharge Elimination System permits, enforce effluent monitoring, and empower the DNR to regulate pollution more strictly than federal standards. The bill also was introduced in the House — House File 368 — by state Rep. Monica Kurth, a Democrat from Davenport.

“They will be required to get a National Pollutant and Discharge Elimination System permit, and that would be all of the medium and large ones, not just 4 percent or whatever that we have now,” Staed said in an interview with Investigate Midwest.

“And they would be mandated to get a permit and monitor their operations for pollution discharges themselves, and report that monitoring data to the DNR.”

Despite its potential to significantly curb water pollution, the bill has faced stiff opposition from agricultural interests and legislative inaction. Staed introduced a similar bill last year, but it failed to advance in the legislature and was never assigned to a committee for review.

Staed said he couldn’t get any support from the legislature’s majority party.

“I can’t get any Republicans to sign off on the bill,” Staed said. “They don’t want to tick off farmers or CAFO operators or large agribusiness, which may or may not be influential. I think that’s the key.”

Michael Schmidt, general counsel for the Iowa Environmental Council, agreed that the influence of industrial agriculture plays a major role in blocking regulatory reform.

“The bill would have aligned Iowa requirements with some states that require permits for concentrated animal feeding operations,” Schmidt said. “But agricultural interests in Iowa have opposed any steps that would increase regulation, or that might hinder the development and expansion of concentrated animal feeding operations.”

Investigate Midwest reporter John McCracken contributed to this report.

Investigate Midwest is an independent, nonprofit newsroom. Its mission is to serve the public interest by serving as a watchdog over influential agricultural corporations and institutions through in-depth and data-driven investigative journalism.