Everyone wants clean water, but not everyone agrees on how to make sure it stays pollution-free. The Clean Water Act is one of the most successful pieces of environmental legislation in American history: Forty years ago, only a third of the country’s lakes and rivers could support fishing or swimming. Now two-thirds do. But when a bill for the CWA was offered up in 1972, Richard Nixon vetoed it, complaining that it would cost too much. It took a bipartisan congressional override to enact the law.

Controversy over the CWA continues, and a particularly ambiguous phrase in the law has been a perennial source of legal trouble. The CWA compels the Environmental Protection Agency and the U.S. Army Corps of Engineers to protect the integrity of the “waters of the United States.” Industrial interests argue that a reference in the text of the law to “navigable waters” limits federal jurisdiction to waters you can boat on. This has let them get away with discharging pollution into smaller waterways. Regulators disagree, since pollutants in these waterways drain into and threaten larger navigable waters, too.

Government agencies set down rules for how to interpret laws they are tasked with enforcing. In April, the EPA proposed changes to how it will define “waters of the United States” in its rules. Howls of protest have followed, particularly from farmers and ranchers. Congress ordered hearings on the subject this summer. Though the rule updates have yet to be finalized—public comment is open until October—this week the House passed H.R. 5078, a bill to prevent the EPA from implementing the proposed rules. Its title—“Waters of the United States Regulatory Overreach Protection Act”—captures the attitude behind the bill.

In theory, the proposed update makes standards clearer by using consistent, scientific terms from hydrogeology to define which waters the Clean Water Act covers. In practice, its critics charge, the update is 80 pages of technical and legal jargon that is “beyond the knowledge of any farmer I know,” says Will Rodger, a spokesman for the American Farm Bureau Federation, the country’s largest farm lobby.

Farmers say some clauses in the proposed rules seem at odds with others. For example, the regulation currently excludes farm ditches and drainage systems from requiring a permit. Normal farm activities, such as watering crops, aren’t subject to regulation under the CWA, either. The EPA says that these standards should stay the same. But because the proposed rule states that water found in wetlands next to larger bodies are “waters of the United States,” farmers fear that they will no longer be exempt. (It is already standard EPA practice to consider wetland waters “waters of the United States,” but they are not explicitly defined as such in the text.)

“A good portion of the water on my rice farm would count as wetland ‘water of the U.S.,’ ” Bob Stallman, head of the Farm Bureau, told me. “Will I now need a permit every time I want to water my rice?” The rule exempts ditches that drain into uplands, but this has not mollified farmers. “No one builds the kind of mythical ditch they say is excluded under these rules,” Stallman claims.

The EPA says this is nonsense—and some of its administrators have expressed exasperation with what they see as willful misinterpretation that has undermined efforts to craft sound policy. “The intent is not to make farmers’ lives harder,” an EPA official told me. Representatives from the agency have been traveling the country to explain their intentions and answer questions. They stress that input from citizens on how to make the language clearer is welcome: Everyone should know just what the rules mean and what they don’t mean.

But writing a rule to everyone’s satisfaction is a tall order. Clear regulations have always been hard to pen, and they have gotten harder. Decades ago, regulatory lawsuits were rare because they could be brought only after an agency charged someone with violating the rules. This changed in 1967, when Abbott Laboratories argued that compliance costs meant those being regulated should have a say in objecting to them. In Abbott Laboratories v. Gardner, the Supreme Court agreed: Now regulators can be sued even before proposed rules are enforced.

The flow of pre-emptive lawsuits keeps increasing: Notices of intents to sue the EPA for how it enforces the CWA have risen 30 percent since 2003. “Regulators undoubtedly have to be more careful now to write things with court preferences in mind,” says Fred Emery, a former director of the Federal Registry who now teaches regulatory writing. Rules are written not just to uphold the will of Congress but also to avoid the wrath of courts.

The rumbling over the EPA’s “waters of the United States” rule is less about its imperfection, though, and more an illustration of deep-seated mistrust of the government. Redefining waters with hydrological terms is unlikely to actually change any farming practices, says Fouad Jaber, an agricultural engineer at Texas A&M University. And in an attempt to clarify the scope of its proposal, the EPA has issued an “Interpretive Rule” to explain its position and purpose, explicitly stating that it intends to leave famers’ current practices alone.

Farmers don’t buy it. “I don’t trust a word out of their mouths,” a Texas farmer told me.

“Don’t let them confuse you,” says Stallman. “Decades of experience tells me that it’s only what’s written that counts and not what they say.” The more cynical farmers and their supporters suggest that the CWA update is an example of government overreach and—some members of Congress would have you believe—an underhanded attempt to impose a “radical green agenda.”

Changes to rules may be intended as broad protective measures, but farmers see them as slapping punitive incentives onto the process. And farmers are already good stewards of their lands and waters, argues Carl Lindgren of Cleremont Farm in Virginia. In Loudon County, where hardy Black Angus cows and prize-winning racehorses graze on verdant fields, it’s common practice to line farm ditches with straw to absorb pollutants. Many farmers voluntarily work with federal agencies to develop conservation plans. “New” EPA rules make ordinary famers feel mistrusted, and then they bristle.

Yet collectively, agricultural runoff contributes 12 million tons of pollution a year to public waters, according to 2004 estimates (the most recent year for which national data is available) from the U.S. Geological Survey. Phosphate and nitrate pollution from fertilizers washes into lakes and seas, causing algae blooms that leave toxins and dead zones behind. This summer in Ohio, algae blooms in Lake Erie spurred by fertilizer runoff caused water shut-offs affecting 400,000 people. The Clean Water Act rules need to be updated. But beyond that, the EPA should interpret its authority more broadly.

Hammering out agreeable standards is proving as difficult as making water run uphill. Suspicion played up for political purposes does not help. Whatever is finally decided about what waters make up the “waters of the United States,” a gusher of lawsuits looms.