Which tributaries should be protected like the rivers they feed?

In September 2008, George Johnson – once dubbed the "king of Arizona's bad-boy developers" – settled a lawsuit brought by the U.S. Environmental Protection Agency, paying a $1.25 million fine for bulldozing a wide swath of the Lower Santa Cruz River and nearby Los Robles Wash. Johnson wanted to flatten 20,000 acres for a 67,000-home development in the parched valley, creating what one local official called a "lunar scape."

Johnson originally argued that he had not violated the Clean Water Act, because he had not damaged a real river as defined by the law. His case and others exemplify a regulatory mess that has swamped regulators in litigation for years.

The problem is this: Thanks to unclear language in the Clean Water Act and a series of ambiguous Supreme Court decisions, no one can say for certain which waterways can be protected from pollution and bulldozing and which ones can't. Things are particularly murky in the West, where streams can stay dry for long periods but remain essential to the health of larger rivers.

In March, the feds offered a fix. The EPA and the Army Corps of Engineers proposed new rules to clarify which waters they regulate. They include better definitions of wetlands and tributaries, particularly those that flow periodically, such as desert arroyos and intermittent mountain streams. EPA officials say the proposed rules also do a better job of recognizing the ecological connections between different waterways, so that they can be better protected. The rules are open for public comment through Oct. 20.

Right now, regulators are often forced to evaluate their jurisdiction over waterways on a case-by-case basis, says Julia McCarthy, a stream biologist for the EPA, and "because of the number of intermittent and ephemeral streams in the West, there's a lot of confusion."

Say a copper company wants to open a mine that would potentially impact dozens of tributaries to a large river, including intermittent streams, dry creeks and seasonal marshes. Under the old rules, each would have to be assessed to determine whether it was covered by the Clean Water Act. Most likely, a contractor would do the assessment and then apply for permits – either from the EPA, to discharge into covered streams, or from the Army Corps, to dredge or fill them. The new rules define "tributary" more clearly, so that individual assessments would be needed less frequently, McCarthy says. "It definitely reduces the confusion about whether they are protected or not and takes away the inefficiencies of the case-by-case basis."

Tributaries will be defined by their physical and hydrological features, and covered if they have a bed, bank and high-water mark, and if they flow into traditionally regulated waters. There needn't be water in the streambed all the time – just proof that it flows occasionally. So intermittent mountain and desert streams will be regulated, as will tributaries that have extensive manmade alterations – rivers  channeled through poured concrete, for example. The EPA expects this to expand waterways under its jurisdiction by less than 3 percent.

As for irrigation, the new rules clearly exclude certain ditches: Those that are built in upland areas or mountains but don't flow out of them could be exempt, while ditches that join tributaries or larger rivers would not be. Wetlands and other watery features – ponds or oxbow lakes – adjacent to major waterways are also covered by the new rules. Other bodies of water will be considered on a case-by-case basis: Prairie potholes, vernal pools and playa lakes, for example, could be regulated if they are ecologically connected to larger waterways.

The new rules are overdue but might not be enough to keep regulators out of court, says Mark Squillace, a water law expert at the University of Colorado Law School. That's because the Clean Water Act's language is the real problem. The law calls for protection of "the Nation's waters," while key sections define "navigable waters" as "waters of the United States," all of which has caused a lot of legal head-scratching.

The courts have sought to redefine those terms, but even the nation's top judges have confused the issue, Squillace says.

In 2006, for example, Supreme Court Justice Antonin Scalia used a simple dictionary definition to figure out which waters were covered by the law. Fellow Justice Anthony Kennedy, on the other hand, argued that if a "significant nexus" existed between a waterway and a "navigable river," it could be regulated.

That kind of ambiguity has landed regulators in countless courtrooms and was at the root of George Johnson's original defense. And the definitions proposed by EPA and the Army Corps won't end the befuddlement. The new rules can't change the law's original language or the court decisions, which still can – and probably will – be disputed.

Only Congress can change the law, Squillace says. "Given the current state of affairs" in Congress – bickering lawmakers and prolonged deadlocks – action seems unlikely. So the new rules will have to do, he says. "That's the world we live in."

• Water
• U.S. Environmental Protection Agency
• Politics