The EPA took a giant step toward finally defining which bodies of water are subject to regulation under the Clean Water Act last week, when it filed a draft rule with the White House regulatory czar designed to settle the confusion created in recent years by a series of court decisions.

The legal battles have centered on the definition and scope of a seemingly innocuous phrase — what exactly are “waters of the United States”?

Judges and regulators have wrestled over how to interpret the term in the absence of legislative action to clarify it. Now, the EPA is not only proposing a regulatory solution — which is not yet publicly available — but is also conducting a scientific review to accumulate evidence to back up the penultimate rule.

That approach to implementing the Clean Water Act (PL 95-217) is the latest example of the Obama administration’s philosophy on environmental policymaking: Act when Congress doesn’t and take steps to shore up the approach against future legal challenges.

“We’re not likely to get that clarity from Congress anytime soon,” said Bruce Myers Jr. of the Environmental Law Institute. “Further clarity from the agencies is beneficial.”

Court Decisions

The Supreme Court has ruled three times on the extent of the law’s application to wetlands since 1985, producing narrow decisions in 2001 and 2006. A split in the 2006 case Rapanos v. United States is the most recent reading of the law to befuddle regulators and the regulated.

Four of the court’s conservative justices ruled that the law could only be extended to cover “relatively permanent” static or flowing bodies of water. Justice Anthony M. Kennedy agreed with their judgment but offered a much different test to determine what exactly constitutes “waters of the United States”— whether a body of water or wetland has a “significant nexus” to waters that are or could reasonably be navigable.

Wetlands are typically found near waterways and floodplains, though sometimes they have no obvious connection to surface water but link up with groundwater sources.

The EPA and Army Corps of Engineers drafted joint guidance documents in response to the decision, most recently in 2011, that sought to advise enforcement officials how to determine on a case-by-case basis which waters meet the test outlined by Kennedy. But the document sat at the Office of Management and Budget for years and an EPA spokeswoman said the agency will withdraw it from interagency review.

Lawmakers have since sought to prevent implementation of the guidance through legislation and policy riders to appropriations bills, though the language was removed from fiscal 2012 spending measures. And the recent practice of funding the government through stopgap measures has precluded most environmental riders from ever getting to President Barack Obama’s desk.

In his opinion, Kennedy left open the possibility that the EPA could establish categories of waters by rule that would meet his significant nexus test, said Robin Kundis Craig, a law professor at the University of Utah.

“And I think EPA is taking him up on that invitation,” she said.

The signal the agencies now appear to be sending with the proposed rule and scientific analysis is that they will use the science to more definitively state that certain types of waters presumptively fall under Clean Water Act jurisdiction, Craig said.

Assembling and reviewing the science of water connectivity helps to move the issue forward and strengthens their legal approach, Myers said.

“I think the obvious benefit for the agencies in a rule-making, from a legal perspective, is that it will likely be entitled to really significant deference from the courts when cases are before them that challenge the regulations,” he said.

Of course, the proposal could change significantly after the OMB — where the EPA and Army Corps’ joint guidance was held up for years — gets through it, and its reliance on the scientific report could also change as it works its way through the executive branch.

Industry and some Republican lawmakers have taken issue with the EPA submitting the proposal to the OMB before finalizing the scientific report about the connections of water bodies. The agencies have created a situation where the independent Scientific Advisory Board is studying the science behind a rule that is already written, rather than first evaluating the science that will later be used to inform a regulation, said Deidre G. Duncan, a partner at Hunton & Williams who works on Clean Water Act issues.

“The timing of it is backwards,” she said.

Many of the same lawmakers who criticized the EPA and Army Corps’ joint guidance registered similar concerns about their latest regulatory approach, wondering whether the accompanying study was just a Trojan horse for the agencies to extend their authority while “allowing the EPA to regulate virtually every mud puddle in America,” as House Science, Space and Technology Chairman Lamar Smith, R-Texas, put it.

At a committee hearing on climate change last week, the former longtime House Energy and Commerce Chairman John D. Dingell — who played a central role in writing the 1972 water pollution law and broadening its definition of “navigable waters” — asked EPA Administrator Gina McCarthy whether the agency will need further clarification of its Clean Water Act authority as climate change affects the nation’s water sources, such as the Great Lakes.

“Yes, I do,” McCarthy replied.

Whether that clarification comes from Congress or the federal courts is anyone’s guess.