The Environmental Protection Agency and the Army Corps of Engineers finalized the Clean Water Rule to protect from pollution and degredation of the nation's water resources in streams and wetlands. (U.S. Environmental Protection Agency via Youtube)

Nearly a decade after the Supreme Court pointed out the confusion over exactly which waters fall under the Clean Water Act, the Obama administration responded Wednesday with a new rule that states what is protected and what is not.

Navigable tributaries, as well as the rivers they feed into, are protected because the flow of streams and creeks, if polluted by farming and development, could affect the health of rivers and lakes, the rule states.

Environmental Protection Agency Administrator Gina McCarthy, who announced the rule, said it safeguards waters such as wetlands that adjoin those waterways and also protects certain distinctive waters, including the Delmarva and Carolina bays, vernal pools in California, and Texas coastal prairie wetlands that flow into waters downstream.

“It’s an important reminder that the Clean Water Act makes it illegal to pollute or destroy our waters without a permit,” Jo-Ellen Darcy, assistant secretary of the Army for Civil Works, said during a telephone conference.

Darcy said that there was confusion over whether a permit was required to pollute everything from a stream near urban development to a ditch on a farm. “Needless to say, it didn’t make sense,” she said. “We’ve always known streams and wetlands determine water quality.”

The EPA and the Army Corps of Engineers looked at 1,200 peer-reviewed studies and held 400 meetings in communities with stakeholders to design the Waters of the United States rule.

In anticipation of criticism from members of Congress, farmers and developers, McCarthy and Darcy emphasized that the new rule does not add to the waters that the act already protected and does not seek to micromanage farming.

“It will not get in the way of agriculture and recognizes the crucial role that farmers play,” McCarthy said. “Farmers, ranchers and foresters are all original conservationists, and we recognize that.”

Artificial ponds and lakes on private property are exempt, along with the majority of ditches, according to an explanation on the agency’s Web site. Darcy said that the rule covers navigable waters but not the large majority of ephemeral streams that do not impact waters downstream or ditches, Darcy said.

Only “ditches that are constructed out of streams or function like streams and can carry pollution downstream” are protected. “So ditches that are not constructed in streams and that flow only when it rains are not covered,” according to the agency’s explanation.

The explanations did not sway powerful critics in the Senate. Sen. James M. Inhofe (R-Okla.), chairman of the Environmental and Public Works Committee, blasted the rule.

When the new rule was proposed, Inhofe and various Republican colleagues asked that it address elements he viewed as an overreach by adding protections for farmers. They wanted a rule that did not include waters in isolated ponds and ditches.

On top of that, they wanted exclusion for “agriculture water, storm water, groundwater, floodwater, municipal water supply systems, wastewater management systems, and streams without enough flow” to impact waters downstream, Inhofe said in a statement in response to Wednesday’s announcement.

But “instead of fixing the overreach in the proposed rule, remarkably, EPA has made it even broader,” Inhofe said. He called on Congress to craft legislation that better defines what the act can protect.

“The EPA has set themselves up to increase federal control over private lands, and I will not allow it,” said Inhofe, whose constituents include farmers. He said his committee will take action in the summer “to halt EPA’s unprecedented land grab and refocus its job on protecting traditional navigable waters from pollution.”

The new rule stems from a 2006 Supreme Court case in which a Michigan developer fought an EPA fine for filling in 54 acres of wetlands on land he owned to build a shopping center without a permit. The EPA and the Army Corps argued that the wetlands were covered by the 1972 Clean Water Act, but the court said the law’s reach was unclear.

In an opinion, two justices wrote that all bodies of water “with a significant nexus” to “navigable waters” are covered by the act. The new rule was drafted to end confusion over the meaning of “significant nexus.”

McCarthy argued that the rule does in fact address the concerns of Inhofe, his congressional allies and farmers.

“We made clear that we’re looking at ditches only when they are tributaries,” she said. “We’ve done a very good job of taking a look at the comments” to the proposed rule. “We are not going to do anything to add regulatory burdens on the agricultural community.”

Brian Deese, a senior adviser at the White House, was more forceful. “This rule undoes confusion without getting in the way of farming,” he said. “The only people with reason to oppose the rule are polluters who threaten our clean water . . . and they will be responsible for their actions.”

Environmental groups and a number of prominent Democrats said the rule brings critical protection to the streams that are most vulnerable to development and pollution. Stopping upstream pollution is key to restoring the health of larger rivers and bays such as the Chesapeake and Puget Sound, said Margie Alt, executive director of Environment America, a Washington nonprofit organization.

“Our rivers, lakes and drinking water can only be clean if the streams that flow into them are protected,” Alt said. “That’s why today’s action is the biggest victory for clean water in a decade.”

Whit Fosburgh, chief executive of the Theodore Roosevelt Conservation Partnership, which works to preserve access for those who hunt and fish, applauded the rule, calling it historic.

“We finally have a rule in place that will stem the tide of wetlands loss and . . . restore water quality protections to trout habitat and salmon spawning waters,” Fosburgh said. “Keeping these waters healthy will also help to ensure the health of local economies that rely on the $200 billion a year generated by the outdoor recreation industry.”

Joby Warrick contributed to this report.