Volunteers clean trash from Watts Branch Stream, where it crosses from Maryland into Washington. (Jahi Chikwendiu/WASHINGTON POST)

The Obama administration announced Wednesday that it will impose stricter pollution controls on millions of acres of wetlands and tens of thousands of miles of streams.

The new guidelines from the Environmental Protection Agency, which will be codified in a federal regulation later this year, could prevent the dumping of mining waste and the discharge of industrial pollutants to waters that feed swimming holes and drinking water supplies. The specific restriction will depend on the waterway.

The question of which isolated streams and wetlands qualify for protection under the Clean Water Act has been in dispute for a decade. The Supreme Court has issued two decisions, and the George W. Bush administration issued guidance in 2003 and 2008 limiting the scope of the act.

EPA Administrator Lisa P. Jackson said in a telephone news conference with reporters that although the new rules will expand the waterways enjoying federal protection, “this is not some massive increase, as far as we can tell.”

The policy change is likely to affect tributaries flowing into water bodies such as the Chesapeake Bay. Sen. Benjamin L. Cardin (D-Md.), who chairs the water and wildlife subcommittee of the Senate Environment and Public Works Committee, joined 13 other senators last month in urging President Obama to expand the application of federal law to such waterways.

In a statement Wednesday, Cardin said the proposed guidance “is designed to address the [Supreme] Court’s concerns in a way that will protect waters that are important for fish and wildlife habitat, flood protection, and supplying drinking water. As we told the president, protecting this incredible network of waters is the first step in restoring them to health.”

Once finalized, the regulations will apply federal water quality standards to a range of waterways, including the headwaters of lakes and rivers as well as intermittent streams.

Although environmentalists welcomed the decision, some groups — including livestock owners and home builders — have said it will impose an economic burden. House Republicans included a provision — subsequently dropped — in their continuing budget resolution this spring that would have blocked the EPA from instituting the rules.

“I’m disappointed that the EPA has decided to issue guidance on this contentious issue. . . . I strongly believe that it is the responsibility of Congress through the legislative process, not the EPA through guidance, to determine whether or not waters currently regulated by the states should be subject to federal jurisdiction,” said Rep. Mike Simpson (R-Idaho), the chairman of the House Appropriations Committee’s environment subcommittee.

Khary Cauthen, director of federal relations for the American Petroleum Institute, called the move “economically significant.”

It remains unclear what portion of the nation’s waterways will now come under stricter regulation. After the Supreme Court issued rulings that questioned whether the Clean Water Act applies to isolated streams that are not connected to navigable waterways, Bush officials said as many as 20 million acres of wetlands fell under that category.

The EPA has also abandoned more than 1,500 pollution probes in recent years, given the uncertainty surrounding what qualifies as “waters of the United States.”

“It’s an incredible mess,” said Jon Devine, a senior attorney in the Natural Resources Defense Council’s water program. He noted that just this week a federal jury in Massachusetts ruled against an individual who, without having a permit, filled in wetlands to grow cranberries, but the case dated from 1999 and could still be subject to appeal.

“It’s a big deal because the resources matter,” Devine said of the new guidance.

Jackson said that “we know that the current guidance is flawed. We also know that it underprotects.”

The administration will take comments on its proposed guidance for 60 days, and will then proceed to draft binding rules on the matter.