Some of the nation’s headwater streams and wetlands would lose federal protection under guidance issued by the EPA and Army Corps of Engineers in June, which sought to interpret a jumbled ruling by the U.S. Supreme Court last year.

The guidance sent to the field staffs of the two agencies, which are the primary federal entities for wetland protection, does not explicitly remove any areas from protection but establishes new tests that must be met before they can assert federal authority over certain areas.

“This interagency guidance will enable the agencies to make clear, consistent, and predictable jurisdictional determinations,” said John Paul Woodley, Jr., the assistant secretary of the Army who oversees the Corps of Engineers.

Under the new guidance, wetlands that are adjacent to traditionally navigable waterways are regulated. Tributaries that are connected to navigable waterways are also protected under the Clean Water Act as long as they are “relatively permanent,” according to the guidance. Wetlands along those tributaries are also regulated as long as they have a continuous surface connection to the tributaries.

But other wetlands that may “significantly affect” traditionally navigable waters, as well as isolated wetlands, will be regulated on a case-by-case basis using a series of tests established in the guidance.

The extent to which wetlands in headwater areas are ruled off-limits for protection could have profound impacts for downstream water quality. “Headwater streams are the ones that have the best chance of removing pollution and doing something with it before it goes downstream,” said Kirk Havens, a wetlands scientist with the Virginia Institute of Marine Science.

An internal analysis, completed in 2003 by EPA Region III—which includes most of the Bay watershed—said that if large areas of headwater streams lost protection, it would make attainment of downstream water quality standards, as well as those for the Bay, “problematic.”

But any immediate impact in the region is likely to be limited. Virginia, Pennsylvania, Maryland and New York all have state programs that could fill the gap.

“Fortunately, all of the states have programs to assert jurisdiction there,” said Carl Hershner, a VIMS wetlands scientist and chair of the Bay Program’s Scientific and Technical Advisory Committee. “That’s presuming the state programs are working efficiently and effectively.”

But wetland officials have long expressed concern that the loss of federal protection could spur legislative efforts to weaken state programs to match federal rules. “It leaves the states as the sole protectors,” Hershner said.

The new federal guidance was intended to clarify last year’s Supreme Court ruling that the EPA and the Corps erred when they denied permits in two Michigan cases where the development was not near “navigable waters.”

Justices expressed a host of views about the extent of the federal government’s ability to regulate wetlands. In the ruling, Justice Anthony Kennedy agreed with four other justices that the federal agencies had overstepped their bounds in regulating the wetlands at issue in the case, but disagreed with the limits the four would have placed in the government’s regulatory power.

Rather, Kennedy wrote that agencies could regulate wetlands that had a “significant nexus” with navigable waters. Since then, agencies have been working to determine how to apply that standard to wetland regulations.

Joan Mulhern, senior legislative counsel for the group Earthjustice said the Supreme Court decision was “clear as mud” and the new guidance “throws even more mud into the mix.”

She and other environmental groups called on Congress to clarify the extent of wetland protections.

A bill offered by Reps. John Dingell, D-MI, and James Oberstar, D-MN, which has 160 sponsors, would make changes in the Clean Water Act to ensure that virtually all U.S. waters, including intermittent streams and wetlands, are covered.

“This guidance leaves protection for these waters murky and to be determined on a case-by-case basis,” Dingell said in a statement. “The guidance…proves once and for all that Congress should…clarify that it was intended that all waters of the United States be covered by the law.”