That project is slated to bury more than seven miles of mountain streams, leading to a protracted legal battle with environmentalists. But last Friday, the Environmental Protection Agency took a giant stride toward halting the operation, when it sent notice to the U.S. Army Corps of Engineers threatening to revoke the mine’s previously granted Clean Water Act permit unless the Corps takes further action to limit the impact on local water quality.

The Charleston Gazette’s Ken Ward Jr. has the latest details:

The judge said  the stay, until Nov. 3, will give EPA and the Corps time to discuss the permit further and consider the next step. Arch Coal’s Mingo Logan Coal Co. subsidiary had wanted [U.S. District Judge Robert C.] Chambers to deny the government’s request for a stay and throw out a lawsuit filed against the Spruce Mine by environmental groups.

EPA’s letter today confirms that all 79 permits initially identified on September 11 must undergo additional evaluation by EPA and the Army Corps of Engineers. EPA’s final list was transmitted in a letter to the Assistant Secretary of the Army (Civil Works) Jo-Ellen Darcy.  The 79 permits represent all of the backlogged surface coal mining projects under review by the Army Corps of Engineers. After a careful evaluation of these surface coal mining projects, EPA determined that each of them, as currently proposed, is likely to result in significant harm to water quality and the environment and are therefore not consistent with requirements of the [Clean Water Act].

As Ward points out, this doesn’t mean that the 79 projects will be rejected. But they could be altered if the EPA — which has been a more aggressive environmental watchdog under this administration than under the last — determines that they do indeed violate the Clean Water Act.

Environmental groups were quick to applaud the decision. Mary Anne Hitt, deputy director of the Sierra Club’s Beyond Coal Campaign, issued a statement saying the further review “will surely prove that this most destructive form of coal mining is incompatible with clean water.”

The ruling extends from a 2002 rule change, with which the Bush administration redefined mining debris — even toxic mining debris — as “fill” rather than “waste.” That seemingly subtle change had the wide-sweeping consequence of shifting mine-waste disposal decisions from the Environmental Protection Agency to the U.S. Army Corps of Engineers — a switch that also helped fuel the popularity of mountaintop mining operations in the Appalachian states in the last decade.

The Obama administration has taken steps in recent weeks to reassert the powers of the EPA to protect waterways surrounding mountaintop sites, but those changes, up to now, are limited to Appalachian projects. Alaskan mines just aren’t subject to the new scrutiny.

That spells bad news for Tongass National Forest’s Lower Slate Lake. In 2005, the Corps had approved permits for the Alaskan gold mine company, Coeur Alaska Inc., to dump 210,00 gallons of waste per day into Lower Slate — waste containing aluminum, copper, lead, and mercury. It was those permits that the Supreme Court upheld 6-3 Monday, overturning an earlier ruling by the 9th U.S. Circuit Court of Appeals.

The reasoning from the court’s majority goes something like this: Because (1) the dumping is expected to raise the bottom of the lake bed by 50 feet over the lifespan of the mine; (2) waste that raises the bottom elevation of waterways is defined as “fill;” and (3) the Corps has sole jurisdiction to issue permits to dump “fill” — then by the transitive properties of jurisprudence the 2005 permits are legitimate, and the EPA is powerless to step in despite the undisputed environmental damage set to be visited upon the lake.

“We conclude that the Corps was the appropriate agency to issue the permit and that the permit is lawful,” Justice Anthony Kennedy wrote for the majority.

The dissenters, however, had another take. Joined by Justices John Paul Stevens and David Souter, Ruth Bader Ginsburg wrote that the majority’s ruling “strains credulity.”

A discharge of a pollutant, otherwise prohibited by firm statutory command, becomes lawful if it contains sufficient solid matter to raise the bottom of transformed into a waste disposal facility. Whole categories of regulated industries can thereby gain immunity from a variety of pollution-control standards. The loophole would swallow not only standards governing mining activities … but also standards for dozens of other categories of regulated point sources.

The court’s ruling clearly defies the intention of the Clean Water Act, Ginsburg added, which states that “the use of any river, lake, stream or ocean as a waste treatment system, is unacceptable.”

Environmentalists also blasted the ruling, warning that it could set a dangerous precedent. “If a mining company can turn Lower Slate Lake in Alaska into a lifeless waste dump,” Trip Van Noppen, president of Earthjustice, said in a statement, “other polluters with solids in their wastewater can potentially do the same to any water body in America.”

At least one voice, however, is joining the mining industry to cheer the decision. Pointing to the 370 local jobs the mine will sustain, Alaska Gov. Sarah Palin (R) said yesterday that the ruling is “great news for Alaska.”

Today’s ruling is a green light for responsible resource development … We truly appreciate Coeur’s tenacity in pursuing the project and its dedication to hiring Alaskans to work at the mine.

The next move lies with the White House.

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A report released today from Waxman’s office — a joint effort with the House Transportation and Infrastructure Committee, headed by Rep. James Oberstar (D-Minn.) — found that the Environmental Protection Agency has shown a lax interest in enforcing the Clean Water Act in recent years, leading to hundreds of instances when investigations have been neglected and waterways have been threatened. From Waxman’s statement:

Our investigation reveals that the clean water program has been decimated as hundreds of enforcement cases have been dropped, downgraded, delayed, or never brought in the first place. We need to work with the new Administration to restore the effectiveness and integrity to this vital program.

The controversy surrounds a 2006 Supreme Court ruling on the Clean Water Act (Rapanos v. United States), which restricted traditional interpretations of the law by requiring the EPA and other federal agencies to show that a waterway is a “significant nexus” to “traditional navigable waters” before officials can apply the environmental protections under the act. Following the Bush administration’s interpretation of that vague ruling, Waxman found, the EPA has whitewashed hundreds of potential violations.

The effects, according to the findings, are nationwide. The EPA branch in Dallas, for example, reported in January that it had 76 cases of confirmed oil spills, “but no follow-up for penalties or corrective action has been sought due to difficulties asserting jurisdiction post-Rapanos.”

That same month, officials in the EPA’s Denver office sent notice to the agency’s headquarters that, “We literally have hundreds of OPA [Oil Pollution Act] cases in our ‘no further action’ file due to the Rapanos decision, most of which are oil spill cases.”

Another example: Last February, an official in the EPA’s San Francisco office announced that the agency was abandoning a case against a potential Clean Water Act violator, explaining the reason thusly:

It is time to pull the plug on keeping this case on life support. With the march of time largely attributable to the impact on the case by Senor Rapanos and his merry band of supreme court justices we had lost many many violations due to statute of limitations . . . . So we will withdraw the referral, and save our ammo for another fight.

Also a subject of the Democrats’ consternation, the EPA redacted many of the documents it provided to the committees — or simply refused to provide them at all. From a summary of the report:

EPA refused to produce hundreds of documents to the Committees and redacted many of the documents it did produce. EPA concealed the identity of corporations and individuals accused of polluting waters and the specific waters that may have been affected.

Waxman and Oberstar also sent the findings to President-elect Barack Obama, complete with a request “to restore the effectiveness and integrity” of the enforcement program.

The first step in that process occurred yesterday, when Obama named Lisa Jackson — former head of New Jersey’s Dept. of Environmental Protection — to lead the EPA next year. In the wake of the mess left behind by current EPA Administrator Stephen Johnson, environmentalists are ecstatic over the thought of the imminent change.

Indeed, the Sierra Club issued a statement yesterday saying Jackson “brings a strong scientific background to an agency where for the past eight years science and knowledge have been systematically corrupted and disregarded.”

Ouch.