The Obama administration finalized its highly controversial new water quality guidance, continuing EPA Administrator Lisa Jackson’s efforts — despite major political pressure on the agency — to reduce the serious environmental and public health impacts of mountaintop removal coal mining in Appalachia.

EPA has posted the final guidance here and there’s a summary available here.

EPA acting assistant administrator for water Nancy Stoner said:

Under this guidance, EPA will continue to work with other federal agencies, states, local communities, and companies to design mining operations that adequately protect our nation’s waters and people’s health. We have a responsibility under the law to protect water quality and this guidance allows EPA to work with companies to meet that goal, based on the best science.

EPA said in a statement:

The guidance, which replaces the interim-final guidance issued by EPA on April 1, 2010, is based on the best-available science and incorporates input and feedback from over 60,000 comments received from the public and key stakeholders. By providing EPA’s regional offices with the latest information on existing legal requirements, the guidance enables them to work together with states, the U.S. Army Corps of Engineers, mining companies, and the public towards a balanced approach that protects communities from harmful pollution associated with coal mining. EPA will apply the guidance flexibly, taking into account site-specific information and additional science to arrive at the best decisions on a case-by-case basis.

In the guidance itself, EPA said:

The environmental legacy of mining operations in the Appalachian region is far-reaching. Recent studies, as well as the experiences of Appalachian coalfield communities, point to new environmental and health challenges that were largely unknown even ten years ago.

The guidance continues:

Since 1992, more than 1,200 miles of Appalachian streams have been filled by Appalachian surface coal mining practices, at an estimated ongoing rate of 120 miles per year. Further, while precise estimates are limited, the estimated scale of deforestation from existing Appalachian surface mining operations is greater in size than the State of Delaware, or 5,700 square kilometers predicted to be affected by 2012.

The full cumulative effects of surface coal mining operations at this scope and scale are still largely unknown.

Appalachian deforestation has been linked to significant changes in aquatic communities as well as to modified storm runoff regimes, accelerated sediment and nutrient transport, reduced organic matter inputs, increased algal production, and altered stream thermal regimes.

And, EPA said in the guidance:

Possible human health impacts from coal mining activities have also been documented, including peer-reviewed public health literature that has preliminarily identified associations between increases in surface coal mining activities and increasing rates of cancer, birth defects, and other health problems in Appalachian communities.

The guidance largely follows the draft guidance issued by EPA back in April 2010 as part of the Obama administration’s promised crackdown on mountaintop removal. EPA based the guidance in part on a detailed report on mountaintop removal’s water quality impacts, a report that was backed up by a review of experts put together by the agency’s Science Advisory Board.

EPA’s actions are also supported by the growing body of peer-reviewed science that concludes mountaintop removal is having “pervasive and irreversible” impacts on the Appalachian environment — not to mention the series of studies by WVU’s Michael Hendryx that suggest large-scale surface mining is linked to negative human health effects.

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EPA Administrator Lisa Jackson right, and Maryland Gov. Martin O’Malley, center, look over a display of soil conservation techniques during a meeting of the Chesapeake Bay Executive Council in Richmond, Va., Monday, July 11, 2011. (AP Photo/Steve Helber)

UPDATED:

Regular readers know that EPA Administrator Lisa Jackson has described the potential impacts of the guidance this way:

Let me be clear. This is not about ending coal mining. This is about ending coal mining pollution.

Minimizing the number of valley fills is a very, very key factor. You’re talking about no or very few valley fills that are going to meet standards like this.

The intent here is to tell people what the science is telling us, which is it would be untrue to say that you can have numbers of valley fills, anything more than say, very minimal valley fills and not expect to see irreversible damage to stream health.

That’s just the truth of it. That’s the science of it.

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The final guidance was issued by EPA just a day after it received the OK from the White House Office of Management and Budget, and just before a deadline tomorrow for Obama administration lawyers to file a key legal brief in a lawsuit challenging the mountaintop removal crackdown.

As discussed here before, the EPA’s actions are being fought in court by the coal industry as well as by the state of West Virginia, in a suit filed by then-Gov. Joe Manchin.

EPA critics have already won one limited skirmish in that litigation, in which a federal judge indicated it appears the agency had implemented significant changes in the permit process without following procedures for required public input and comment. It will be interesting to see how the fact that EPA has not finalized its guidance impacts that ongoing litigation. While an EPA brief is due tomorrow, substantive hearings in the part of the case challenging the EPA guidance aren’t scheduled until late October.

EPA also acted today despite the growing political pressure from the Republican-controlled House of Representatives, from the coal industry and from the industry’s friends among Democratic coal-state lawmakers.