A federal appeals court issued a stay Thursday delaying construction of parts of the Mountain Valley Pipeline in West Virginia.

The case, brought by the Sierra Club and four other conservation groups, challenges a stream-crossings permit issued by the U.S. Army Corps of Engineers.

While the underlying attack of the permit remains pending, a three-judge panel of the 4th U.S. Circuit Court of Appeals granted a late-afternoon stay that puts construction in southern West Virginia on hold until further court proceedings can be held.

“The effect of today’s court order is to prohibit MVP from construction activities in 591 streams and wetlands in West Virginia and it may affect construction along the entire route of the pipeline,” the Sierra Club said in a statement.

Filed in May, the request for a stay takes issue with a permit the Army Corps granted for four pipeline river crossings in West Virginia — even though it knew that Mountain Valley could not complete them within the 72 hours required by state regulators.

Shortly after the challenge was filed, the Corps temporarily suspended work on pipeline crossings of the Elk, Gauley, Greenbrier and Meadow rivers. Even before the court filing, river-crossing construction was not expected to start until late this summer.

But the stay granted Thursday covers all streams along an approximately 80-mile stretch of the pipeline in West Virginia — and as a result, it could impact the schedule for construction of the entire project, which will run through six counties in Southwest Virginia.

The Virginia portion of the pipeline was not directly impacted by the stay.

However, attorneys for Appalachian Mountain Advocates, a law firm representing the conservation groups, are arguing that the flaws with the four West Virginia river crossings are serious enough to invalidate other permits for stream crossings along the pipeline’s 303-mile route.

That includes a so-called Nationwide Permit 12 issued by the Army Corp’s Norfolk division for a stretch of the pipeline that passes through the New River and Roanoke valleys.

“When it comes to NWP 12, one bad apple spoils the bunch,” attorney Derek Teaney wrote in a motion seeking the stay. “That is, if even one stream crossing is ineligible for NWP 12, then all the pipeline’s crossings are ineligible.”

In a June 6 letter to the Army Corps, Teaney asked the federal agency to revoke a permit that covers nearly 500 streams and wetlands to be crossed in Virginia. Thursday’s stay came too late in the day to seek a comment from the Army Corps.

A spokeswoman for Mountain Valley said the company expects to seek a rehearing on the stay.

“While disappointed with this temporary setback… the MVP team is evaluating options to understand its ability to continue with construction activities that do not include stream and wetland crossings along this portion of the route,” Natalie Cox wrote in an email.

In court filings arguing against the stay, attorneys for the Pittsburgh-based company said it would be forced to delay work on an 80-mile stretch of the pipeline in West Virginia – at a cost of $600 million.

Such a delay would push back completion of the $3.7 billion project, which had been slated for the end of this year, by at least eight months, the filing stated.

At this point, the next step in the legal process is a hearing scheduled for September. Joining the Sierra Club in the petition for review of the Army Corps permit are the West Virginia Rivers Coalition, the Indian Creek Watershed Association, Appalachian Voices and the Chesapeake Climate Action Network.

At the heart of the case is the method that Mountain Valley proposes to use to cross four major rivers in West Virginia, and how long the process will take.

To run the 42-inch diameter steel pipe across the water bodies, the company plans to use a dry-cut method, in which a temporary dam diverts the water flow along half of the river’s width while construction crews dig a trench along the exposed river bed to bury the pipe. The process is then repeated on the second half of the river.

That is expected to take four to six weeks for each major river, Mountain Valley told the Army Corps.

The Corps then granted a permit for all water bodies and wetlands in southern West Virginia, despite a requirement by state regulators that the work on each crossing take no longer than 72 hours to limit its environmental impact, the Sierra Club maintains.

In her statement, Cox said both Mountain Valley and the West Virginia Department of Environmental Protection agree that the 72-hour limit only applies to “wet-cut” crossings, which involve digging an open trench while the river is flowing.

“While significantly more environmentally protective, the ‘dry-ditch’ technique also requires a longer completion time as compared to traditional ‘wet’ crossing methods to which the time limitation provision applies,” Cox wrote.

While the company evaluates it options, Cox wrote, it continues to target a late 2018 completion date for the pipeline.

But at least for now, pipeline opponents were optimistic about the first major court ruling to go their way.

“It brings a sense of relief to see this pause button hit,” said Angie Rosser, executive director of the West Virginia Rivers Coalition. “What we’re seeing is that short-cuts and easy-outs just won’t work for this massive project.”

“Already with MVP, we’re seeing its early construction causing problems for our waters. It’s encouraging that the court agrees a more intensive review of this permit is required before risking any further damage.”

Laurence Hammack covers environmental issues, including the Mountain Valley Pipeline, and business and enterprise stories. He has been a reporter for The Roanoke Times for more than three decades.

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