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Staff scientists at the U.S. Environmental Protection Agency had serious concerns last year that the PolyMet copper-nickel mine might not be able to meet state and federal water quality standards under the Clean Water Act, according to documents released Thursday.

The scientists' comments were written more than a year ago in response to a key permit the Minnesota Pollution Control Agency issued to PolyMet Mining. But they were never submitted. Instead, they were released this week as part of a Freedom of Information Act case an environmental group filed against the EPA in an attempt to make them public.  

In court filings, the St. Paul-based advocacy group WaterLegacy questioned whether the EPA comments had been suppressed as the MPCA developed the final water quality permit it eventually granted to PolyMet last December. 

WaterLegacy and Minnesota U.S. Rep. Betty McCollum applauded the documents' release. 

"All Minnesotans have a stake in ensuring that the quality of our water is protected, and the public has a right to access essential information about whether a project of this magnitude meets the spirit and letter of the law," said McCollum, who, as chair of a House subcommittee with jurisdiction over the EPA, 

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The water quality permit and an air quality permit were the last two state approvals PolyMet needed to move ahead with its NorthMet copper-nickel mining project, which would be located near Babbitt and Hoyt Lakes in northeastern Minnesota. It capped a review and permitting process for the controversial development — which is set to become Minnesota's first copper-nickel mine — that's stretched well beyond a decade.


Copper-nickel mining poses potentially more severe environmental risks than the state's long-established iron ore mining industry because the process used to extract the minerals from the sulfide rock can result in acid mine drainage, which can leach heavy metals and other pollutants into nearby surface and groundwater. 

That's why the project's water quality permit, which sets limits on the pollutants that can be released into groundwater, lakes and streams, was so heavily scrutinized when 

Four environmental groups — the Minnesota Center for Environmental Advocacy, the Center for Biological Diversity, Friends of the Boundary Waters Wilderness and WaterLegacy — along with the Fond du Lac Band of Lake Superior Chippewa, quickly 

 at the Minnesota Court of Appeals. They argued the permit failed to comply with federal and state standards.

Soon after, in January, retired EPA attorney Jeffry Fowley filed a complaint with the agency's inspector general, alleging that administrators in the EPA's Chicago office had "suppressed" staff comments that were critical of the PolyMet water quality permit.

But in a brief filed Wednesday in the appeals court case, the MPCA acknowledged it had come to an agreement with the EPA "that EPA would provide oral [rather than written] comments to MPCA." 
 
The documents EPA released Thursday show that EPA staff had significant concerns about the permit. EPA scientists were especially concerned that it failed to include specific limits on the amount of pollutants the mine can discharge, — known as "water quality-based effluent limits" — which are put in place to ensure that projects can meet federal environmental standards. 

EPA staff had prepared detailed written comments, but the agency never filed an objection to the MPCA's permit plan. And instead of publicly submitting those comments in writing during the public comment period part of the permitting process, staffers at both agencies agreed that the EPA would read them to MPCA staffers over the phone. 

As a result, the EPA scientists' concerns did not become a part of the administrative record, which appeals courts rule on — and which the Minnesota Court of Appeals will rely on in its review of the MPCA's decision to issue the permit. 

Fowley, the former EPA attorney who filed the inspector general complaint, said in a filing included in WaterLegacy's appeals court case that it was "highly unusual" that written comments on such a complex permit would not be part of the public record. 
 
"In all of my years of experience," he wrote, "I have never heard of a situation where EPA personnel have read written comments on a permit to state personnel over the phone."

Fowley worked for 37 years at the EPA office in Boston and specialized in Clean Water Act compliance.
 
"The apparent purpose for only receiving such comments over the phone would be to obtain them off the record — to avoid the MPCA receiving written comments which it would then need to be put into the administrative record for the permit and to which it would then need to respond," he wrote.

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Fowley told the court last week that the EPA's inspector general had begun a preliminary inquiry into his complaint. The office announced Wednesday it was beginning an audit of the water quality permit issued by the MPCA "to determine whether the EPA followed appropriate Clean Water Act ... regulations to review the PolyMet permit approved by Minnesota and issued in 2018." 

But in interviews and court filings, the MPCA argues it engaged in a robust back-and-forth with EPA staffers for several years in developing PolyMet's water quality permit. Officials insist it was neither out of the ordinary — nor unethical — for the agency to receive comments from federal regulators over the phone.

"I think it was the most effective way for [EPA] to make the comments and for us to react to them," said John Linc Stine, who was MPCA commissioner while the PolyMet water quality permit was being developed. 

"There had been years and years of document exchange and comment back and forth," he continued. "So, it seemed right to me to handle it by phone calls, so that we could get the permit finally resolved and drafted." 

Linc Stine said it wasn't unusual for the EPA not to submit written comments. MPCA officials said the agency's staffers engaged in regular conference calls with their EPA counterparts, and continually incorporated their feedback into the draft water quality permit. 

But Paula Maccabee, WaterLegacy's attorney and advocacy director, said it's commonplace for the EPA to provide written comments on major industrial permits in Minnesota — and for the MPCA to provide detailed responses. 

MPCA spokesperson Darin Broton emphasized that staffers from the state and federal agencies had frequent conversations during the permitting process. Those conversations, he said, resulted in substantive changes to the permit along the way, including additional limits on the discharge of several pollutants — including arsenic, lead and mercury — and "language prohibiting violation of water quality standards."

Broton said that's why the EPA did not object to the MPCA's final permit when the state agency sent it to them for final review. 

But the Fond du Lac Band and environmental groups that brought the appeals court case argue that the limits included in the permit are weak and unenforceable, and aren't the same kind of restrictions that EPA scientists asked for in the comment letter released Thursday. 

They also argue the permit, as written, could actually act as a shield to protect the company from potential liability. 

"Without those effluent limits, Minnesota water quality won't be protected from the state's first proposed toxic sulfide mine," Water Legacy's Maccabee said.

WaterLegacy's appeals court case is one of several lawsuits making its way through state and federal courts seeking to overturn various approvals PolyMet received to build its mine. 

Barring a successful legal challenge, PolyMet is clear to begin construction of the state's first-ever copper-nickel mine, once it raises the estimated $1 billion it will cost to build it. Later this month, PolyMet is expected to conclude a stock offering to clear debt from its balance sheet, which could result in the Swiss mining and commodities giant Glencore winning majority ownership of the company.

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Staff scientists at the EPA had serious concerns last year that the PolyMet copper-nickel mine might not be able to meet state and federal water quality standards under the Clean Water Act, according to documents released Thursday.

Newly released documents detail EPA's concerns over PolyMet

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