Mineral leases near the Boundary Waters Canoe Area Wilderness will not be renewed, the U.S. Department of the Interior and the Department of Agriculture announced Thursday.

The federal agencies cited broad concerns from thousands of public comments and input about potential impacts of mining. They also initiated steps to withdraw key portions of the watershed from new mineral permits and leases.

Affected is land near Ely where Twin Metals Minnesota has conducted extensive research and found rich concentrations of copper, nickel and other precious metals. The firm previously filed a lawsuit challenging the agencies’ authority to deny mineral leases.

“The Boundary Waters is a natural treasure, special to the 150,000 who canoe, fish, and recreate there each year, and is the economic life blood to local business that depend on a pristine natural resource,” USDA Sectetary Tom Vilsack said in a prepared statement. “I have asked Interior to take a time out, conduct a careful environmental analysis and engage the public on whether future mining should be authorized on any federal land next door to the Boundary Waters.”

U.S. Sen Amy Klobuchar (D-Minn.) said the proposed project preferably would have followed the established review process.

“I had advocated for making a decision on this project based on the environmental review process that has been utilized for other mining projects. I am concerned that with the federal government using the leasing standard, we will end up in endless lawsuits and will not get an outcome—regardless of whether the science supports granting or not granting a permit—based on a thorough scientific review," she said in a Dec. 19 statement. “That’s why, earlier this summer, I asked the Administration a series of written questions — though I have yet to receive a response — about why the Administration would utilize a lease renewal process instead of the normal environmental review process that the U.S. government has used in the past. Without any answers after nearly six months, I will pose the same questions to the new administration"

Officials of Twin Metals expressed disappointment in the action announced by the BLM and the USFS to deny renewal of two of the company’s mineral leases.

"If allowed to stand, the BLM-USFS actions will have a devastating impact on the future economy of the Iron Range and all of Northeast Minnesota, eliminating the promise of thousands of good-paying jobs and billions of dollars in investment in the region. Further, this unprecedented decision is contrary to the overwhelming majority of local and regional citizens and communities who support mining and believe mining can be done responsibly in this region," Twin Metals responded Thursday afternoon in a news release.

The agency said Congress set aside the Boundary Waters more than 50 years ago “in recognition of its irreplaceable resources. Today, more than 150,000 annual visitors help drive the local economy through tourism and outdoor recreation.”

“There's a reason that the Boundary Waters is one of the most visited wilderness area in America: it's an incredible place,” said U.S. Secretary of the Interior Sally Jewell. “Today's best available science is helping us understand the value of the land and water and potential impacts of development in places like the Boundary Waters. This is the right action to take to avoid irrevocably damaging this watershed and its recreation-based economy, while also taking the time and space to review whether to further protect the area from all new mining.”

Twin Metals Minnesota filed its lawsuit Sept. 12 in U.S. District Court in Minnesota. It followed a decision by Gov. Mark Dayton to order the Minnesota Department of Natural Resources (DNR) not to authorize or enter into any new state access agreements or lease agreements for mining operations on state lands in close proximity to the Boundary Waters. The U.S. Forest Service later expressed concern about renewing two Twin Metals Minnesota non-ferrous mining leases because of the lands’ close proximity to the BWCA.

The lawsuit seeks to invalidate an opinion by Department of the Interior (DOI) Solicitor Hilary Tompkins, who instructing the Bureau of Land Management (BLM) that it has the discretion to deny renewal of Twin Metals’ federal mineral leases. The lawsuit challenges the solicitor’s opinion as being inconsistent with federal law, the terms of Twin Metals’ leases, and the federal government’s established precedent in supporting and renewing the leases over five decades.

“The solicitor’s opinion has cast a cloud of uncertainty over Twin Metals’ federal mineral rights creating significant challenges for the company to engage in long-term planning, investment, development, or operational decisions,” Ian Duckworth, chief operating officer of Twin Metals, said in September. “Affirming the validity of Twin Metals’ federal mineral leases would eliminate that uncertainty and facilitate responsible project development activities moving forward.”

The company said the leases in question were issued by the federal government in 1966 with a right of unlimited, successive 10-year renewals. The leases were renewed by the BLM without controversy in 1989 and 2004. Twin Metals filed the pending lease renewal application in mid-2013.

In not consenting to the lease renewals, the Forest Service cited the potential risk of environmental contamination of the surrounding watershed as a key concern.

“The two leases are located directly adjacent to and within three miles of the BWCAW, respectively. It is well established that acid mine drainage is a significant environmental risk at sulfide ore mine sites like the one proposed for these leased lands and in a water-based ecosystem like the Boundary Waters because contaminated water could have dramatic impacts to aquatic life, sport fisheries, and recreation-based uses and communities,” the agency wrote.

Last summer, the Forest Service held two listening sessions and a 30-day public input period related to the potential lease renewals and received more than 30,000 comments.

“The decision to withhold consent and study the impacts of this type of mining near the Boundary Waters echoes the concerns of many in the area, including former Vice President Walter Mondale and Minnesota Governor Mark Dayton, who has similarly said that the state will not authorize or enter into any new state access or lease agreements for mining operations near the Boundary Waters Canoe Area,” the agency said.

Late in November, the industry said a poll revealed wide-scale support for nonferrous mining. By large margins, Northeastern Minnesotans support the development of new copper-nickel mines and oppose new federal restrictions on mining throughout the region, said the poll, which was conducted by Twin Metals and the industry trade group Mining Minnesota.

“Support for the mining economy and for the development of copper-nickel mining projects is overwhelming across northeastern Minnesota and the Iron Range,” Bob McFarlin, Twin Metals spokesperson, said of the findings. “This extraordinary support reflects a strong belief that copper-nickel mining can help revitalize the region’s economy, protect the environment and create jobs for generations of Minnesotans.”

Beyond Thursday's ruling, the Forest Service also submitted an application to the Secretary of the Interior to withdraw key portions of the watershed that flows into the BWCAW from new mineral permits and leases.

Twin Metals, which is owned by Antofagasta PLC, has invested more than $400 million in acquisition, exploration, technical, environmental and other project development activities. The company has said it did so while relying on the federal government’s repeated affirmation of the validity of the mineral leases.

The agencies went a step further in its Thursday announcement.

“BLM will review the withdrawal application and issue a notice in the Federal Register to segregate the lands – essentially, place them in a 'time out' – for up to two years, subject to valid existing rights. To preserve the status quo during that 'time out,' no new mineral exploration or development applications would be accepted while a thorough, scientific environmental analysis is conducted. Upon publication of the Federal Register notice, there will be an initial 90-day public review period for the proposed withdrawal and additional analysis during the segregation period that will include further public involvement, including public meetings,” said the government’s news release.

During the segregation period, BLM and the Forest Service will conduct an environmental analysis to determine if the lands should be withdrawn for a period of 20 years. This process will invite participation by the public, tribes, environmental groups, industry, state and local government, as well as other stakeholders. By law, the Department of the Interior can only withdraw these lands for a maximum of 20 years. Only Congress can legislate a permanent withdrawal.

Klobuchar said the federal agencies used language that was not specific enough to prevent misinterpretation or abuse.

“While I have long been an advocate for preserving our natural resources and protecting our wilderness, I am also very concerned that the use of the term ‘minerals’ in the announcement is so broad that it could be interpreted to include taconite mining," she said.

The segregation or any future withdrawal would not prohibit ongoing or future mining activities on any valid existing rights or prohibit any other authorized uses on private lands. Other National Forest management activities that are not related to mineral exploration or development, including permits, licenses, and cooperative agreements compatible with the intended use on the lands, would still be permissible at the discretion of the authorized officer.

Twin Metals said it is assessing the impact of the agencies’ lease renewal decision, adding that the company is "committed to progressing our project forward and will continue to pursue legal avenues to protect our contractual mineral rights.”

Klobuchar said mining and environmental protection can co-exist.

“For generations we have been able to successfully preserve our wilderness and natural resources in northern Minnesota while allowing responsible mining to continue. I have worked very hard to protect our environment while at the same time preserving mining jobs in northern Minnesota. In fact taconite plants have recently reopened after more aggressive action has been taken on illegal steel dumping. We will of course not have success until every worker has their job back.

Minnesota's Republican Party seized on the opportunity and blamed Democrats for the decision.

"In a cruel attack on Iron Range families right before Christmas, Democrats effectively killed the Twin Metals' mining project today and likely all future mining with an order from the Obama administration," Chairman Keith Downey said Thursday in a prepared statement. "The Democrats' cynical and pathetic show of rejecting the "kill mining" Resolution 54 at their State Central Committee meeting last Saturday (Dec. 10) is the absolute worst of politics.  Shamefully, Mark Dayton, Rick Nolan and Amy Klobuchar claim to support mining, all the while they must have known that this order was coming. It is no coincidence that this order effectively accomplishes the intensions of Resolution 54. The order requires that equipment must be removed from the site and all activity shut down. We'll say it again, watch what Democrats do, not what they say, when it comes to killing mining and destroying the economy of Northeastern Minnesota."

“My goal here is to have a decision based on science and the facts,” Klobuchar said.