A federal judge blocked construction of a giant copper mine in Arizona’s Coronado National Forest, overturning a decision by the federal government and handing a major victory to environmental groups and tribes that have been fighting plans for the mine.

Federal District Judge James Soto said in his decision Wednesday that the U.S. Forest Service “abdicated its duty to protect the Coronado National Forest” when it failed to consider whether the mining company held valid unpatented mining claims.

Conservation groups sued the government seeking to stop construction of the $1.9 billion Rosemont copper mine by Toronto-based Hudbay Minerals Inc. The company secured federal approvals for the open-pit mine in the Santa Rita Mountains southeast of Tucson, but opponents argued it would tear up the landscape, destroy streams and ravage habitat for rare animals, including endangered jaguars that roam the wilds of southern Arizona.

“This is a crucial victory for jaguars and other wildlife that call the Santa Ritas home,” said Randy Serraglio of the Center for Biological Diversity, one of the groups that filed cases seeking to stop the mine. “The judge’s ruling protects important springs and streams from being destroyed. We’ll move forward with everything we’ve got to keep protecting this southern Arizona jewel from this toxic mine.”

Other groups that sued to challenge the federal government’s approval of the project included the group Save the Scenic Santa Ritas and three Native American tribes: the Tohono O’odham Nation, the Pascua Yaqui Tribe and the Hopi Tribe. The tribes object to plans to excavate remnants of ancestral villages and burial sites, and say the mine would dewater springs and seep they consider sacred.

Soto said in the ruling that he was overturning the Forest Service’s decision and environmental impact statement “such that the Rosemont Mine cannot begin operations at this time.”

MORE: Plans for the giant Rosemont mine have unleashed a battle

The judge said the Forest Service had “no factual basis to determine that Rosemont had valid unpatented mining claims” on 2,447 acres, and that the claims are invalid under the Mining Law of 1872.

“The unauthorized dumping of over 1.2 billion tons of waste rock, as well as about 700 million tons of tailings, and the establishment of an ore processing facility no doubt constitutes a depredation upon Forest Service land,” Soto wrote in the decision. He said the agency implemented the wrong regulations, misinformed the public, and “failed to adequately consider reasonable alternatives.”

The mining company said it will appeal to the Ninth Circuit Court of Appeals.

"Hudbay believes that the Court has misinterpreted federal mining laws and Forest Service regulations as they apply to Rosemont," the company said in a statement. It said the Forest Service issued its decision in 2017 after a "thorough process of ten years involving 17 co-operating agencies at various levels of government."

Peter Kukielski, Hudbay's interim president and CEO, said the appeal will proceed as the company evaluates its next steps on the project.

"We are extremely disappointed with the Court's decision," Kukielski said. "We strongly believe that the project conforms to federal laws and regulations that have been in place for decades."

Representatives of the Forest Service were unavailable to comment on the decision.

The judge said “defects pervaded” the Forest Service’s review and decision, and “led to an inherently flawed analysis from the inception of the proposed Rosemont Mine.”

Stu Gillespie, an attorney with the group Earthjustice who is representing the tribes, said the ruling “affirms the fundamental principle that nobody gets a free pass to destroy our public lands.”

“As the Court explained, the Forest Service provided no basis for assuming Hudbay had a right to destroy thousands of years of the Tribes’ cultural heritage,” Gillespie said in an email. “Because this crucial error tainted the entire process, the Court threw out the Forest Service’s decision and enjoined Rosemont from destroying these sacred public lands.”

MORE: Arizona tribes challenge permit for open-pit copper mine near Tucson

The tribes' leaders praised the judge’s decision. Ned Norris Jr., chairman of the Tohono O’odham Nation, called it a victory for “all of Southern Arizona.”

“The devastation that the Rosemont mine would bring to our land, water, and cultural resources is well-documented and cannot be allowed to happen,” Norris said in a statement. “The Nation will continue to fight to ensure that our sacred lands and the region’s water are protected.”

Hudbay has disputed the concerns raised by opponents, stressing that the project has gone through a thorough vetting process involving multiple government agencies and lasting more than 12 years, with a long list of studies that have examined the potential effects on the environment. Hudbay has argued that various agencies concluded the company will be able to operate the mine in compliance with environmental laws.

The company says Rosemont would be the third-largest copper mine in the United States.

Serraglio called the judge's decision a “momentous precedent.”

“The judge essentially ruled that the mining company does not have an automatic right to dump their toxic waste on our public lands, and that the Forest Service’s interpretation of the law to that effect undermined the entire EIS (environmental impact statement) process,” Serraglio said in an email.

While the company appeals the decision, the judge made clear that no work on the mine may proceed in the meantime.

Reach reporter Ian James at ian.james@arizonarepublic.com or 602-444-8246. Follow him on Twitter: @ByIanJames

Environmental coverage on azcentral.com and in The Arizona Republic is supported by a grant from the Nina Mason Pulliam Charitable Trust. Follow The Republic environmental reporting team at environment.azcentral.com and at OurGrandAZ on Facebook, Twitter and Instagram.