A federal agency gave the proposed Rosemont Mine its final biological clearance Tuesday, saying the mine won’t jeopardize a dozen imperiled species living on or near its site or illegally destroy their habitat.

The Final Rosemont Biological Opinion from the U.S. Fish and Wildlife Service acknowledged that the mine will cause significant adverse impacts on many of the species. It went into more detail on impacts on endangered and threatened fish and birds than it had in previous opinions.

This opinion, a rewrite of a 2013 report, was ordered after authorities discovered an endangered ocelot living near the site and concluded they had to take a second look at impacts on surrounding streams and wetlands.

The new opinion says many of the mine’s negative impacts on species will be ameliorated by a host of mitigation measures, some new, some previously disclosed. The new ones include the hiring of a biologist/project manager for monitoring of impacts on wildlife, a $3 million program to manage and remove invasive species and a $1.25 million program to upgrade habitat for the endangered Southwestern willow flycatcher and the threatened Western yellow-billed cuckoo.

The opinion is one of the key legal hurdles that Rosemont Copper and its parent company, Hudbay Minerals Inc., needed to clear before getting final federal decisions on the proposed copper mine in the Santa Rita Mountains southeast of Tucson. The U.S. Forest Service and the U.S. Army Corps of Engineers must make those decisions.

Mine opponents contend the opinion won’t survive a court challenge. That’s in part due to their view that the service improperly decided the mine won’t jeopardize jaguar existence or illegally destroy jaguar habitat. The only known U.S. wild jaguar has lived near the mine site in recent years.

The new report acknowledges that the mine’s lowering of the water table to create the open pit could or would dry up a stretch of Empire Gulch, a key tributary to Cienega Creek, a nationally recognized stream running east of the mine site.

But the report agrees with the Forest Service’s conclusions that the water-table decline won’t be enough to cause major drying of Cienega, even after 150 years. The creeks and surrounding wetlands are home to many of the endangered fish, frogs and birds that were among the species reviewed.

The opinion says many of the imperiled species have healthy populations elsewhere, including the jaguar, and noted that the mining company will monitor groundwater levels. It also mentioned a long-debated, highly controversial plan by the mining company to buy water rights to Lower Cienega Creek to keep water from being diverted onto a golf course. That water could be used downstream to create more wildlife habitat, the wildlife service says.

Patrick Merrin, Hudbay Minerals’ vice president for its Arizona Business Unit, issued a written response Tuesday, saying the biological opinion “was completed through a 23-month-long science-based evaluation.

The process included the participation of five federal agencies and more than 720 studies and reports. We acknowledge the diligence of the agencies and their staff participating in the Final Biological Opinion’s development and their hard work required to complete the document. Our leadership remains committed to the permitting process.”

Two mine opposition groups sharply criticized the report.

“The agency charged with protecting America’s most vulnerable wildlife thinks it’s just fine for a foreign mining company to harm our only known jaguar. This outrageous decision, which was contradicted by the agency’s own scientists, will not withstand judicial scrutiny,” said Randy Serraglio, a conservation advocate for the Tucson-based Center for Biological Diversity.

“The Rosemont project will destroy the habitat of endangered species with its half-mile deep open pit and mine waste piles stacked 600 to 800 feet high spread over five square miles of the Coronado National Forest,” said Gayle Hartmann, president of the group Save the Scenic Santa Ritas.

Contact reporter Tony Davis at tdavis@tucson.com or 806-7746. On Twitter@tonydavis987