A federal judge on Monday ruled in favor of the Pebble mine project and put a temporary halt on the U.S. Environmental Protection Agency's efforts to protect Bristol Bay.

The ruling is a "procedural victory," but it doesn't settle Pebble's claims that EPA overstepped the law, Tom Collier, Pebble Ltd. Partnership CEO, said Monday afternoon in a written statement. It will take months more to resolve the lawsuit at issue, Pebble said.

Activists fighting the mine noted that U.S. District Judge Russel Holland rejected two of Pebble's three arguments to halt EPA over a theory that it colluded with anti-mine activists and scientists. Rather, the judge determined that Pebble had a chance of winning on one claim, that EPA improperly turned to an anti-mine team as it worked on its study of how a big mine would affect the Bristol Bay watershed.

The EPA in July announced that it intended to take extraordinary steps to protect Bristol Bay's world-class salmon runs and proposed restrictions that would prevent the mega-mine from being advanced by the Pebble Partnership. While it stopped short of an outright veto of the project, the EPA said it would place caps on how many miles of streams and acres of wetlands could be lost if the mine were developed.

Pebble responded with three lawsuits.

In U.S. District Court in Anchorage on Monday, the focus was on one of them, and whether Pebble has a chance of winning.

The 138-page lawsuit is rooted in an obscure 1972 federal law, the Federal Advisory Committee Act, that requires the government to follow basic rules of open government.

Pebble asserted the EPA relied on "de facto advisory committees that worked behind the scenes, and out of the public eye," for its Bristol Bay watershed study, which Pebble derided as "biased, junk science." EPA worked secretly with Pebble critics, the lawsuit contended.

An anti-mine team played a critical role in developing EPA's strategy of using the Clean Water Act to restrict a big mine, "precisely the kind of backroom influence peddling that FACA was enacted more than 40 years ago to prevent," the lawsuit contends.

In his ruling from the bench, Holland granted Pebble's request to block EPA from taking additional steps to finalize its restrictions on the gold and copper mine until the lawsuit is fully aired and decided.

The judge also directed Pebble to rewrite the complex lawsuit "as soon as possible."

"We expect the case may take several months to complete," Collier said. "This means that for the first time EPA's march to preemptively veto Pebble has been halted."

Pebble is separately challenging whether EPA has the authority to impose restrictions through the Clean Water Act even before a mine plan is submitted. It lost the first round and has appealed. It also is suing the EPA for public records. Records already released show more than 500 contacts between EPA and activists, Collier said.

"We fully expect that once we have access to all the documents that there may be many times that number," he said in the statement.

EPA said it was waiting for the written ruling.

The decision wasn't on the merits of Pebble's claims, EPA said.

Its work leading up to the decision to restrict the mine was based on extensive, peer-reviewed science, EPA said. The mine would be nearly as deep as the Grand Canyon in a region rich with salmon and with unparalleled natural habitat. It would straddle the headwaters of salmon-producing streams that feed into Bristol Bay.

Advocacy groups that have been fighting the mine were disappointed with the ruling. They said that Pebble's characterization of EPA's work is wrong.

The process that EPA used to develop its Bristol Bay watershed study was a model of good government, said Kim Williams, executive director of Nunamta Alukestai, a group that now includes 10 tribes opposed to Pebble.

She participated on EPA's intergovernmental technical team as a representative of Curyung Tribal Council, the tribe for Dillingham. The team also included representatives from the state of Alaska, which sued the EPA over Pebble, and tribal organizations that support Pebble, Williams said.

"I sat in on those meetings. It wasn't one-sided. EPA has this model process where they allowed all the stakeholders to participate," Williams said. "That's government in action as it should be. It's very transparent."

EPA didn't follow every critical thread, she said. For instance, she questioned whether power generation at the mine site would create environmental problems, but EPA didn't include that angle in its study.

EPA spent more than three years on its Bristol Bay assessment. Tribes have been asking for protections even longer.

"It is unfortunate that Judge Holland does not see harm in delaying a final decision that would provide our residents the peace of mind they have been waiting on for nearly a decade," Alannah Hurley, executive director of United Tribes of Bristol Bay, said in an email.

Sue Aspelund, executive director of the organization that represents driftnet fishermen, the Bristol Bay Regional Seafood Development Association, said in a written statement that "political games and courtroom stalling tactics" were bringing uncertainty to the region.

The stakes are huge. The Pebble prospect is estimated to be one of the largest deposits in the world. Half of the world's wild runs of sockeye salmon originate in the Bristol Bay watershed. The state Department of Fish and Game has predicted next year will bring the biggest run of Bristol Bay sockeye salmon in 20 years.

"This decision is far from damning, but it does nonetheless represent an unfortunate example of Pebble throwing up legal and procedural roadblocks against scientific fact and the will of Alaskans, which has consistently spoken out against Pebble Mine," said Tim Bristol, Alaska program manager for Trout Unlimited, a trout and salmon conservation organization.