BANGOR, Maine — A federal judge Wednesday said he will create a panel of engineers and scientists to recommend “cost-effective and scientifically effective” ways of removing mercury deposits left by the former HoltraChem plant in Orrington from the bed of the Penobscot River without causing further damage to the ecosystem.

After hearing closing arguments in a lawsuit that began 15 years ago, U.S. District Judge John Woodcock said he will issue a written order next month creating the panel and most likely seeking a special master to oversee it.

Woodcock also found in favor of the plaintiffs — the Maine People’s Alliance and the Natural Resources Defense Council — and accepted the results of a study filed in 2013.

The judge rejected the request of defendant Mallinckrodt Inc. that the company oversee remediation.

Woodcock said he would follow the lead of now retired U.S. District Judge Gene Carter, who issued an order creating the study panel in 2002.

“The great genius of Judge Carter’s order is that it placed trust in a group of scientists whose loyalty ran to the court,” Woodcock said. “And by the court what we really mean is the public.”

Woodcock said the new group would recommend solutions to the problems outlined by the scientists Carter appointed to determine the severity of the mercury pollution. The original panel was not tasked with making specific recommendations about remediation or determining how much the cleanup would cost.

Wednesday’s decision essentially was an oral verdict in the jury-waived trial held last June before Woodcock.

The judge expressed concern Wednesday about testimony last year that mercury is making its way from the Penobscot River into Penobscot Bay.

“We need to find out what we can do to prevent that,” Woodcock said.

In May 2014, concerns over elevated mercury levels found in lobsters prompted the Department of Marine Resources to close permanently a 7-square-mile area of the lower Penobscot River to lobster and crab fishing. The source of the mercury, the level of which is little more than what is found in canned white tuna, was traced to the defunct HoltraChem plant, according to previously published reports.

Woodcock also said Wednesday he would not award damages in the case.

“How do I pay a lobster?” he asked.

Attorneys for Mallinckrodt, a global pharmaceutical corporation, declined to comment after Wednesday’s nearly four-hour hearing, but the firm issued a statement in an email.

“Mallinckrodt remains committed to appropriate environmental remediation of the Penobscot River,” it said. “Mallinckrodt has fully supported the study panel’s work for the past decade. We continue to believe that targeted remedies offer the greatest chance to address risk without adding further unnecessary delays to this process. Mallinckrodt is prepared to work with NRDC on the next phase of this project.”

Representatives of the NRDC and MPA declined to comment after the hearing but held a press conference outside the Margaret Chase Smith Federal Building before the hearing began. The executive directors of both groups said they would continue their efforts to hold Mallinckrodt responsible for the mercury cleanup.

The cost of remediation has been estimated at $130 million, according to court documents. A study of the amount of mercury in the river submitted in April 2013 recommended establishing a remediation program that could include removing contaminated mobile sediments in the entire upper estuary and replacing them with clean sediments.

The case stemmed from a U.S. Department of Justice order in 1986 that forced Mallinckrodt to develop a “corrective action” plan under the guidance of the U.S. Environmental Protection Agency after repeated pollution problems at the plant and concerns about contamination of the river were voiced. The HoltraChem plant closed in 2000 because of bankruptcy, which left Mallinckrodt as the only remaining former owner still in business.

The MPA and NRDC filed the lawsuit against Mallinckrodt in April 2000, claiming state and federal regulatory agencies were not doing enough to address mercury pollution problems in the Penobscot River below the plant, which sat on 235 acres.

The two environmental groups won a landmark legal victory against the company in 2002. The company was found responsible for the pollution that occurred between 1967 and the early 1970s, when tons of mercury were dumped into the river.

Since 2002, Mallinckrodt has funneled millions of dollars into the river study but until Wednesday had fought the implementation of the cleanup phase, the plaintiffs have said.

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