ANCHORAGE — The U.S. Supreme Court will not review a federal appeals court decision that said coal falling into Resurrection Bay from the Alaska Railroad’s loading system in Seward violates the federal Clean Water Act.

A three-judge panel of the 9th Circuit Court of Appeals in September reversed a decision by U.S. District Court Judge Tim Burgess, who ruled that incidental coal falling from the Seward Coal Loading Facility was allowed under the railroad’s permit to discharge stormwater. The judges said coal was not a list of substances that could be discharged with storm water.

The district court will decide whether the railroad committed specific violations of the federal Clean Water Act, whether there will be penalties, and whether the parties will be directed to pay attorney fees, Alaska Railroad corporate communications officer Stephanie Wheeler said.

“We are disappointed that the Supreme Court would not hear the case. But we are prepared to return to the Alaska District Court,” Wheeler said.

The ruling was made in a lawsuit filed in December 2009 by Alaska Community Action on Toxics and the Alaska chapter of the Sierra Club. The groups said dust from coal stored in Seward was polluting Resurrection Bay, dust-covered snow was plowed into the water and coal improperly entered the water by falling from a conveyor belt and other equipment as it was loaded onto ships.

Burgess rejected all three claims. The plaintiffs appealed only the third point.

Pam Miller of Alaska Community Action on Toxics said the decision was good news for keeping coal and coal dust out of Resurrection Bay. “We fully intend to hold them accountable to do that,” she said.

The railroad has invested hundreds of thousands of dollars in measures to control dust and incidental coal loss, Wheeler said. The latest investment was a larger, secondary containment system under the coal conveyor.

“We believe this is working really well to minimize any incidental coal from dropping into the water,” she said.

Russ Maddox, a Sierra Club activist in Seward, said the first coal ship of 2015 arrived Sunday.

“This is the exercise that will show whether or not the containment efforts so far have been effective,” he said. “They’ve claimed that they fixed the issue. We can’t determine the efficiency of it until it’s in action.”

As of Monday, he had not seen any coal falling into the water, he said.

Maddox said he continues to be irked by the expense of the matter, including an expensive appeal to the Supreme Court. “In a time of austerity — it is a state-owned railroad — and they’ve wasted a lot of money just to avoid putting in containment,” he said.

In 2013, when the railroad and Aurora Energy Services LLC, the operator of the coal-loading facility, had prevailed at the district court level, they asked for $2.2 million reimbursement in legal fees.

Wheeler said she was unable to immediately calculate how much the railroad has spent on the lawsuit.

Aurora Energy Services, meanwhile, has applied for a wastewater-discharge permit that would allow the discharge of incidental coal during loading operations. The details of a final draft permit are expected to be released within two weeks.

Wade Strickland, program manager for the Department of Environmental Conservation’s wastewater discharge authorization program, said the agency will collect public comment for 45 days and will schedule a public hearing in Seward, likely in late July.