CHARLESTON, S.C. — A federal judge ruled Tuesday that both the Georgia Ports Authority and South Carolina’s Savannah River Maritime Commission may take part in a lawsuit challenging the $650 million deepening of the river shipping channel.

But U.S. District Judge Richard Gergel denied a motion to expand the lawsuit to rule on what South Carolina environmental laws pertain to the project. So the suit will now center solely on the issue of whether the work needs a South Carolina pollution permit.

Environmental groups in both South Carolina and Georgia originally sued the U.S. Army Corps of Engineers, charging a permit is needed because the deepening work will mean toxic cadmium from river silt will be dumped on the South Carolina side of the river.

The suit was brought by the Southern Environmental Law Center on behalf of the Savannah Riverkeeper, based in Augusta as well as the South Carolina Coastal Conservation League and the South Carolina Wildlife Federation.

The Georgia Ports Authority had asked to intervene on the side of the corps; the Maritime Commission on the side of the plaintiffs.

Supporters of the deepening project say it is needed so the river can handle the larger container ships that will routinely call at the Georgia ports when the Panama Canal is expanded in 2014.

The plaintiffs wanted the suit amended so the court would decide if other South Carolina environmental law applies. They noted that the corps has said repeatedly it can proceed without South Carolina approval under exemptions in the Clean Water Act.

They argued both the Department of Health and Environmental Control and Gov. Nikki Haley cited the corps’ position as part of the rationale for giving state approval to the project. Their filing quoted Haley speaking last fall at the Charleston Propeller Club.

“I have in writing, your DHEC board had in writing, a letter from the Corps of Engineers saying we don’t need a permit from DHEC to give Georgia their dredging,” Haley was quoted as saying. “It’s not they didn’t need it. They were gonna do it anyway.”

But both the corps and the Georgia Ports Authority — in court filings Monday opposing amending the suit — said no final decision has been made on whether the exemptions will be used.