COLUMBIA, S.C.—A federal judge will not dismiss a lawsuit over a pollution permit for the $650 million deepening of the Savannah River shipping channel.

U.S. District Judge Richard Gergel wrote in an order released late last week that the time is right to hear the case against the U.S. Army Corps of Engineers over the project. The deepening of the 38-mile channel is expected to begin in the spring.

The lawsuit was filed by the Southern Environmental Law Center on behalf of the Augusta- based Savannah Riverkeeper, the South Carolina Coastal Conservation League and the South Carolina Wildlife Federation. The deepening is being sought so the Georgia ports can accommodate larger container ships that will routinely be calling when the Panama Canal is deepened in 2014.

The environmental groups say the long-awaited project will dredge up toxic cadmium in river silt that will be dumped on the South Carolina side of the river that divides the state from Georgia. They want Gergel to decide if the corps needs a pollution permit issued by a South Carolina agency, arguing that they don't have to wait until environmental damage actually occurs before they try to prevent it.

The corps had asked Gergel to dismiss the suit, saying the plaintiffs have not been harmed and that the case is premature. But on Friday, Gergel wrote that this is a good time to hear the case, given that construction on the project is set to begin in less than a year.

"This long and arduous planning and approval process is rapidly coming to completion," Gergel wrote. "Plaintiffs need not wait for dissolvable oxygen levels to drop in the Savannah River or cadmium contaminated clay to be discharged into the environment before they have standing to sue."

Gergel has also asked the parties to give him an update on other lawsuits over the deepening project.

Environmentalists have also sued in South Carolina state court, alleging that a permit approved by the Department of Health and Environmental Control last year is illegal because authority over river dredging decisions rests with the state Savannah River Maritime Commission.

Chief Justice Jean Toal said during a hearing that DHEC broke state law when it shut out the river commission dredging negotiations and the agency "rubber stamped" an agreement with Georgia officials. DHEC staff had initially turned down the permit, but the agency reversed itself after Georgia Gov. Nathan Deal flew to Columbia to meet with Gov. Nikki Haley, who appoints members of the DHEC board.

The Savannah River Maritime Commission is already appealing the certification through the State Administrative Law Court.