COLUMBIA — The board that runs South Carolina’s environmental agency decided today not to consider a request to allow deeper dredging in the Savannah River, setting up a courtroom showdown next week in the fight over helping bigger ships reach the port in Savannah, Ga.

The South Carolina Department of Health and Environmental Control board debated in secret for about 30 minutes before holding a brief two-minute public session where members voted unanimously to not consider the request from the Georgia Ports Authority and the U.S. Army Corps of Engineers at its June meeting.

Instead, the board will wait for the South Carolina Supreme Court to rule on a lawsuit between environmentalists and the corps and authority over the $650 million project in the river that serves as the state line for South Carolina and Georgia. The justices will hear arguments Tuesday.

“This is an active case moving through the legal system right now,” department board member Mark Lutz said during the conference call, suggesting the board’s best course was to wait this lawsuit out.

Supporters of the dredging project are fighting a decision by a committee set up by South Carolina lawmakers to limit the depth of a channel to the Georgia port to just 45 feet. They want the channel in the Savannah River leading from the Atlantic Ocean to the Savannah port at least two feet deeper.

The Savannah River Maritime Commission in a decision earlier in May sided with environmentalists who said a deeper channel would bring down water quality. The commission was created by South Carolina lawmakers in 2007 and has become a big player in the port battle since last fall, when the department’s board reversed course and approved permits allowing the digging to begin so bigger ships could reach the Savannah port when the Panama Canal is widened in two years.

The sudden reversal came after Georgia Gov. Nathan Deal flew to Columbia to meet with South Carolina Gov. Nikki Haley, who appoints the members of the department’s board. The board made a last minute compromise with the Georgia Ports Authority and the U.S. Army Corps of Engineers to approve the project.

South Carolina lawmakers were furious, accusing Haley of selling out the port in Charleston, which will compete with the port in Savannah. The move also put in doubt a proposed joint port between the two states that was supposed to be closer to the Atlantic Ocean.

South Carolina legislators passed a bill this session retroactively suspending the department’s ability to make dredging decisions involving the river. The governor rejected the bill, but lawmakers overrode the veto with just one dissenting vote.

Next week, the South Carolina Supreme Court will hear arguments in a lawsuit over who should make some decisions about the river. A suit filed by the Southern Environmental Law Center on behalf of the Savannah Riverkeeper, based in Augusta, Ga., the South Carolina Coastal Conservation League, the South Carolina Wildlife Federation and the Conservation Voters of South Carolina said it is the Savannah River Maritime Commission because lawmakers have given authority over dredging decisions to the group.

The Georgia Ports Authority is getting ready to argue its case in court and will point out the decision to dredge a deeper channel is based on 14 years of careful study, authority spokesman Robert Morris said.

“DHEC’s action today regarding agency jurisdiction is understandable in light of the ongoing case before the SC Supreme Court,” Morris said in a statement.

The dredging project is also facing an additional legal fight. Environmental groups have an ongoing lawsuit in federal court saying the dredging project cannot begin until the project gets a pollution permit from the state.