Georgia ports want the channel deepened to accommodate larger ships that will be calling when the Panama Canal is widened in 2014.
Last month three conservation groups from both states sued in South Carolina court.
The suit contends the corps needs a South Carolina pollution permit because the deepening work will dredge up toxic cadmium that will be placed on the South Carolina side of the river.
The suit was moved from state to federal court in Charleston earlier this month. Federal law allows that when a federal agency or official is sued in their official capacities.