SAVANNAH, Ga. — The federal government said Saturday it has given final approval to a $652 million project to deepen the river channel to the Port of Savannah to make room for supersized cargo ships.

The project has been a priority for Georgia for 16 years, but it also still faces a court challenge in neighboring South Carolina. And budget cuts have made it difficult in recent years to get federal funding approved by Congress, though President Barack Obama promised in July to expedite work expanding Savannah and other ports his administration deemed nationally significant.

“This is a major milestone, but we’re not popping corks just yet,” Gov. Nathan Deal said in a statement. “There’s still much to get done, and Georgia is ready and able to pay its (share) of the cost.”

The Army Corps of Engineers said construction on the massive project could begin as early as summer 2013, and Georgia port officials hope to have the work finished by 2016. It will involve scooping 5 feet of mud and sand from the riverbed along 38 miles of the Savannah River, deepening the stretch between the port and the Atlantic Ocean from 42 feet to 47 feet.

“The Record of Decision affirms that deepening Savannah harbor to 47 feet is economically viable, environmentally sustainable, and in the best interests of the nation,” said Col. Jeffrey Hall, commander of the Army Corps’ Savannah District.

Georgia, along with other East Coast ports, is scrambling to deepen its harbor to accommodate giant ships expected to begin arriving through the Panama Canal after a major expansion that’s scheduled to be finished in late 2014 and fully operational the following spring. The upgraded canal will handle ships needing 50 feet of water.

Georgia officials say the Savannah port needs deeper water to remain competitive. Savannah has the fourth-busiest container port in the U.S. and handled nearly 3 million cargo containers in the fiscal year that ended June 30.

Curtis Foltz, executive director of the Georgia Ports Authority, has long said Savannah shouldn’t worry about losing port business as long as it can show progress on the deepening by the time the Panama Canal expansion is finished.

“All of us are excited to get this thing going and get beyond studying it to the point where we can finally see progress,” Foltz said. “This is welcome news to trade, our current customer base and is equally important to those customers considering Georgia for a home in the future.”

The Army Corps said the document giving final approval was signed Friday by Jo-Ellen Darcy, the assistant Army secretary for civil works. Hall noted three other federal agencies — the Department of Commerce, the Department of Interior and the Environmental Protection Agency — had previously given their approval.

The decision comes six months after the Army Corps issued its final report recommending the harbor deepening. But Georgia ports officials have been waiting much longer. The corps spent $41 million studying the project since it was first proposed.

The port at Charleston, S.C., one of Savannah’s nearest and fiercest competitors, is seeking to deepen its harbor from 45 to 50 feet. Meanwhile, lawmakers in South Carolina, which shares the Savannah River with Georgia, have opposed the harbor deepening in Savannah. Environmental groups have filed three legal challenges to the project that are pending in South Carolina courts.

Deal has made the Georgia harbor expansion an economic priority. State taxpayers would foot 30 percent of the cost, with the federal government paying for the rest.

The Army Corps says more than $292 million will go to environmental mitigation. That includes building a river bypass around a dam near Augusta to let endangered shortnosed sturgeons reach waters expected to boost their spawning success. Savannah’s water treatment plant would get a 38-acre retention pool to serve as a backup water source for when pipe-corroding chlorides get too high during droughts.

The Corps also plans to create 2,200 acres of new wetlands to make up for an estimated 223 acres of valuable freshwater marsh expected to be lost to saltwater intrusion, most of it within the Savannah National Wildlife Refuge. And it plans to install machines to pump oxygen to the river bottom to make up for a loss in dissolved oxygen.

Environmentalists say the oxygen machines — which the Corps acknowledges will have to run forever — are just one example of how the project would do irreparable harm to the river.

“From now until the end of time they will have to operate these bubblers,” said Chris DeScherer, an attorney for the Southern Environmental Law Center, which has a lawsuit over the project pending in federal court. “We do not think they have shown that strategy will be effective. And that’s just one of a number of concerns we have.”