COLUMBIA — The S.C. Supreme Court on Friday overturned state approval to dredge Savannah’s harbor for larger ships, saying South Carolina regulators didn’t have the authority to cut a deal with Georgia for the $650 million project.

The Supreme Court’s ruling is a strong rebuke to state regulators and Gov. Nikki Haley, and it further muddies the picture of when the dredging project will go forward. The U.S. Army Corps of Engineers signed off on the project last week and asked Congress to bypass the need for a key environmental permit in South Carolina so the dredging can start.

Congress might not act on the request for some time, but for now, Friday’s Supreme Court decision is a setback for Georgia officials who have sought for nearly two decades to dredge Savannah’s harbor, just across the state line.

Frank Holleman, an attorney representing the environmental groups that brought the suit, said the court’s ruling was “very important” for South Carolina residents concerned about the toll the project would have on wetlands, water quality and wildlife along the lower Savannah River.

“It upholds South Carolina’s rights to protect the environment without the intrusion of this unlawful negotiation,” Holleman said.

The negotiation Holleman referred to follows Haley’s involvement last year in the permit decision that was under review by the S.C. Department of Health and Environmental Control.

In November 2011, DHEC reversed a decision by agency staff that denied a water quality permit needed for the dredging.

Haley had asked the agency board, which she appoints, to review the staff decision after she met with Georgia Gov. Nathan Deal, a fellow Republican. The agency’s board signed off on a settlement – negotiated in a matter of hours with Georgia officials – that DHEC said resolved its concerns about the project’s impact on water quality.

The Supreme Court’s decision, however, said DHEC didn’t have authority to negotiate the agreement.

State law says the Savannah River Maritime Commission is “empowered to negotiate on behalf of the state of South Carolina” on matters involving the lower Savannah River, the court said. DHEC didn’t involve the commission in the agreement it reached with Georgia.

“This is good news and expected news,” said state Sen. Larry Grooms, a Berkeley Republican who also is on the Maritime Commission. “I knew DHEC had overstepped its bounds. I hate we had to take the legal route to tell DHEC what they had done wrong.”

Attempts to reach spokespeople for Haley and for Georgia Gov. Deal were unsuccessful. But DHEC issued a statement Friday night saying it would follow the Supreme Court’s order.

Georgia’s push to deepen Savannah’s harbor by about five feet has been a point of contention for years because of the project’s potential effect on endangered fish, water quality and rare freshwater wetlands. Hundreds of acres of tidally influenced wetlands would be destroyed by the project. Some studies suggest the project also will reduce oxygen levels in the Savannah River, which is why Georgia officials say they will artificially inject air bubbles into the water. But environmentalists say that is a risky precedent and might not work.

The dispute intensified this year, however, because of concerns the Georgia project would set back efforts to attract larger ships to the port of Charleston, a major competitor for maritime business on the Southeast coast that also wants to deepen its harbor.