The S.C. Supreme Court has tossed several but not all claims in a lawsuit challenging Carnival Cruise Lines’ operations in downtown Charleston, saying it will issue a final ruling after lawyers submit more information.

The court has dismissed allegations that Carnival’s year-round cruises violate the city’s noise and sign ordinances. But it also requested new written arguments from attorneys by July 5 about whether the cruises are a public nuisance or violate city zoning rules.

In a case that has attracted national attention, the Preservation Society of Charleston, the Coastal Conservation League and neighborhood groups sued two years ago, seeking to block cruise operations.

The high court said in a June 5 order that it agreed with the recommendations that a court-appointed referee made earlier this year, including tossing out allegations of that Carnival was violating sign and noise ordinances as well as a state pollution act.

The referee, Judge Clifton Newman, also said in his report that the plaintiffs should be allowed to argue that the vessels are a public nuisance based on noise and pollution and that they violate city zoning rules. The five-member Supreme Court has asked both sides to submit new briefs addressing those allegations within 30 days.

Carnival spokeswoman Aly Bello-Cabreriza declined to comment. Gordon Schreck, an attorney for the cruise line, said in an e-mail that the order was “self-explanatory.”

Blan Holman, a Southern Environmental Law Center attorney who filed the lawsuit, said he was glad the court is taking up the nuisance argument and the allegations that Carnival is running an accommodations business in an area not zoned for that use.

“We are pleased that our seven strongest claims remain and look forward to showing that Carnival cannot ignore the rules every other business plays by in making Charleston a great city,” Holman said in a statement.

Charleston Mayor Joe Riley said Tuesday that he was “very pleased” with the latest order. Jim Newsome, SPA’s chief executive, also lauded the decision.

“We are grateful to the Supreme Court for taking this important case in its original jurisdiction, and we are optimistic that this action will lead to an expeditious resolution to the remainder of the lawsuit,” Newsome said in a written statement.

The SPA and the city are helping Carnival fight the lawsuit.

The dispute over cruises in downtown Charleston heated up in 2010 after Carnival permanently based its 2,056-passenger ship Fantasy at a berth near the City Market.

Neighborhood groups and environmentalists also have filed lawsuits to block the SPA from opening a new $35 million cruise terminal at the north end of Union Pier, alleging it will bring more tourists, traffic congestion and fumes to the historic district.