David Gilbert tongs oysters from the cat point oyster reef in Apalachicola Bay, subject of a Supreme Court case argued Monday. Justices seemed sympathetic to Florida officials who say Georgia is using too much water in a basin. (Mark Wallheiser/For The Washington Post)

Supreme Court justices on Monday seemed sympathetic to Florida officials who complain that their neighbors to the north in Georgia are hogging water in a way that endangers a sensitive Sunshine State estuary.

But while the court seemed to think “common sense” and maybe even physics favored Florida, the powerful U.S. Army Corps of Engineers does not — it favors Georgia, and even the Supreme Court’s clout might not be enough to overcome that.

“There’s nothing common-sense about the operations of this basin,” said Craig S. Primis, a Washington lawyer representing the state of Georgia, who spent much of his time at the lectern during oral arguments fighting questions about why capping Georgia’s consumption of river water would not necessarily result in more water downstream.

“It is incredibly complicated,” he said.

So complicated that the states have been fighting for three decades over the waters in the ­Apalachicola-Chattahoochee-Flint basin, which covers more than 19,600 square miles in three states. The current Supreme Court battle alone has eaten up a combined $100 million in legal fees.

At stake in the decades-long litigation is whether the flow of waters will favor Atlanta and the farmers of southwestern Georgia or the seafood producers of the Florida Panhandle.

The Chattahoochee River flows from north of Atlanta, and there are five federal dams controlled by the Corps of Engineers that provide flood control, hydropower and recreation, as well as drinking water for the nearly 6 million residents of metro Atlanta.

The Flint flows from a spring near Atlanta’s Hartsfield-Jackson International Airport and sweeps through southwestern Georgia, where farmers depend on irrigation for growing ­cotton, corn, soybeans, peanuts and pecans, among other crops in a more than $4 billion industry.

The two rivers converge at the state border to become the Apalachicola, which runs for 106 miles to the bay. Its wide flood plain through the Florida Panhandle serves as a spawning ground for crabs and Gulf fish, and the famed bay once accounted for 90 percent of the oysters produced in Florida.

Florida has sued to impose consumption caps on Georgia, saying the reduced flow of the water, especially during droughts, has harmed its ecosystem.

Ralph I. Lancaster Jr., a special master appointed by the Supreme Court to study the issue, agreed Florida had been harmed. But he ruled that the Corps really controls the flow of water and that Florida had not met its obligation to show that the caps it would impose in Georgia would actually benefit Florida.

Lancaster, of Maine, reasoned that when the water is most needed — during drought conditions — the Corps would be more likely to store the water in its reservoirs than to send it down to Florida.

Justice Elena Kagan told Florida’s lawyer, Gregory G. Garre of Washington, that “you have common sense on your side.” But she added “there seems to be a real dearth of record evidence specifically quantifying how much more water you would have gotten, exactly what benefits would have followed from that.”

Justice Sonia Sotomayor pressed for more evidence, as well.

Garre responded that Florida didn’t have to show with “absolute precision” how it would benefit. But he said even if the water flowed during non-drought conditions, that would help stave off drought.

Chief Justice John G. Roberts Jr. was critical of Georgia’s argument that the Army Corps’ decision on how the water should be regulated is beyond question.

A finding by the Supreme Court that Florida has not gotten its equitable share of the water, Roberts said, “will at the very least change the facts on the ground and, according to the Corps itself, cause them to adjust its operations accordingly.”

But Primis added that “the Corps is governed by a panoply of federal statutes, congressional dictates and mandates” about its responsibilities in the basin.

“And it is not as simple as if extra water comes in, then you just pass it through to Florida because they have articulated one concern,” he added.

Florida pressed its claims against Georgia without the Corps of Engineers as a party to the suit. The Corps has sovereign immunity and cannot be sued without its consent. Its absence made the case more difficult.

Justice Anthony M. Kennedy Jr. complained about that to Deputy Solicitor General Edwin S. Kneedler, who was representing the federal government. He said the parties were left to speculate what the Corps might do even after the court’s ­decision.

Kneedler said the Corps has gone through the process of deciding how the water should be allocated to carry out the obligations it has been given by Congress. But those are not completely in sync with what Florida says it needs.

For instance, Kneedler said, it is not clear whether the Corps even has the authority to provide more water to the bay to help the oyster industry. Its jurisdiction probably stops when the river meets the bay.

The case is Florida v. ­Georgia.