WASHINGTON (CNN) -- The Obama administration struggled to keep its legal head above water at the Supreme Court Tuesday as it defended a series of federally controlled and managed floods that caused major timber damage along an Arkansas river.

A majority of the justices appeared inclined to believe that the periodic release of water from a U.S. Army Corps of Engineers dam project begun two decades ago was a government "taking." That legal designation would require the federal government to compensate the state for damages.

The property rights dispute is narrow and unique in many ways, but could clarify the standards for determining the scope, length of time, and impact of government actions affecting many property owners -- private and public.

At issue for the high court is whether the resulting downstream flooding was effectively "permanent" and therefore a "taking," or was merely "temporary" and only a "trespass."

The state of Arkansas owned the flooded land and had earlier won a $5.6 million judgment. Several on the bench appeared inclined to side with the state.

"You knew when you opened up the dam that this is where the water was going to go," Chief Justice John Roberts said to the federal government lawyer.

"Your position seems to be that if it's downstream, somehow it's not the government's water," said Justice Anthony Kennedy. "It's like the old moral refuge that the rocket designers take: I only make the rockets go up; where they come down is not my concern."

The Army completed the Clearwater Dam in 1948, along the Black River in southeastern Missouri, in response to prior natural flooding. About 110 miles downstream, in northeastern Arkansas, is the Dave Donaldson Wildlife Management Area, 23,000 acres of state-owned riparian land used for duck and game hunting, wildlife management, and timber harvesting.

Federal rules for decades had managed normal release of the water, and provided for both "planned" and "unplanned minor deviations." Beginning in 1993 the Corps launched a series of planned, irregular deviations -- quick releases of water during the summer growing season in part to give upstream farmers more time to harvest their crops without their fields becoming inundated.

Under the unique dynamics of stream flow and hydraulics, the result was higher water levels downstream, and long-term flooding of the state property during the critical growing period. The series of deviations lasted until 2000.

The Constitution's Fifth Amendment forbids "private property be taken for public use without just compensation." Even thought the land in question is state property, all sides have treated the land as "private" in nature for purposes of settling the "takings" dispute.

Attorney James Goodhart, arguing for Arkansas, said 100,000 trees were destroyed in 1999 alone, as the controlled, temporary flooding exacerbated a drought at the time. "This management area sat in water during June, July, into August, basically, stagnated water that choked the oxygen from the roots of these trees," he said.

But Justice Sonia Sotomayor questioned the premise. "The problem with this case," she said, "is that flooding is going to occur naturally anyway. The (federal) government generally builds dams to control that flooding to the benefit of all of the interests along its affected route. And at some point, either the government is going to going to make a decision that's going to help someone and potentially hurt someone. And the question is, are all of those situations going to be subject to litigation."

Sotomayor was later equally tough in her questioning of the federal government.

Justice Stephen Breyer was more blunt. "The problem with a flood is you don't take all the land. You send some stuff in. And the stuff is there for a while, and then it comes back. It's called water."

But Justice Department lawyer Edwin Kneedler got into trouble when he argued the controlled dam releases created only "incidental consequences downstream from the dam as a result of the flowage" and that the flooding was not an "occupation by the government."

"So if the government comes in and tells a landowner downstream that every March and April we are going to flood your property so that you can't use it from now on -- that's part of our plan -- that's a taking for those two months, correct?" interjected Roberts. When Kneedler said no, the chief justice shot back, "That's not a taking?"

Justice Antonin Scalia added that this is clearly a case of "a 'foreseeable and certain' incidental consequence."

Kneedler replied it is "hard to explain" how a government action affecting land 110 miles downstream is "direct" in nature. He also argued the congressional Flood Control Act of 1928 -- resulting in a hundreds of federally funded dams across the country -- would not have become law if the government believed it would to be liable for all its good-faith efforts.

"Of course, that (congressional action) can't overrule the (Constitution's) Takings Clause, can it?" replied Scalia. "I mean, that's nice that Congress doesn't want to be liable," he joked.

Sotomayor said she had "significant problems" with the administration's articulation.

The high court has dealt with several flooding cases over the years examining whether damages should be paid by the government. In a similar 1924 dispute, the high court concluded a taking required an "actual, permanent invasion of the land, amounting to an appropriation of and not merely injury to the property."

It is that gateway question the justices must first navigate: whether the Corps of Engineers' flood deviations were in fact a taking. The compensation questions would come later.

In one of the Supreme Court's most controversial recent eminent domain cases, the majority in 2006 allowed a Connecticut city to condemn a private, mostly residential neighborhood, in order to lease the land to a private developer for a high-end development project. The city justified the seizure as a "public use," generating jobs and higher tax revenues.

Justice Elena Kagan is sitting out the Arkansas appeal and did not attend the one-hour oral arguments. She had litigated the case in some form during her previous job as the administration's solicitor general. Her absence could result in a 4-4 high court tie, which would be a victory for the U.S. government, but would set no precedent.

The case is Arkansas Game & Fish Commission v. U.S. (11-597). A ruling is expected by spring.