The Army Corps of Engineers said yesterday that it could cost $3 million during the next decade to remove some of the hydrilla that is threatening the Potomac River.

But the project, a spokesman said, would destroy only 1 percent of the furiously growing green waterweed.

Spread of hydrilla during recent summers has alarmed many biolo- gists and officials, who say it will clog river access, choke vegetation and thwart fishing and boating.

"The cold, hard truth is that to try to stop or eradicate it is impossible," said Noel Beegle, the chief federal engineer working on a hydrilla project. "It's just not as easy as putting up the Berlin Wall."

District, Virginia and Maryland officials who met at the Metropolitan Washington Council of Governments offices yesterday appeared ready to endorse a new cost-sharing plan with few revisions if the Corps of Engineers attacks hydrilla mechanically.

Some of the officials rejected the use of chemicals against the weed and said hydrilla is hardly a monstrous problem.

"Hydrilla is not Godzilla . . . . The threat is overblown," said Neil Fitzpatrick of the Audubon Naturalist Society.

Fitzpatrick, who represents an area group of 7,000 environmentalists and conservationists, said that the aquatic weed, which first sprouted in the Potomac in the summer of 1982, is a sign of a cleaner river.

Even so, he agreed yesterday that some hydrilla, particularly when it forms impenetrable mats and travels into river channels or marinas, should be removed.

Army engineers estimated that if hydrilla, which now covers 600 acres in the Potomac, continues to multiply at rabbit speed, it could blanket 34,000 acres of the Potomac by 1995.

To eliminate a strategically placed 1 percent of those 34,000 acres, the Corps' preliminary report estimated, the cost will be between $238,000 and $320,000 each year for the next decade.

The federal government will absorb half the cost, and the District, Virginia and Maryland will share the rest of the cost, assuming the plan wins approval this fall from the Corps of Engineers, Congress and local governments.

Robert S. Pace, a Corps of Engineers spokesman, said that by rejecting the use of chemicals the states will have to pay more, because the federal government will pick up half the cost of only the most cost-effective method. The biggest hurdle now, Pace said, is to get local governments to agree on how they will divide their half of the annual fee for mechanical harvesting.

Because Maryland has jurisdiction over the Potomac, one option unveiled yesterday would have that state pay the largest bill, $73,000. Virginia would pay $44,000, and the District, $1,000. Another plan, based on the number of usable boat slips in each jurisdiction, had Virginia paying $68,000, Maryland $33,000 and the District $17,000.

Corps of Engineers officials said they were optimistic that the states would promptly approve a cost- sharing plan so that hydrilla control could start next spring.