Scientists have turned up evidence that acid rain is not only poisoning northeastern lakes but also is activating potentially hazardous aluminum in mountain soil, water and streams.

Researchers at Cornell University, Dartmouth College and the University of Vermont, as well as scientists in Europe, have found aluminum in sufficient concentrations in high-altitude streams to be toxic to fish and aquatic life and apparently damaging to trees and plants.

Some medical researchers suspect that aluminum, one of the most common elements on earth and long thought to be harmless, also may be implicated in several forms of human brain degeneration, particularly Alzheimer's disease, a common but devastating form of senility. The theory is far from proven, however.

Normally, aluminum is tightly locked to other elements in the soil. The metal is now being knocked loose by such ingredients of acid rain as sulfuric and nitric acids.

Acid water is most concentrated at high altiutdes. But as it flows downhill, it often passes over limestone bedrock, which progressively reduces the acidity. As the water approaches the neutral state, the aluminum particles begin combining with other elements and sink to the stream bottoms.

What no one knows is the precise extent to which this free aluminum is getting into drinking water.

Without exception, the scientists and medical researchers are cautious about claiming broad significance for their findings, but taken together they represent a gathering consensus that acid rain's apparent tendency to mobilize aluminum poses a potential public health problem.

"I see enough potential threat from aluminum in my studies to indicate we'd better start looking with much more energy at the environmental issue," said Dr. Daniel Perl, a neuropathologist at the University of Vermont Medical School.

This consensus could affect the political debate about acid rain in the United States. The assumption, unproven, has been that midwestern power plant emissions somehow undergo chemical changes in the atmosphere and return to earth as rain and snow. Acid rain's primary effect has thought to have been on aquatic life in the Northeast and in Canada.

The Reagan administration and midwestern congressmen have deflected strong federal action on the grounds that the precise cause of acid rain is still in dispute and that the economically strapped midwestern states cannot afford the cost of significantly cutting such air pollution. Evidence that humans are affected could change that.

The University of Vermont's Perl, who works with a team from the National Institutes of Health, has found high concentrations of aluminum in the damaged brain cells of Alzheimer's victims in the United States and in victims of other types of brain degeneration from Guam.

Guam, along with a remote region of Japan and an area in New Guinea, has high concentrations of aluminum in its garden soil and water supplies.

Perl and Dr. Joseph Cotruvo, director of the Environmental Protection Agency's drinking water standards division, said that no one knows now whether aluminum shows up in the brains of senility victims because they are sick, or whether the aluminum causes the sickness. If it does cause the sickness, no one knows how much aluminum will do it or how.

Dr. Noye Johnson, a geologist at Dartmouth, said that in the past the metal combined with organic substances and was ingested that way. Aluminum mobilized by acid rain, however, is combining with inorganic materials, and that raises the public health question.

Perl dismissed the idea that humans will suffer from small amounts of aluminum such as they might get from using aluminum pots and pans.

"We have bodily barriers to keep aluminum out," he said. "So you would have to flood the system." Even if aluminum is an agent of brain disease, he added, there is probably another factor involved, such as lack of calcium or magnesium.

While medical research is filled with uncertainty, research has reached broad agreement on several points--that in acid water, mostly found at higher altitudes in the Northeast, large amounts of aluminum are being mobilized, that it is toxic to fish and aquatic life, and that it probably damages trees and plants.

In a 1979 study, Christopher Cronan of Dartmouth and Carl Schofield of Cornell University found aluminum concentrations three times the level toxic to fish in a mountain watershed in New Hampshire. They also found that high-altitude lakes in the Adirondacks of New York had aluminum concentrations 10 to 50 times higher than low-acid waters in the same region.

A team of botanists from the University of Vermont has found that more than half of the red spruce trees on the upper slopes of unspoiled Camel's Hump Mountain have died since 1965 and that the aluminum in tree cores from the same study area has increased threefold in that period.

In a statement on the brain degeneration research, the National Institute on Aging said the work done by Perl, Dr. Carlton Gajdusek and other scientists at NIH supports a "developing hypothesis that environmental factors may be an underlying cause" of brain disease.

"It may be that high intake of aluminum over a long period of time, coupled with chronic low intake of vital minerals such as calcium and magnesium, ultimately results in a breakdown of the normal mechanisms which metabolize minerals," the statement said.