Acid rain has damaged some lakes in the northeastern United States and is increasing the acidity of streams in the Southeast in a way directly related to increases in industrial sulfur emissions, the National Research Council reported yesterday.

But the report, culminating a three-year study of the causes and effects of acid rain under the auspices of the National Academy of Sciences, said the damage was not uniform. Some lakes showed almost total loss of fish life, while others in the same area showed little effect or became more alkaline instead of acidic.

"In other words, the connection between acid rain and environmental damage is real, but it is more variable and complex than many people have supposed," said James H. Gibson of Colorado State University, who headed the research team.

A summit meeting next week between President Reagan and Canadian Prime Minister Brian Mulroney is expected to dwell on the politically sensitive subject of acid rain. Canada is seeking a U.S. commitment to reduce sulfur emissions, a multibillion-dollar program that Reagan has been reluctant to endorse.

The report contains no recommendations for Reagan, however, and at a news conference yesterday Gibson and other members of the scientific panel declined to offer any advice on behalf of the academy.

Speaking for himself, Gibson said he believed the report buttressed Mulroney's argument that emission reductions are needed to prevent further damage to sensitive aquatic systems in Canada and the U.S. Northeast.

"Am I personally concerned?" he said. "The answer would be yes, because I think we've established a definite link."

Industry groups said the report confirmed their belief that new controls on coal-burning boilers were unnecessary. "We don't see it as being overly conclusive," said Susan Roth of the Edison Electric Institute.

Environmentalists said the report adds important new detail to the academy's basic 1981 conclusion that sulfur emissions are directly related to acid rain.

"This report dotted the i's and crossed the t's on what was known years ago," said Richard Ayres of the National Clean Air Coalition. "Before, they had dead fish and lakes that were acid. This report uses all sorts of sophisticated techniques to measure the time line, and what they found is that lakes that used to have fish don't. And it's because they're acid."

The report is based in part on relatively new evidence from the fossil remains of tiny microorganisms called diatoms. Using sediments dating back to 1800 from nine lakes in New York's Adirondack Mountains, researchers found clear signs of recent acidification in six of them.

According to Gibson, acidity in one such lake dropped markedly beginning in 1950, coinciding with increases in industrial emissions. Yet within 16 years, the number of fish species in the lake had been cut in half.

The report did not examine why some lakes showed this reverse response or no response at all. Gibson said some soils and watersheds are able to buffer acid, and some lakes may be affected by other results of human activity, such as sewage pollution and agricultural runoff.