The grades are B-minus and below in lakes cleanup

The water in the Great Lakes, the sparkling jewels of the Upper Midwest that hold 95 percent of the nation's fresh surface water, are a lot cleaner than they used to be - but not nearly as clean as they could be.

That's the assessment of the 15-year battle against Great Lakes pollution as seen by Lee Botts, co-director of the Environmental Policy Program of Northwestern University's Center for Urban Affairs and Policy Research.

She points out that the water in the Great Lakes, particularly in Lake Erie where swimming and walleye fishing have returned, looks clearer. She gives highest marks (''B-'') to states and cities that have reduced phosphorus levels in the lakes through phosphate detergent bans and improved sewage treatment. She gives the same mark to industries in the region, which have cut back on direct discharge of pollutants into the lakes.

''There has been a concerted effort - it has had a big payoff,'' she says.

Attempts to stem agricultural runoff (often containing pesticides and herbicides) into the Great Lakes, however, rate a ''D-.''

But she reserves an ''F'' for what she calls the failure to curb toxic pollutants. The invisible and odorless chemical pollution consists largely of chlorinated hydrocarbons from PCBs to toxaphene and heavy metal deposits from cadmium to lead.

In her view it is the worst of the Great Lakes pollution problems and the one with the potential for the most serious long-term effects. The US Fish and Wildlife Service's Great Lakes Fishery Laboratory, she notes, recently reported that traces of 476 toxic substances have been found in fish throughout the Great Lakes system. If the problem is to be solved, she says, there must be increased recognition of the danger posed by toxic chemicals over time and a change in existing clean-air law standards.

Ms. Botts credits industry with making some changes that may help. She says many businesses are finding it is good economics to change their manufacturing processes to produce less total waste and to recycle more of what is left. Great Lakes Waste & Pollution Review Magazine, for instance, a new bimonthly publication, regularly prints a list by companies of waste products available and wanted.

''Industry is finding there is a tremendous savings in pollution control management and is doing more than most people realize,'' Ms. Botts says.

Her interest in the Great Lakes environment has deep roots. She is a founder and first president of the Lake Michigan Federation, a coalition of citizen groups founded in 1970 in four states. President Carter appointed her to chair the Great Lakes Basin Commission in Ann Arbor, Mich., where she served until the Reagan administration ended its funding two years ago. Now Ms. Botts wrestles with environmental policy questions from a top-floor office in an old wood frame house serving as the Urban Policy Center on the Northwestern campus. From her attic window, one can see past the trees to the blue waters of Lake Michigan.

Why does she feel that further reduction of Great Lakes pollution is so important? Because scientists are concerned, she says, about the tendency of toxic chemicals to accumulate and concentrate over time. Current levels of toxic substances in the Great Lakes are low, and direct exposure is not considered a hazard to human health. But a long-term buildup could affect not only the quality of drinking water (some 25 million Americans and Canadians already rely on Great Lakes water for that) but the level of toxic pollutants in Great Lakes fish.

Sport fishing on the Great Lakes continues unabated. But Great Lakes states now warn their residents not to eat large lake fish such as salmon and whitefish more than once a week. Such species have ample fatty tissue, which readily absorbs and holds toxic chemicals. The state of Indiana urges its residents not to eat any Great Lakes fish.

Ms. Botts regards it as vital for people to think of the water and air as an ''ecosystem.'' She says, ''We can't continue to deal with air and water as separate problems.''

She notes that while the Clean Water Act of 1972 has an ecological aim - making waters clean enough for fish to survive and humans to use without danger - the earlier Clean Air Act has a more limited goal of protecting human health in local areas. Under that concept, she says, tall smokestacks that carry pollution away from immediate areas, and toxic substances that in low levels pose no human health hazard, were condoned. She argues that a different standard must be set that takes long-term effects into account.

Though the manufacture of such toxic substances as DDT and PCBs have been banned and direct discharges have been curbed, Ms. Botts argues that toxic contamination of the Great Lakes continues to grow. An estimated 50 percent of all toxic substances getting into the Great Lakes are carried in the atmosphere. And one-fourth of the overall pollutants in the lakes are deposited from the air. Significant amounts continue to be picked up in the atmosphere from landfills, waste treatment systems, and incinerators and are deposited in the lakes. Ms. Botts says that situation makes it imperative that a more earnest effort be made to reduce pollutants at their source.

''We now know we have only displaced (much of) the waste - we haven't really destroyed it,'' she says.

''We can't control what happens in the atmosphere so we have to control pollution where we can even more - unless we just want to give up,'' she says. ''With a (lake) system this large it's very difficult to reverse any change - the real challenge is to prevent it in the first place.''