Helping to save the great Amazon River -- the Cousteau way

''There's still hope to save the world's last great river system, the Amazon, from pollution,'' according to Jean-Michel Cousteau. Jean-Michel, with his father, Jacques Cousteau, directs the continuing global expeditions of the research vessel Calypso and produces the films that have made the Cousteau name a hallmark of high-quality wildlife and undersea television documentaries. If you used to watch the shows on PBS and you've been wondering where they had gone, ''The Undersea World of Jacques Cousteau'' appears now as repeats on the Turner Broadcasting System's SuperStation, WTBS (Sundays, 5:35-6: 35 p.m., check local listings).

For the past two years, the Cousteaus have been in Brazil's Amazon region, charting the wilderness that makes up one-third of the world's forest and one-fifth of the world's river water. Recent development in the region has caused nearly 1 million trees to disappear and, according to some scientists, ''the lungs of the planet'' are in jeopardy.

Jean-Michel is in New York to tell the world about what is happening in Brazil . . . and, incidentally, to promote a new Cousteau series, which should start appearing on WTBS late this year or in early 1984. The 48-member team of explorers, photographers, divers, and scientists, he explains, is developing a continuous profile of the Amazon's water quality and filming animal and plant life in the river and its tributaries and tropical forests. ''The mission will produce the first global picture of the Amazon,'' he says, ''from its source high in the Andes in Peru to the estuary flowing into the Atlantic, a stretch of some 4,000 miles.''

Since his brother, Philippe, was killed in an airplane crash four years ago, Jean-Michel has taken over his responsibilities in the Cousteau Society. ''We have never been involved in such a large undertaking of a territory which is almost as large as continental US,'' he explains in as charming a French accent as his father's, which many TV viewers are familiar with. ''Communications are extremely complicated, transportation difficult. In addition to the Calypso, we have a helicopter, a Hovercraft, a riverboat, an amphibian truck, an Iveco amphibious truck of totally new design which allows us to go places where we couldn't go otherwise.''

Aside from the TV films, what is the purpose of the expedition?

Without any hesitation Jean-Michel says: ''To communicate with the rest of the world what we discover about the Amazon. To make it part of their lives, since more than 20 percent of all fresh water coming out of landmasses is from the Amazon. As it reaches the Atlantic, it is taken on by an equatorial current and taken up northwest, and it goes right up to the Caribbean and literally feeds it with its nutrients. The life in the Caribbean would not be what it is if it were not for the Amazon. In addition, we trace either in the air or water additional impacts of outpour . . . and ultimately with the Gulf Stream. So half of the Amazon is really linked with the rest of the world.''

Is the river being polluted?

''There are signs, but I am happy to say that it is not as dramatic a pollution as has been reported. Nothing compared with what has been happening to waters of our great rivers like the Mississippi, the St. Lawrence, the Yangtze. The Amazon is really the river of the future . . . still comparatively unspoiled.''

Is there some organized attempt to prevent the despoliation of Amazon land and water?

''There are hopeful signs. We are working with something wonderful called the Amazonas Pact. Nine countries - Brazil, Peru, Bolivia, Colombia, Ecuador, Venezuela, and the three Guyanas - all signed an agreement to treat the Amazon as one entity. Border or no border, it is one water system.''

Mr. Cousteau says the expedition has made contact with the native Indian population that inhabits the northern part of the Amazon region. ''There are some Indians who unfortunately are not even recognized as human beings. They do not have citizenship, although they must technically respect the laws of the countries in the area.

''We found four different types of Indians. One - those who have been adapting to tourism. They put on their feathers when the tourists come; then when the tourists go they put back on their jeans and continue their normal way of life. Two - the ones controlled by the missions, some good, some bad, depending upon the personality of the missionary at the particular spot. Three - those forced into the drug culture. They produce cocaine for the drug traders, who manage to keep them in enough debt so they must continue to produce cocaine. Four - the Indians never contacted by the white man. There are still a few of those, and they are gloriously free of the evils of our civilization.''

Mr. Cousteau explains that he has just returned from a stay with the Jibaro Indians, commonly considered to be headhunters or head shrinkers. ''They do not shrink heads anymore,'' he hastens to explain. ''In 40 years they haven't shrunk one single human head, although until not long ago they used to practice on sloths and monkeys.'' Life among this tribe will be seen in the Amazon series.

The Calypso goes up and down the river, as far north as Iquitos, Peru, 2,200 miles inland.

What is Jean-Michel's major function on the expedition?

''I am the son of my father, which means the No. 1 guy, which means I get all the detail work. But I have the fun of organizing the expedition, the logistics. And I am in the field about 50 percent of the time.

''Also, I'm the executive producer of the six one-hour specials that are being produced. Since Turner is the co-producer, they will probably be shown on WTBS. Maybe a special on the highlights of the expedition even before Christmas.

''The first two hours will be essentially the spectacular part of the Amazon. Then there are segments on medicinal plants, on animal traders and poachers, on industries in the area, on the Indians and their way of life. Plus, of course, the show on the gold fever, which resembles in many ways the gold rush of the West Coast.''

Has Jean-Michel found any gold?

''Only dust. And I didn't keep it, because if I had I wouldn't have lived long. I quickly turned it over to the settlers who were there.''

Will this be the last big expedition for his father, Jacques Cousteau?

''No! He's going to be working for another 25 years. He is driving everybody off the wall, he is so energetic.''

So what comes after the Amazon?

''We would like to do the Mississippi. And the Nile, the St. Lawrence and the Great Lakes, and the Yangtze in China. On the way we will go to New Zealand, the Great Barrier Reef, the Philippines, Batavia, New Guinea, the Great China Sea. That's five years. Still 20 to go.''

Does Jean-Michel Cousteau think there is any way to prevent the parts of the world that have not already been spoiled by civilization from becoming spoiled?

''Yes. People can learn. By projecting in the media what may happen, we believe people will realize they must preserve their heritage. I think probably the Amazon will be preserved in large national parks, which will become either totally no man's land or laboratories for other generations to study. There are hundreds of thousands of plants and animals there which have yet to be identified.''

But are the governments of Brazil, Peru, Colombia, and Venezuela enlightened enough to do what is necessary to protect the Amazon? And for that matter, is the US government enlightened enough to protect the American wilderness?

''I don't believe the governments are. But governments come and go. I believe the public will become enlightened and the public will demand it of the governments. The people are moving ahead of their governments in the area of conservation. And that is very encouraging.''