The eagles are back, the fishing is good and, 40 years after the passage of the Clean Water Act, the length of the Mississippi River that flows through the Twin Cities is healthier than it's been in a generation.

The findings, released Thursday, show that decades of effort have reduced the flow of industrial pollutants, storm water runoff and human waste into the nation's largest river at the point where it begins its journey to the Gulf of Mexico.

At the same time, they focus attention on the river's emerging threats. The Mississippi also contains rising levels of new contaminants from household products and pharmaceuticals that could affect the health of both wildlife and people, bigger surges of water from bigger storms and significantly more pollutants from agriculture and urban runoff.

The first-ever State of the River report was compiled by the National Park Service, which oversees the 72-mile Mississippi National River and Recreation Area, and Friends of the Mississippi River. It used 13 indicators to grade the river's ecological health from Dayton to Hastings.

The analysis was conducted in part to answer questions the public often asks -- if and how they can use the river for swimming, fishing and boating, said Park Service spokesperson Lark Weller.

The answer, mostly, is yes. The Father of the Waters has proved to be remarkably resilient.

"The river was dead in 1926," said Trevor Russell, watershed program director for the river advocacy group. Old surveys show that only two living fish were recorded downstream of St. Anthony Falls. Decades of sewage, industrial pollutants and dam construction destroyed the fisheries.

All the way through the 1970s, the river was in essence a conduit for sewage.

"That was the practice," said Tim Scherkenbach, a retired deputy commissioner of the Minnesota Pollution Control Agency. "The river was seen as a natural flushing system."

Putrid mats of solid waste used to build up behind the Ford Dam, he said, and nothing lived at the bottom of river.

All that began to change with the passage of the Clean Water Act in 1972, and subsequent state and federal laws that required permits for industrial discharges, separation of storm water and sewage systems, and increasingly sophisticated technology to remove contaminants from wastewater treatment plants.

"It is good to remember back to that time," said Whitney Clark, executive director of the Friends of the Mississippi. "We took some decisive actions to reverse those trends."

Eagles and pelicans

Once the pollution stopped, the river began to heal itself.

Today, it supports quality fisheries for catfish, walleyes and smallmouth bass. The number of walleye catches has tripled since 1979, according to data from the Minnesota Department of Natural Resources. Of the 120 native species of fish that used to ply the water below St. Anthony Falls, a natural fish barrier, 119 are back.

The bald eagles, once endangered, are now commonplace, thanks to the Endangered Species Act and bans on destructive pesticides such as DDT. Today, there are 36 active nests along the 72-mile stretch of the river, and each produces on average two nestlings per year, according to the Park Service counts.

Other fish-eating birds are thriving as well.

"I saw my first white pelican in 1985 or 1986," said Hokan Miller, a birdwatcher who has worked on barges and commercial boats on the river for years. "I said, 'What is that!'"

Now, he said, every spring flocks of the huge white birds fly in lazy circles over the river near downtown St. Paul.

But the river continues to reflect the human life and land uses around it. The eagles carry contaminants in their blood -- mercury from power plants, carcinogens from air pollution, and pesticides that run off the land. So do some fish, which sometimes makes eating them a risk for young children and pregnant women.

The amount of water in the river has increased by more than 25 percent on average since 1975. Some of that is the result of the much larger rainfalls that some experts believe may be associated with climate change. But most of it comes from draining the vast agricultural fields around the Minnesota River, which flows into the Mississippi at Fort Snelling.

With bigger rains comes sediment that clouds the water, carrying pollutants like phosphorus and nitrates that all drop to the bottom when the river widens into Lake Pepin. Phosphorus, which causes blue-green algal blooms, has dropped significantly, largely as a result of new water treatment processes. But compared to 1975, nitrates from fertilizers, pet waste and organic material have increased by up to 47 percent in some recent years. Eventually, they flow into the Gulf of Mexico, contributing to a "dead zone" around the mouth of the river that cannot sustain life.

A new dioxin

Equally worrisome, say scientists, are new contaminants, many from consumer products used by millions of people.

Scientists found that concentrations of a contaminant formed by triclosan, a common antibacterial product, have jumped more than 200 percent since it was invented in the 1960s. It's commonly used in soap, toothpaste, deodorants and other household products that are flushed through water treatment systems and into the river. Exposure to chlorine and sunlight turn it into a dioxin, a potentially harmful toxin for people and wildlife.

Other dioxins that come from waste incineration have declined in the last 50 years, meaning that those from triclosan now make up 31 percent of the total mass of dioxins in Lake Pepin.

The irony, said researchers, is that triclosan provides little or no benefit in the products that contain it. "It's a marketing tool," said Bill Arnold, a researcher at the University of Minnesota Duluth who studied the dioxins in sediment cores from Lake Pepin.

The lesson, said Scherkenbach, is that the cleanup never ends.

"But we are getting better, and getting smarter as a society in understanding how complex nature is," he said. "And the next generation of kids will be even more aware."

Josephine Marcotty • 612-673-7394