It was a monumental task.
One area known as the Black Triangle at the junction of Germany, Poland and the Czech Republic was notorious. A concentration of coal mines and heavy industry suffocated the region under industrial ash and gas. Some 80 million tons of lignite, or brown coal, were burned annually, pouring 3 million tons of sulfur dioxide into the air that caused chronic breathing ailments, higher cancer rates, and heart and immunity problems. Satellite images showed half the pine forests in the surrounding hills disappeared between 1972 and 1989.
With help from the EU, the three countries mothballed factories, switched to cleaner fuels, and installed new technologies in the area, about the size of Maryland or Belgium. Within a decade, sulfur dioxide emissions fell 91 percent, nitrogen oxide fell 78 percent and solid particles dropped 96 percent, according to the UN Environment Program.
For the Danube, the cleanup was more than just an environmental project. The Danube Convention changed mindsets, breaking down barriers between former enemies, forcing countries and riverside populations to work together across previously hostile borders.
"The Danube is a living river that is bound up with the culture and the peoples who live there," says Philip Weller, the commission's executive secretary.
"It is not a wild river, in the sense of salmon jumping or white water," Weller said. "It is the lifeblood, the circulation system" that connects the richest part of Europe in western Germany to the poorest in Ukraine and Moldova.
The river is still not pristine, but "over the past 20 years much has changed for the better," said Andreas Beckmann of the World Wildlife Fund. After 150 years of abuse and the loss of 80 percent of the river's wetlands, "the Danube has significantly recovered."
With the fund's support, dikes were torn down and severed river systems were reconnected, restoring 50,000 hectares (123,000 acres) or one-fifth of the retrievable wetlands, Beckmann says.
Still, the river bears irreparable scars from the Soviet era.
Romania's Iron Gate dams and hydroelectric stations cannot be dismantled, forever blocking the migration route of the majestic sturgeon. Two of the five sturgeon species native to the Danube have virtually disappeared, though efforts are on to revive stocks in the lower Danube.
Economic progress brings modern threats: more packaging, more waste, more household detergents containing phosphorous that stimulate river-choking algae.
Sergei Rudenko, a teacher at a vocational school in Dniprodzerzhynsk, has been throwing a fishing line into the Dnieper for 50 years. Springing from the mountains of central Russia, the 2,285-km (1,420-mile) river was once rich at this spot in eastern Ukraine with perch, carp and bream.
Now its yield is miserly, he says.
"The Dnieper is destroyed," Rudenko said, casting his line from a highway bridge, from which the horizon is obscured by smoke from the metallurgical plant. "The fishing is not like in earlier times. My father always brought home many fish, many bream, and now there is none."
Dniprodzerzhynsk, a name that combines the river with that of Felix Dzerzhinsky, the founder of the Bolshevik secret police, once was so crucial to the Soviet economy that it was closed to outsiders. With 250,000 people, it has 60 factories, some looming over the city in a permanent haze.
On the outskirts of town eight fields are fenced off with barbed wire, hung with yellow triangles warning of radioactivity. Nuclear waste was dumped here many years ago. Uniformed officers patrol the area, and stopped two Associated Press journalists to ask why they were there.
Next to a chemical plant is the city dump, where three decades worth of garbage is now a steaming landfill 30 meters (100 feet) deep. Dozens of trucks arrive daily, dropping more refuse into the ravine, cut through by a stinking scum-filled stream.