It's a tale of environmental redemption in the Twin Cities: On the Mississippi River between Minneapolis and St. Paul, a variety of native mussel species once wiped out by pollution are making a comeback.

Decades ago, mussels were everywhere in this part of the river. But then we started filling it with sewage, industrial waste and farm runoff. Mussels suffered.

But about 15 years ago, well after the 1972 Clean Water Act and other efforts led to water quality improvements, biologists surveyed the river and found some native mussels had started coming back.

Holdhusen held the shell of a Threehorn Wartyback mussel she found in the Mississippi River. Courtney Perry for MPR News

"Mussels are kind of like the canary in a coal mine," said Tamara Smith, an endangered species biologist with the U.S. Fish and Wildlife Service. "When mussels are doing poorly, that's a sign that the water quality isn't doing well. When they're doing well, that's a good sign and it's also good for humans."

Mussels play an important role in the aquatic food web. They're filter feeders. They capture organic matter in the water and make it available to the small organisms that fish and other animals eat. And: "They cleanse the water," says Bernard Sietman, a mussel biologist for the Minnesota Department of Natural Resources.

More from the DNR: Mussels of Minnesota

Byron Karns, center, an aquatic biologist with the National Park Service, returned to a boat after diving for mussels. Dan Kelner, right, is with the U.S. Army Corps of Engineers. Courtney Perry for MPR News

"About 15 minutes of searching along this line, I was able to find a couple," said National Park Service aquatic biologist Byron Karns as he exited the river wearing scuba gear. Karns pulled out a winged mapleleaf with a tag attached to its shell. "That's the guy you want right there," he said. It's one of the mussels the researchers have placed here.

A Winged Mapleleaf mussel with a tag is found near Pike Island. Courtney Perry for MPR News

"It's good to be able to go back and relocate stuff that we've put out in the river, because a lot happens in this river over the course of a year," Karns said. "But it seems like really good habitat. There's tons of other mussels down there. If I had been collecting everything that bag would have been full."

But finding evidence that the reintroduced mussels are surviving is only half the battle. The ultimate goal, Karns says, is to see these mussels multiply.

"You know that you have been successful when you find the evidence of new babies," he said.

Researchers have found signs that's happening with the Higgins' eye mussels — in 2011, and again this year.

Dan Kelner of the U.S. Army Corps of Engineers held the shell of a Higgins' eye mussel, a federally listed endangered species. Courtney Perry for MPR News

Army Corps of Engineers biologist Dan Kelner held the shell of the Higgins' eye mussel divers found in recent days.

"We think it dropped off a fish that was infested with the glochidia, the larval form of native mussel," he said. "We think this is an individual that was recruited in, lived for a few years. Just the fact that we found one this year and that we found a couple live ones in 2011 means there could be potentially thousands within this reach because it really is like looking for a needle in a haystack with divers at near zero visibility. It's a good sign, a very good sign."

And it's evidence that the Upper Mississippi River, despite years of abuse, has come back to life.