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Great Lakes Today was created to highlight issues affecting the lakes. The main partners are WBFO (Buffalo), ideastream (Cleveland) and WXXI (Rochester).Browse more coverage here. Major funding for Great Lakes Today is provided by the Corporation for Public Broadcasting, a private corporation funded by the American People. Additional funding comes from the Northeast Ohio Regional Sewer District.

Crystal Clear Great Lakes May Not Be So Healthy -- Here's Why

Beach along Lake Superior [Dan Kraker/Minnesota Public Radio]

By Dan Kraker

At Brighton Beach outside Duluth, the waters of Lake Superior are stunningly clear. Looking into about six feet of water, it’s easy to see smooth rocks at the bottom.

But Lake Superior has lost its long-held title as the clearest of the Great Lakes. A recent study showed that lakes Michigan and Huron have changed drastically.

"And not only did they show big changes, but they also passed Lake Superior in terms of water clarity," says Gary Fahnenstiel, who co-authored the study in the Journal of Great Lakes Research.

"And this was really profound, because if anyone’s been in the Great Lakes for years, you recognize that Lake Superior is kind of always held as the clearest, most pristine lake of all five Great Lakes."

For the study , scientists analyzed satellite images captured between 1998 and 2012. Over that period, the depth that light could penetrate into the water increased by about 20 percent in lakes Michigan and Huron.

So what's going on? Fahnenstiel, a senior research scientist at Michigan Tech University, says it's partly due to less runoff of phosphorous, which is common in farm fertilizer.

But the dominant factor, he says, is the explosion of invasive zebra and quagga mussels in the lakes in the past twenty years or so. He says some of the world’s highest concentrations of quagga mussels are found in Lake Michigan.

"So in a somewhat figurative sense, you can almost walk on a bed of mussels from one side of Lake Michigan to the other," he says.

And all those mussels filter a lot of water.

"It’s estimated in Lake Michigan right now the mussels can filter the entire volume of water in six days," he says.

The mussels eat the plankton in the water. Those plankton are the dominant light absorbers. So remove plankton, and the water gets a lot clearer.

That's good, right? After all, if you've been to the eastern shore of Lake Michigan, you know, it's gorgeous. The water is this aqua blue color, and you can see down 30 or 40 feet.

"And I feel the same way when I’m on my sailboat in Lake Michigan, it reminds me now of the Caribbean," says Robert Scuchman, co-director of the Michigan Tech Research Institute and a co-author of the study. 

He says you have to think about the ramifications of that water clarity. The plankton that the mussels filter also are the base of the food chain. If they’re  gone, the rest of the chain risks starvation.

"So, it’s very disconcerting, because if you take it to the limit, the Great Lakes may be totally clear and you’re kayaking, and you’re seeing the bottom, but they may end up being literally ecological deserts,” Scuchman says.

The clearer water also has led to a surge in a dangerous algae.

Cladophora is a hotspot for the growth of a harmful bacteria that in turn produces a botulism toxin. And  that has killed large numbers of fish and birds, including migrating loons.

But there may be a bit of good news, says Fahnenstiel. The number of invasive mussels may have peaked in Lake Michigan. And he hopes the improved water clarity in lakes Michigan and Huron sparks a new sense of pride and stewardship.

Back at Brighton Beach, 70-year-old Rob Hall knows firsthand just how clear Lake Superior is. The retired firefighter is a scuba diver who's done about 500 dives in the big lake.

"I drink it, I swim in it, I eat the fish that come out of it," he says. “It’s still the best. They call it Superior for a reason."

Even if it's no longer the clearest of the Great Lakes.