The Chicago Sanitary and Ship Canal is a navigation corridor for goods such as coal, fuel, grains and ores. It also has become a superhighway for invasive species. Credit: Gary Porter

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Standing on the banks of the Chicago River, you realize that maybe the best thing about this filthy waterway is that it was reversed over a century ago so it flows away from Lake Michigan instead of into it.

Water isn't even the first thing you notice where the river merges with a notoriously fouled little tributary, dubbed Bubbly Creek for the gases still belching from untold tons of cow carcasses dumped into it by the city's old stockyards.

Floating on the surface is the crinkly corpse of a pink Mylar balloon that's wrapped itself around a 40-ounce beer bottle. Nearby is a pumpkin stuck in the muck, orbited by an array of tampon applicators and plastic bottle caps. Just below a sewer pipe that excretes a septic stew when big rains hit, a boot floats sole-up next to a tennis shoe; if the pair were a match you'd fret they were attached to feet.

Above it all, gleaming in the midafternoon sunlight a few miles to the northeast, are the two white tusks atop the Willis Tower, pinnacle of Chicago's lakeshore skyline. The Chicago River no longer flows that direction, toward Lake Michigan - the city's drinking water source. It instead tumbles into a man-made canal that whisks it across a continental divide, away from the Great Lakes, and into the Mississippi River basin.

At least it does for now.

Some regional leaders have begun to explore a multibillion-dollar plumbing project to rechannel the Chicago River so it once again does what nature designed it to do - sustain Lake Michigan instead of drain it.

The threat of Asian carp swimming up the Chicago Sanitary and Ship Canal from the Mississippi River basin and into Lake Michigan spawned talked of re-engineering Chicago's waterways several years ago, but today it is more than talk.

A $2 million study by the Great Lakes Commission and a group representing the region's mayors provides the most detailed prescription yet on how to restore the natural divide between the Great Lakes and Mississippi basins that Chicago destroyed over a century ago in a desperate move to channel its sewage and industrial wastes away from the lake.

Today the region is feeling a different kind of desperation.

Biologists predict the number of unwanted organisms moving on the Chicago canal will only grow until the waterway is somehow plugged. And it is much more than a Great Lakes problem because biological pollution travels both directions on this invasive species superhighway.

Not only do rapacious Asian carp threaten to unleash havoc on the lakes' multibillion-dollar fishery, but some troublemakers such as pipe-clogging zebra and quagga mussels already have ridden canal waters in the opposite direction - out of the Great Lakes and into the Mississippi basin. From there they have hitched rides on recreational boats towed over the Rocky Mountains and now plague irrigation and hydroelectric systems across the West.

The cost of these unwanted organisms is hard to comprehend, but it is growing. The U.S. Fish and Wildlife Service predicts that if the fingernail-sized zebra and quagga mussels get into the Northwest's Columbia River hydroelectric dam system, they could do more than a quarter-billion dollars in damage. Per year.

Other noxious invaders are poised to make the same trip. A fish-killing virus now menacing the Great Lakes could do incalculable damage were it to slip down the canal and into the South's aquaculture industry.

In this sense, the Chicago canal system isn't so much a waterway as it is an open wound.

"This is not about Asian carp," said Peter Annin, a Great Lakes author who is managing director of the University of Notre Dame's Environmental Change Initiative. "This is about two artificially connected watersheds that many people argue never should have been connected."

Fixing the problem would be a massive public works project that would likely cost at least $4 billion and take years to accomplish. But beyond stopping invasive species, it could lead to dramatic improvements in water quality and flood control, as well as fuel a navigation boom on Chicago's increasingly neglected canal network.

It would require dramatic sewage treatment upgrades for the Chicago region, which is unique among Great Lakes cities in that it still does not disinfect the discharges from its three main sewage treatment plants.

But the people behind the study say it can be done.

The reason: This is no longer 1900, and it is no longer necessary to protect public health by diluting Chicago's sewage discharges with billions of gallons of Lake Michigan water and flushing it all into the Mississippi basin.

Even some of those most opposed to putting barriers in the canal system acknowledge that a river reversal is doable.

"Sure it can be done," Del Wilkins, president of Illinois Marine Towing Inc., said on a gray October afternoon while standing in the pilot house of the tugboat Lemont Trader as it rumbled down the canal, about 30 miles downstream from a proposed barrier site.

"But at what cost?" he asked, as black clouds built in the west. "What's the price and what will be the consequences?"

The storm clouds burst later that afternoon, dumping nearly a half inch of rain on Chicago neighborhoods. That storm was followed by a second deluge less than a week later that overwhelmed Chicago's sewage treatment system. For the 27th time this year, raw sewage was unleashed into the river and canal system, and it did exactly what the city has wanted it to do for more than 100 years.

It became someone else's problem.

Destroying the divide

The words Continental Divide conjure images of a cloud-scraping mountain crest stretching like a spine down the middle of North America that forces raindrops and melted snow to flow one way or the other - down a western slope and out to the Pacific Ocean or down the other side toward the Atlantic.

The pink Mylar balloon floating near Bubbly Creek would have once faced an equally fateful reckoning on the continent's other great divide, the one that split the Mississippi River basin from the waters of the Great Lakes.

Here the divide wasn't a mountain range, or even a perceptible bump in the landscape. It was essentially a marsh at the headwaters of a branch of the Chicago River, then a sluggish creek that started several miles southwest of what is now downtown and drifted more than flowed toward Lake Michigan.

Because the five Great Lakes are actually one giant, slow-motion river flowing east to the St. Lawrence, Chicago River water that historically flowed into Lake Michigan ultimately tumbled over Niagara Falls, down the wild, massive St. Lawrence River and out to the North Atlantic.

Water on the other side of that marsh trickled into a river that fed the Gulf of Mexico-bound Mississippi River. In big rains, the marsh occasionally, temporarily, turned into a sloshing swamp where water could drift in either direction.

Chicago destroyed the natural separation between the basins in the mid-1800s with a relatively crude navigation channel that opened a pathway for goods and people to float between the Great Lakes and Gulf of Mexico. That leak in the continental divide turned into a torrent in 1900 with the opening of the Chicago Sanitary and Ship Canal, a man-made waterway between the two basins wide enough (160 feet) and deep enough (about 25 feet) to actually pull the Chicago River - and all its waste - backward.

The river reversed direction because the 30-mile-long canal that linked with the Mississippi-bound Des Plaines River was at a lower elevation than Lake Michigan. So the water had no choice but to oblige gravity, reverse its course and head for New Orleans.

Chicago leaders felt they had no choice but to undertake what amounted to a replumbing of the continent. The city's namesake river doubled as its sewer and as long as it flowed toward its drinking water intakes in Lake Michigan, people were bound to suffer. As many as 2,000 Chicagoans in the 1890s were dying each year from typhoid fever.

The canal project was considered an environmental success in an era before the lakes were open to global shipping, when nobody pondered the biological costs of bridging the two massive basins. But now the threat posed by dozens of unwanted crustaceans, protozoa, algae, plants, mollusks and fish spilling through the breached divide has become clear as a zebra mussel-infested lake.

Today the canal is recognized by many as one of twin blunders that destroyed the ecological isolation of the Great Lakes. The other was construction of a shipping channel between the Great Lakes and Atlantic Ocean.

The St. Lawrence Seaway, which was completed in 1959, tamed obstacles such as Niagara Falls and the roaring St. Lawrence River with a system of canals, channels and locks to allow deep-draft ocean vessels - and all the biological pollution clinging to their hulls and lurking in their ballast tanks - to sail into the lakes from ports around the globe.

The Great Lakes are now home to 186 non-native species, some of which have ravaged native fish populations, spawned noxious algae growth and triggered botulism outbreaks that have killed tens of thousand of birds. Federal regulators this year ordered a multiyear phase-in of ballast water treatment systems on Great Lakes-bound freighters to block new seaway invasions, though many are dubious the regulations are stiff enough to solve the problem.

This would be mostly just a Great Lakes dilemma were it not for the back door from the lakes that Chicagoans opened to the middle of the continent.

Pressed by the Asian carp threat to examine the extent of ecological danger posed by the canal, the U.S. Army Corps of Engineers last year identified dozens of "high risk" organisms poised to ride its waters into or out of the Great Lakes. Most are species few have ever heard of. The tubificid worm. The testate amoeba. The bloody red shrimp.

But how many North Americans heard of zebra mussels or Asian carp just 25 years ago?

The Army Corps study illuminated a startling fact for many. While Great Lakes states fretting an Asian carp invasion have been making the most noise about the trouble caused by the Chicago canal, they don't necessarily have the most at stake in the matter.

The Army Corps identified 29 invaders set to spill out of the Great Lakes and into the Mississippi basin if a barrier system isn't erected between the watersheds. It also listed 10 species - including Asian carp - poised to invade the Great Lakes from the Mississippi basin.

"The problem is the people who live in the Great Lakes region are very aware of this issue, but the basin that may have the most to lose, the Mississippi, is the least engaged on this topic," said Notre Dame's Annin.

That is beginning to change.

Last year 17 attorneys general from South Dakota to Missouri to Arkansas wrote congressional leaders demanding "immediate federal action" to "completely sever the ecological connection between the basins."

"All our states, which are in or connected to these basins, face severe harm as non-native aquatic species, such as zebra and quagga mussels, invade our waters, disrupting ecosystems and damaging our economies," they wrote. "We all face the threat that more invasive species will move, in both directions, between the basins through the key artificial pathway that connects them" - the Chicago canal system.

Daley grasped the stakes

In spring 2003, former Chicago Mayor Richard M. Daley was among the first politicians to recognize the threat posed by the canal when he called dozens of researchers to downtown Chicago to scheme ways to prevent Asian carp from using the canal to invade the Great Lakes.

Daley urged the scientists to be audacious with their strategies, telling them an aggressive, proactive solution to a problem like this is almost always cheaper than trying to fix the damage later.

"Sometimes we have to be bold about it and not be afraid of taking some active steps protecting us against invasive species," he said.

At the time - and still today - the only thing standing between the carp and the Great Lakes has been an electric, fish-shocking barrier on the Chicago canal, about 35 miles downstream from Lake Michigan. While it's been fortified in recent years and is now actually three separate barriers, the federal government has called the system an "experimental and temporary fix."

The barrier also has suffered unexpected shutdowns and questions remain about how effective it has been at repelling juvenile fish.

After two days of debating options to stop the flow of unwanted organisms back in 2003, Daley's group reached a radical conclusion: "A project should be established that would result in the hydrologic separation of the Great Lakes and Mississippi River basins within 10 years."

Six years later, with Asian carp maybe only a day's swim below the electric barrier, the U.S. Army Corps of Engineers had secured federal funding and began trying to figure out a permanent solution to prevent the spread of nuisance species between the basins.

The Army Corps has long been in the business of moving barges - not stopping fish - and some Great Lakes advocates doubted the agency's commitment to a project that might harm navigation. Their worries intensified when Army Corps officials quickly changed the congressionally ordered focus of the study from one that would explore options to prevent the spread of nuisance species to one that will "prevent or reduce the risk."

That opened the door for the Army Corps to look at a host of alternatives that conservationists said were a waste of time and money in terms of finding a permanent fix - things like shooting bubbles, acoustic blasts and strobe lights into the canal to disrupt species migrations.

The agency also has exhaustively assessed the risk posed by 18 substantially smaller potential pathways between the basins, something Great Lakes advocates acknowledge is necessary but, like paper cuts compared to a severed artery, should be given a much lower priority.

Army Corps officials initially said they would finish the Chicago canal system portion of the study by the end of this year. Then officials said it would be 2015, at the earliest.

The carp might not wait that long.

At the end of 2009, DNA evidence emerged indicating that Asian carp had breached the electric barrier.

Because the DNA extracted from canal waters, like any other material, does not float upstream, the scientists who developed this genetic fish detection tool concluded that because DNA was found upstream of the barrier, carp had already made their way past it.

Army Corps officials countered that the Asian carp DNA likely was coming from some other source - bird feces, contaminated bilge water, even the toilet flush of someone who had consumed the fish.

Illinois' neighboring states responded to the DNA evidence by demanding that the Army Corps close two navigation locks near the Lake Michigan shoreline as an emergency barricade to protect the lakes and that the agency expedite its study into how to permanently separate the basins.

The Army Corps evidently didn't share that urgency.

"No need to close the locks at this time - the Corps electric barrier is effectively repelling any Asian carp invasion!" tweeted the Army Corps' Dave Wethington in spring 2010, two months after DNA was detected near the Lake Michigan shoreline. At the time, Wethington was project manager for the Army Corps canal study.

Three months after that tweet, in summer 2010, a 20-pound Asian carp was netted in Lake Calumet, a harbor directly connected to Lake Michigan - the only actual Asian carp found to date above the barrier, despite intense fishing, shocking and poisonings during the past three years.

Wethington headed for an agency job in Washington, D.C., late this summer. But he left town evidently convinced everything was under control, even after the barrier mysteriously crashed this past May and the door to Lake Michigan swung wide open.

"Barrier loses power for 13 mins; Continues to keep the Asian carp at bay for 2,600,000+minutes and counting!" he tweeted.

A frustrated Congress this summer ordered the agency to complete its canal study by the end of next year. The Army Corps took the full three-month time period it was given to respond to the congressional directive. Then agency officials said they would offer a range of options to solve the problem by the deadline, but said they couldn't provide an actual prescription by that time.

Lawmakers urging a plan of action were incredulous.

"I plan to hold the corps accountable for openly flouting the direction given to it by Congress," said U.S. Rep. Dave Camp, a Michigan Republican.

Pressure on the agency also is coming from the group that represents the region's mayors and the Great Lakes Commission, a body appointed by the region's governors and state legislatures. Concerned about the pace and focus of the Army Corps' study, the two groups hired their own team of engineers to figure out what it will take to restore the continental divide Chicago has destroyed.

"We were not convinced this was going to get fair consideration in the federal process," said David Ullrich, executive director of the mayors' group - the Great Lakes and St. Lawrence Cities Initiative.

"Nobody really trusts the corps," said Wayne State University law professor Noah Hall, who was instrumental in drafting the Great Lakes Compact that prohibits new water diversions out of the Great Lakes basin. "But the corps can't really solve the big problem on its own anyway. It will only happen if (and) when Congress appropriates several billion dollars to do it."

It also will only happen if it can be demonstrated that it can be done - and that it's worth the price.