Notwithstanding the bacteria, the canal is also an expressway for invasive species in both directions.
Chicago has a rare distinction among major American cities: It does not employ a disinfection stage at its three main sewage treatment plants.
The result is a river and canal system running so thick with fecal coliform that signs along the banks warn that the contents below are not suitable for "any human body contact."
Those fish farmers brought in the Asian carp as a way of boosting productivity. I'm told it's tasty for a bottom-feeder, and there's a lot of export potential.
The canal had indeed been a forceful solution to the city's 19th century sewage problem. But by the beginning of the 21st century, the true costs of destroying a continental divide - which some conservationists refer to as Chicago's "original sin" - were finally coming into focus as water, waste and noxious species mixed in a manner nature never intended.
Pipe-clogging invasive mussels from the Caspian Sea region - which have shredded the Great Lakes' food web and cost billions of dollars to industries and municipalities - rode Chicago's canal waters out of Lake Michigan and into the rest of America. They were followed by round gobies, a prolific predator of native fish species' eggs. Today a fish-killing, ebola-like virus is threatening to spill inland from southern Lake Michigan, an invasion that could have dire consequences for fish farmers in the South.
The drainage canals are pretty, but not exactly recreational waters.
They serve, however, as freight transportation corridors, and closing the canal without provision for transportation will be costly. Chicago does not think of Lake Michigan as both water source and water sink, and that would change.
The leafy North Shore channel is a training ground for college crew teams, as well as high school rowers, many of whom see the dirty water as the best route to a varsity letter, and perhaps college scholarship.
Space for all rowers is tight on busy training days, and on weekends they have to dodge droves of kayakers and canoeists.
All of them float past the warning signs lining the banks that caution against any body contact at all.
Only a fool - or an unsupervised child trying to beat the heat on a hot summer day - would purposely take a dip in the North Shore Channel, but that doesn't mean people aren't getting wet.
New Trier Township High School assistant crew coach Hope Poor says her kids are schooled to wash well after practice, scrub popped blisters and keep their heads above water on the rare occasion someone takes an accidental plunge.
Kenosha County, where the Root River, which drains into Lake Michigan, and the Des Plaines River, which drains into the Illinois River (on the opposite side of the sub-continental divide), could be Conflict Zero in a future civil war.
The postcards of a shiny city perched on the shore of a deep blue lake belie an unfortunate reality for the Chicago area. Pockets of it could be headed for a water shortage in the coming decades if the region doesn't stop flushing billions of gallons of water away a day.
Chicago is unlike every other Great Lakes city in that it doesn't pull its water from the lake, use it and send it back as part of a sustainable water management system that allows people to live and industries to thrive without diminishing the lakes.
In this sense, Chicago really isn't a Great Lakes city at all; it is just another American metropolis that has a limited freshwater supply heading into a century where many believe water will supplant oil as a primary economic driver.
The 1900 river reversal means virtually every drop Chicagoans take from the lake - whether it's to wash cars, brush teeth, fight fires or make ice - is a drop sucked away from the lakes and sent to the Gulf of Mexico.
That's why the U.S. Supreme Court decades ago slapped a 2.1 billion gallon-per-day cap on Illinois diversions from Lake Michigan.
It is an immense amount of water - about 20 times what Milwaukee takes from the lake per day - but it might not be enough.
Chicago's western suburbs, like Milwaukee's, are dependent on an ever-shrinking groundwater supply, and it's probably just a matter of time until they'll push to poke their straws into Lake Michigan for a share of that 2.1 billion gallons.
Compounding the problem, the amount of water available right now isn't even close to 2.1 billion gallons because every drop of rain that falls in the south-flowing Chicago River watershed is a drop that counts against its court-allowed allocation.
The canal system, however, provides relief capacity for railroads and highways that are congested with little relief in sight.
To meet that challenge while separating the Great Lakes from the Mississippi River calls for some thought.
Freight train tonnage is expected to grow 70% by 2030, according to a report LaBelle's group put together called The Metropolitan Freight Plan.
The roads are similarly choked, and getting worse faster than most people may realize. In 1982, the average Chicago driver spent about 16 hours a year in traffic jams. By 2002, that number had grown to 56 hours, and it has been projected to reach 80 hours - the equivalent of a typical person's two-week annual vacation - within the next 25 years.
Truck traffic is driving much of the problem.
In the next 25 years, according to the report, the number of trucks on Chicago-area roads is going to grow by a staggering 80% and will account for more than half of the extra vehicles on Chicago-area roadways.
Yet at the same time, some people are beginning to eye the massive canal system as an underutilized asset.
"Fifty percent of commercial goods nationally go through this region, $570 billion is on trucks, and $380 billion is on rail, and they're subject to all kinds of constraints," says Henry Henderson of the Natural Resources Defense Council. "The Great Lakes and Chicago's inland waterway transportation systems are really not part of that, and they need to be integrated into it."
I saw pictures once of a barge elevator in the Netherlands or north Germany that did this, and the Allegheny Portage Railroad did so on a somewhat larger scale.
The Alliance for the Great Lakes report offers a glimpse of how it might be accomplished.
It suggests that the most logical place to explore restoring the destroyed divide would be on the Chicago River, about three miles west of Navy Pier.
One dam-like structure here and you would effectively solve the problem for Navy Pier and Wilmette, where a second canal flows in from Lake Michigan and eventually merges with the Chicago Sanitary and Ship Canal.
That would mean the water currently treated at the North Side treatment plant would flow back into Lake Michigan instead of down to the Mississippi, requiring sewage treatment upgrades.
A structure at this location about 3 miles west of the lake would still allow thousands of Chicago tour boats and private vessels to sail along much of the downtown river and into Lake Michigan - a huge advantage over putting a barrier at the lakeshore near Navy Pier.
A second barrier could be installed on the Calumet River near the Lake Michigan shore, south of downtown, the report suggests. This would prohibit the free flow of barges into the lake, but it has an advantage in that much of the sewage and storm water discharges from that area would still flow away from Lake Michigan.
There are two smaller access points to Lake Michigan on the Grand Calumet River and Little Calumet River that would need to be plugged with some type of physical barrier, perhaps a berm. Neither have heavy commercial navigation.
As for the areas where barges would be blocked, [Illinois Senator Dick] Durbin and others expect the new Army Corps study to explore options to transfer that cargo overland, or perhaps transport entire barges overland.