The lake, however, was also the source of drinking water. During a tremendous storm in 1885, the rainfall washed refuse from the river far out into the lake, past the water intake cribs. Typhoid, cholera and other waterborne diseases from the contaminated drinking water took their toll. The Chicago Sanitary District (now The Metropolitan Water Reclamation District) was created by the Illinois legislature in 1889 in response to a terrible epidemic which killed thousands of residents of this fledgling city.

This new agency devised a plan to construct channels and canals to reverse the flow of the rivers away from Lake Michigan and divert the contaminated water downstream where it could be diluted as it flowed into the Des Plaines and eventually the Mississippi.

On September 3, 1892, a workforce of 8,500 men, most of them newly arrived immigrants, swung into action. Using every type of earth moving equipment available, including wheelbarrows, mule drawn plows, steam shovels, drag scrapers, drills, liberal shots of dynamite and bare hands, they completed the 28 mile Sanitary and Ship Canal in 1900. The North Shore Channel was completed in 1907 and the Cal-Sag Channel in 1922. Altogether the District built 56 miles of canals, all designed to divert water from Lake Michigan into the Des Plaines and Calumet rivers, rather than having the rivers flow into the lake.

Other Great Lake states began to worry that Chicago's diversion of Lake Michigan water would lower the water level of the lake. So the District installed locks at the lakefront intake points to control the amount of diversion.