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There was a time when the Chicago River did what all rivers do when confronted with a downhill run and a large body of water at the end of that run: it flowed east into Lake Michigan. Then, as the city grew with people, railroads, more people, more freight—both rail and ship—more people, manufacturing, retail, people, the river became the premier sewer of the region, moving all its waste into Lake MIchigan. Oh, my! Polluting the lake! What do we do?!?! Reverse the flow of the river, of course, to move the stuff somewhere else.
Here is a concise history of the river from the Encyclopedia of Chicago. And
here is a USGS map of the river system today.
Ah, what we do to clean up our messes, eh?
The Chicago Harbor Lighthouse was first built in 1893 at the mouth of the Chicago River. In 1917, after the Navy Pier was built, it was moved out here at the end of the breakwater in the harbor.