The flow was reversed because people in Chicago were getting sick due to the presence of human waste and other contaminants in the river. Reversing the flow reduced the spread of disease because it no longer gathered in Lake Michigan. However, that stuff didn't disappear. How did the reversal impact public health along the Mississippi River, the new destination for Chicago's waste and sewage?
In a sense, that stuff does disappear in waterways where there is sufficient dilution and natural bacterial action in the flowing streams to oxidize organic matter, and Chicago was able to fend off legal challenges by proving that the hundreds of miles of flow through the Des Plaines and Illinois Rivers made the city's effluent harmless by the time it reached Peoria or St. Louis. However, the city's rapidly expanding population and the Supreme Court's 1930 decision limiting the amount of water that Chicago could take from Lake Michigan made it clear that sewage treatment would become necessary, and the Sanitary District of Chicago began planning for that in the 1920s. The district's massive treatment plants were completed in the 1930s.
More recently, the district has been constructing the Deep Tunnel system of tunnels and reservoirs so that untreated sewage, even the results of huge rainstorms, can be treated prior to release. The district has recently begun complying with EPA orders to sterilize water being discharged, to kill any pathogens.