You’ve reminded me, just in time for summer: Chicago’s south side beaches were notorious for being closed more days than they were open during the summer because of dangerous e coli levels. We would have to check a website or automated phone message in the morning to find out if the levels that day were below a certain level before heading out. And then they brought hawks to the south side. Magically, our beaches are useable again. Turns out that’s all it was: pigeon guano.
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Where you are (Chicago), the beach problem’s the same as where I am (L.A.): (mostly) seagulls and broken sewer lines. 
From 2011
“A leaking sewer line was to blame at 63rd Street in 1999, when the beach was closed 22 times.”
"DNA testing confirmed that the droppings from seagulls and other birds were a “significant E. coli source,” according to the report. "
When they sent in dog teams to scare seagulls away from the food left at Chicago beaches, the contamination levels sharply dropped!
Not only that, Chicago also decided to work on their infrastructure.
From 2012
“As part of the program, Chicago will spend about $US 1.4 billion to fix its water system, a quarter of which is more than 100 years old. Last year, there were more than 3,800 pipe breaks in Chicago, costing the city tens of millions of dollars[.]”
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P.S. As the articles note, high concentrations of E. coli don’t necessarily mean a lot of people will get sick. It’s hard for people to get sick off of bird E. coli. Mammal E. coli (from dogs, toddlers swimming and pooping, or broken sewers are more likely suspects.
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