The 24-year-old, who was a contractor with Kenney Construction, was relining a sewer at 8:30 p.m. Wednesday when a rush of rainwater hit him.
His body was found two hours later and 500 feet away from where he disappeared, WMAQ-TV, reported.
"When we first got here, the contractor had the camera going both ways in the sewer to see if we could find him faster and maybe make this a rescue instead of a recovery, but it didn't turn out," chief of the Chicago Fire Department Special Operations, Michael Fox, said.
The man's name is not being released.
Chicago received 1.5- to 3.5 inches of rain Wednesday night, and winds knocked down trees and power lines, leaving 15,000 without power.
Minor flooding also hit areas of Chicago, WMAQ-TV reported.
Storms continued Thursday.