A Flood Watch was in effect for most of the area Saturday, but it has since expired.
Flash flooding was a concern in the south and southwest neighborhoods that already saw about 3.6 inches of rain on Friday.
The Department of Water Management planned to work through the overnight hours into Saturday morning to ensure sewers were flowing and moving the excessive storm water out.
In Darien, the police department was flooded on Friday, officials said.
There were ground stops at both Midway and O'Hare airports Friday afternoon due to thunderstorms.
Also on Friday, funnel clouds were reported in Illinois and there was a Flash Flood Warning for parts of the Chicago area Friday.
The National Weather Service issued a special weather statement for funnel clouds from LaSalle County through southern Cook County and south of that line.
Funnel clouds rarely touch the ground and typically do not pose a hazard, Butler said. Some were spotted earlier Friday near Ottawa.
Trees and power lines were knocked down Thursday by strong winds.