The heavy rain started falling Wednesday night and continued well into the morning hours.
Areas to the north and west of Chicago took most of the hit from the storm.
In Lake Forest, several drivers had to be rescued from their vehicles when they tried to get through a flooded viaduct. Authorities said there were two cars underwater beneath the underpass, a Honda and a Chevy. The motorists who were in those cars are safe.
Floodwaters have covered the Deer Path Golf Course in Lake Forest, where most of the greens are submerged.
Along Route 41, firefighters swept the overflow waters to find out if there was anyone else that may not have been able to make it out or escape from their vehicles. Rescue crews plucked several motorists to safety.
The heavy rainfall overnight and Thursday morning prompted road closures throughout Lake, northern Cook and McHenry counties. Route 41 between Lake Forest and Lake Bluff was closed for part of Thursday, but as of 10 p.m. Thursday night, the southbound lanes through the area had reopened.
In Lake Bluff, many motorists, homeowners and area businesses continue to be affected by the weather.
"This happens every time it rains like this, so the area here, we have a little lake. I brought my fishing pole...It will affect the business here," said Chris Larsen, Thybony Paint & Wallcovering.
Business owners say they never really get used to it. They just try to deal with it.
In Lake Zurich, firefighters and county work crews sandbagged and pumped out streets and some homes near the Cedar Creek subdivision after standing water as high as two feet washed out the area.
The heavy rain also caused problems for homeowners in a subdivision in suburban Hanover Park. For a while, the water was so high, some residents could not get into or out of the community.
The minor flooding in Hanover Park soaked some basements and garages. At least one apartment parking lot has turned into a swimming pool, with several cars that may be stuck in the high water.
The flash flooding drenched parts of Hanover Park. The standing water trapped Tremaine Brown as he was driving to work. Emergency crews towed his car while he stayed inside it.
"It didn't look as deep to me as it was," Brown said.
Much of the high-standing water did go down, but the rain still soaked yards and homes.
Pablo Castillo will spend the day cleaning out a few inches of water in his garage, a wet rec room, and a backed up tub.
The flooding got so bad in one part of Hanover Park that some residents were trapped for a while.
Yards and homes were flooded, and some residents found water had backed up through their tubs and toilets.
"All of the wood inside, all of the drywall, probably we have to fix them because this is the second time that happened. I don't know how bad it is, we'll have to see," said Castillo.
Castillo said Thursday afternoon he's still not sure how bad the damage is.
The wet weather has also closed several streets and caused heavy delays for the morning rush hour.
Chicago was not entirely spared, however, as cars and trucks had to navigate a small lake that appeared in the middle of the street at 17th and Union.
The weather system reportedly dumped at least two inches of rain in the region with the threat of more to come.
At one point, standing water rose to two feet high, waterlogging 18-year-old pizza delivery driver Kevin Faetz's car.
"There's still water in there," said Faetz. "I lost my wallet, my iPod - a bunch of stuff of value. It was kind of inconvenient."
Wednesday night's storms left thousands of homes and business without electricity Thursday.
ComEd reports, at the height of the storm, more than 9,000 customers lost power.
As of 4 p.m., that number had dropped to 2,283.
Most are in an area near Dixon.
The weather is also affecting air travel.
More than 200 flights have been cancelled at O'Hare Airport, and there are delays of up to 30 minutes.
Average delays of 40 minutes are also being reported at Midway Airport.