Flooding closed the Edens Expressway at Pratt Avenue for about three hours this morning and shut down the McHenry branch of Metra’s Union Pacific Northwest Line for the entire day. 
The expressway was closed in both directions around 7 a.m. The inbound lanes were opened around 10:20 a.m. and the outbound lanes were opened soon after, according to the Illinois State Police.
Many north and northwest suburban highways and streets were also flooded. The National Weather Service issued a flash flood warning for Lake and McHenry counties and the northern part of Cook County as up to 7 inches of rain fell in parts of the Chicago area. The warning had been scheduled to expire at 11:30 a.m., but was extended until 4:30 p.m.
The McHenry branch of Metra’s Union Pacific Northwest Line has been shut down indefinitely because of tracks undermined by washouts, Metra spokesman Michael Gillis said. The line will not be opened for the evening rush, but Metra officials hope to have the trains running again Thursday morning.
Making matters worse, unrelated communication issues temporarily halted trains on other branches of the UP Northwest line.
Trains began running between Palatine and Chicago around 7:45 a.m. and trains between Barrington to Harvard/Crystal Lake started moving after the communications issues were cleared up about 15 to 30 minutes later, Metra said.
But later this morning, Union Pacific lines were further delayed by a freight train near Barrington, with trains running up to two hours late.
For updates on Metra, check the agency’s website.
For nearly an hour, riders at the Cary station on the line repeatedly heard the announcement: “Attention commuters. Due to weather problems, inbound and outbound trains are stopped. Estimated time of this delay is unknown. Thank you for your patience and understanding.”
Finally, around 7:45 a.m., the riders boarded train 616 for Chicago instead of their usual 620.
Many commuters grumbled and made calls to work. Several left and opted to drive.
Chris Payne, 40, of Algonquin, said he has been taking the train every week day for four months. “I’m missing a conference call that I needed to be on.”
At 7:42 a.m., he boarded the train he had planned to hop on at 6:58.
Rescue workers evacuated people by boat out of a flooded area in Buffalo Grove Wednesday morning, officials said.
The village launched its emergency operations center at 7 a.m., after the storm began overnight around 3 a.m., said Terry Vavra, Buffalo Grove fire chief.
“We had over three inches of rain overnight. That’s an incredible amount of rain in that short period of time,” he said.
For flooding in the area of Saint Marys Parkway and Raupp Boulevard, the fire department called in swift water divers on three boats to rescue nine people and two pets, Vavra said.
“It was enough water that they couldn’t walk out,” Vavra said.
McHenry County, where residents are still recovering from flooding this spring, was hard hit again by flash flooding, officials said, with some basements taking water, particularly in Cary, Crystal Lake and Fox River Grove
The rain was torrential in spots, with Crystal Lake reporting almost seven inches of rain overnight, while Woodstock got about three inches, said David Christensen<CQ>, director of the McHenry County Emergency Management Agency. Nippersink Creek almost doubled in depth since Saturday, to nearly 8 feet, and the Fox River below the dam in Algonquin reached a moderate flood stage at 11 feet, according to the U.S. Geological Survey.
Horses had to be moved out of flooded stalls to higher ground at the Midwest Center for Children’s Development in Crystal Lake, Christensen said.
While no human evacuations were required, more than 30 roads in McHenry County had to be closed this morning due to high water, authorities reported.
In Barrington, near Kelsey Road and Old Barrington Road, Flint Creek overflowed, flooding a nearby running path and bringing out emergency workers in inflatable pontoons, as well as divers.
Meanwhile, heavy rains and flooding resulted in road closures that snarled traffic in Park Ridge this morning. About 20 vehicles were stranded and disabled after drivers tried to pass through flooded streets, said police Deputy Chief Lou Jogmen.
The city is still seeing spotty closures as water levels recede, but Jogmen said the focus is on Dempster Street, which remains closed in both directions at Dee Road.
The city relied on volunteers, many of whom left their own flooded homes to help the city’s storm response, Jogmen said. “Our resources were certainly strained,” he said.
No injuries have been reported, he said.
Flash flooding early this morning forced street closures throughout south and southwestern Lake County, from Buffalo Grove to Lake Zurich, said Kent McKenzie, the county’s emergency management coordinator.
“A couple of rain gauges got 5 or more inches of rain since midnight, which is a ridiculous amount of water,” McKenzie said. “We have had multiple reports of flooded basements and homes in and around Lake Zurich, Deer Park and Kildeer.”
Officials anticipate more flooding is possible along the Des Plaines River south of Lincolnshire, where the water level has risen four feet, he said. They also are concerned about the rising water level in Fox River, throughout Cuba Township.
“We have sent sandbags to Deer Park,” McKenzie said. “The problem with a flash flood is it is difficult to predict where the rain is going to fall.”
Flood debris collections will begin Monday for one week. Residents can place flood debris — but no electronics — at their curbs for free pickup, Jogmen said.
Tribune reporter Robert McCoppin and Tribune photographer Stacey Wescott contributed
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