More torrential rain worsened flooding in the American midwest, spawning high water that swept away an Iowa teenager, caused a traffic nightmare near one of the nation's busiest airports and threatened to swamp a Missouri town for the fifth time in less than a decade.

More than 3in of rain fell over much of eastern Iowa and northern Illinois Monday night and Tuesday morning, and some areas got up to 5in of rain, National Weather Service meteorologist Mark Fuchs said, capping a week of downpours in the region.

Six midwest states – North and South Dakota, Minnesota, Iowa, Illinois and Missouri – were dealing with significant flooding and there were pockets in some other states. By the weekend, the Mississippi River will be at major flood stage along many Iowa, Illinois and Missouri communities, forecasters said. River flooding could close highways, potentially top levees and threaten some homes and businesses.

The Mississippi River rise came suddenly after a spate of thunderstorms in the last month, Fuchs said.

"The spring wasn't that terribly bad. It was minor flooding, kind of ho hum," he said. "We had a very wet June, and it looks like, initially at least, July will follow suit."

In Iowa, rescue crews were searching for 17-year-old Logan Blake, who was swept away in a Cedar Rapids storm drain Monday night. The storm sewer drains into a lake and rescue crews were using sonar and boats to search.

The sudden rain overwhelmed the Kennedy Expressway, a major Chicago thoroughfare that runs to O'Hare International Airport. All but a single lane of traffic heading to the airport was closed for several hours Tuesday because of standing water. Some desperate air travelers were getting out of taxis and hauling luggage the rest of the way to the airport.

Karen Pride, a spokeswoman for Chicago's aviation department, said Tuesday that some 125 flights at O'Hare had been canceled. A dozen more were scrapped at Midway International Airport.

A Chicago area water authority released millions of gallons of storm runoff and sewage into Lake Michigan to relieve tunnels and reservoirs, the Metropolitan Water Reclamation District of Greater Chicago said. The exact amount won't be known for a couple of weeks, it said.

Storm clouds hang over the downtown Chicago skyline as rain and high winds move into Illinois from Iowa. Photograph: Kiichiro Sato/AP Photograph: Kiichiro Sato/AP

In Kane County, Illinois, west of Chicago, storms washed out a stretch of an unlit, rural road and created a 10ft sinkhole that a Ford Taurus drove into early Tuesday morning, trapping both occupants. A pickup truck followed suit a short time later. No one was seriously hurt.

The fast-rising Mississippi River prompted sudden flood-fighting efforts in several towns from southern Iowa to near St Louis. The timing was worrying for Mark Twain's hometown, Hannibal, Missouri. The community's popular National Tom Sawyer Days festival over the Fourth of July weekend should go ahead because all of the major events – the fence-painting and frog-jumping contests among them – are inside the flood levee.

The situation was far more serious for Clarksville, Missouri, about 70 miles north of St Louis. The town of only about 400 residents draws tens of thousands of visitors every year to one of the widest and most scenic spots on the Mighty Mississippi.

It also has no flood protection. In four of the past eight years, Clarksville has been forced to spend $400,000 to $700,000 in city funds to pay for sandbagging operations – the entire annual city budget is $350,000.

The flood is expected to crest nearly 10ft above flood stage on Tuesday. That's enough to put water into several homes and most downtown businesses. But Mayor Jo Anne Smiley said there will be no organized sandbagging this year.

"The city has no funding to deal with this flood," Smiley said. "Individuals and business owners are on their own."

Homeowners and merchants are already using sand and bags left over from last year to fortify their own properties. Smiley is also trying to get prisoners to help fill and place the bags.

In Minnesota, fresh off its wettest June in more than a century, there were signs that the worst flooding may be receding. The flooding has already forced St Paul to relocate a major food festival and the annual Fourth of July Fireworks display away from the Mississippi river.

Parts of the Dakotas saw record rainfall over the weekend. In North Dakota, crews in Bottineau and Renville counties were cutting open some roads to keep water flowing and away from farmhouses. Weekend storms dumped as much as 9in of rain.