Rain and storms also hit the Chicago area, flooding some lanes of Interstate 190 near O'Hare International Airport.
Cedar Rapids Fire Department Battalion Chief Brian Gibson was hopeful the first teen,17, could still be alive.
"It's a possibility that he could be caught in the sewer system and just unable to free himself and get himself out," he said. "There is that chance. ... We're certainly hoping for the best."
About 5 inches of rain fell in the area Monday, inundating storm drains and sewers. Officials said the first boy was swept away at about 7:20 p.m.
The second boy traveled about 1 1/2 miles through the sewers into Cedar Lake. He walked to a hospital, where he was being treated for his injuries.
A third teen called 911, setting off the search.
Thousands of people lost power in the storm.
In Chicago, travelers trying to reach O'Hare early Tuesday faced a massive traffic jam, police said. Illinois State Police Sgt. Henry Spight told the Chicago Tribune many people being driven to the airport got out of cars and taxis and trudged along the side of the highway with their luggage.
Storms late Monday brought trees down and left many in the region without power. Police in Kane County rescued a woman and her teenage son after a sinkhole swallowed their Ford Taurus and a pickup truck came down on top of them.