Wisconsin had a few tornado injuries, and at least one injury was reported near Chicago. Indiana had been spared any reported deaths or injuries due to flooding.
"At this point, mercifully, we believe all Hoosiers are secure," Gov. Mitch Daniels said at a news conference. "We hope that will continue."
Daniels declared an emergency in 10 counties as the Coast Guard was called in from the Great Lakes to help with flooding that has forced hundreds of people from their homes.
Ninety percent of the small town of Paragon, southwest of Indianapolis, was underwater, State Homeland Security Director Joe Wainscott said.
Water reached the first floor of Johnson Memorial Hospital in Franklin, but no patients had to be moved, county Commissioner Tom Kite said, and cars were submerged up to their windshields in the county government building parking lot.
"We have dams failing in the Prince's Lakes area," threatening the town of Nineveh, about 30 miles south of Indianapolis, Kite said.
Indiana State Police reported evacuations in the Lake Lemon area about 10 miles northeast of Bloomington. Dams near Gold Point were close to collapse, police said.
Near Martinsville, southwest of Indianapolis, Ben Pace watched motorboats rescuing neighbors. The rain didn't appear that bad when he woke up, Pace said, but he then watched water rise 6 to 8 inches in his backyard shed.
"Then I realized that it's worse than it's ever been," he said.
A rescuer came by boat to his front door to get him. He managed to grab some clothes and his dog, leaving the home with knee-deep water in his bedroom.
Interstate 70 was closed in Clay County in west-central Indiana, and Interstate 65 and another major route, U.S. 31, both were closed near Franklin.
Residents of Helmsburg, a town of about 6,000 just 40 miles south of Indianapolis, were taken by bus to a YMCA in Nashville, said Wayne Freeman, Brown County Red Cross chairman.
In western Indiana, water more than a foot deep surrounded homes on Terre Haute's east side. U.S. 41 was the only route open into Terre Haute, and it was down to one lane by mid-afternoon.
J.D. Kesler, deputy director of the Vigo County Emergency Management Agency, said more than 200 people had to be rescued from their homes, vehicles and nursing homes there.
Peter Perdoue, 35, a mortgage broker from Terre Haute, heard a trickle Saturday morning and checked his daughter's basement room. The water had risen above the window.
"It was almost like I was standing inside an aquarium," he said.
Within a few hours, sewage started backing into his basement, and it wasn't long before the waters had filled his basement up to the 10-foot ceiling.
More than 30,000 electricity customers lost power, the Indiana Utilities Regulatory Commission said.
Near Chicago, Will County Sheriff's Department spokesman Pat Barry said a tornado damaged several homes in the Wilmington area and toppled trees and power lines.
A person was injured on Interstate 57 in the southern suburbs, and a swath of the major highway closed as authorities worked to clear overturned trucks, said state Trooper Mark Dorencz.
Tornadoes were also reported in Lake County, north of the city, and in Livingston County, to the southwest.
Central and southeastern Wisconsin were pelted with baseball-size hail in a storm that blew roofs off homes, toppled trees and power lines, and injured at least six people. Heavy rains also pelted the area, causing flash flooding.
Flooding built up around Milwaukee, where water as deep as 2 feet in roads caused parked cars to drift and closed parts of an interstate highway.
On the south side of town, two vacant buildings partially collapsed because of the heavy rains, authorities said. No injuries were reported there.