Two Michigan newspaper carriers drowned this morning when their car was submerged along a washed-out road.
Another person was killed in Indiana, where record flooding is continuing along several rivers.
Hundreds of people have been evacuated from Indiana homes, a hospital and a flooded nursing home.
In Nebraska, the National Weather Service has confirmed at least one category EF 2 tornado touched down in a neighborhood in west Omaha.
Emergency management teams are reporting no deaths or major injuries, but dozens of homes have been damaged including some that may be total losses.
Omaha Mayor Mike Fahey toured the damage in the Millard area and said, "I'd say it was a miracle no one got killed."
Meanwhile, rain continues to fall today in Wisconsin. Strong storms there yesterday brought baseball-size hail and blew roofs off homes. At least six people were injured.
Michigan Thunderstorms Bring Flooding; 2 Drown
The National Weather Service issued thunderstorm warnings for six Michigan counties this afternoon, hours after two people drowned in a flooded creek.
The victims were delivering newspapers for The Grand Rapids Press when their car sank in a creek swollen from weekend of thunderstorms that continued this afternoon.
The storms blacked out at least 232,000 Michigan homes and businesses, and about 42,000 remain without power today.
The fatal accident happened about 4 a.m. today near Lake Michigan in Allegan County's Saugatuck Township - about 40 miles southwest of Grand Rapids.
1 Dead, 1 Missing In Indiana Flooding
Rescuers in boats were still plucking people from rising waters Sunday, and parts of Indiana braced for more flooding that has caused at least one death.
As much as 11 inches of rain swamped the state Saturday, flooding homes, threatening dams and closing several roads and highways. One person drowned, and 23 of the state's 92 counties were declared disasters, said John Erickson, a spokesman for the Indiana Department of Homeland Security.
Another person also was reported missing after falling off a boat in a flooded area, state police 1st Sgt. Dave Bursten said.
In Morgan County, southwest of Indianapolis, about 150 residents were taken out of a flooded nursing home. Floodwaters that were moving south to eventually drain into the Ohio River prompted officials to evacuate more than 250 patients and employees from Columbus Regional Hospital in southern Indiana. Workers pumped water out of the basement, and a couple inches of mud covered the first floor of the facility that was forced to close.
Jack Elkins, 67, has lived in Columbus since 1963 and said he has never experienced such serious flooding.
His and other condominiums near the hospital were inundated with water in a matter of minutes Saturday night, he said. Once the storm drains filled up, it took 15 minutes for about 8 inches of water to ruin his place.
"It looked like a river in front of my house," he said as he took a break from ripping up carpeting and flooring.
Gov. Mitch Daniels said many of the flood victims he spoke to told him similar stories about how quickly floodwaters rose, catching them off guard.
"This thing came on fast with such a radical deluge of water that people were describing going from a feeling of security to waist-deep water in a matter or 15 or 20 minutes," he told reporters Sunday.
Elkins estimated it would take at least $25,000 to fix his house, since he can do the work himself. He and his neighbors do not have flood insurance because the area has never dealt with the problem.
In western Indiana, Terre Haute also was dealing with serious flooding. Daniels said that there had been some looting reported in the city but that extra police had been sent to prevent it from happening again.
Travel was getting easier on two major north-south highways. Indiana State Police said Interstate 65 from Indianapolis to Louisville, Ky., and U.S. 31 north and south of Columbus were reopened after being closed for about a day by the flooding. But several state highways remained closed as a result of the record flooding that continued along the White, Wabash and Flatrock rivers.
A Johnson County dam was breached by the high water but had not failed, Erickson said.
"It's in bad shape," Erickson said.
A shelter set up in Columbus filled with people, Erickson said. Shelters were also open in several other counties.
"Obviously we don't need any more rain," he said.
Indiana caught a break on that front, at least for a day, as most of the state was hot and dry. However, more thunderstorms could hit central Indiana Monday and continue into Tuesday, possibly dropping another inch of rain.
"If you get another inch or so of rain where they've already had 11 inches of rain, it doesn't help their situation, but it doesn't return to flooding anywhere near what they already saw," weather service Hydrologist Al Shipe said. "We're not out of the woods yet."
Part of southern Indiana from Spencer to Edwardsport could see high water as bad or worse than record flooding in 1913, forecasters say.
In northern Indiana, a line of thunderstorms swept through Saturday night, and one tornado touched down briefly northwest of Marion, according to the National Weather Service. No deaths or injuries were reported, and the twister caused minor property damage.
Besides high water, residents were also dealing with power outages. Duke Energy reported that 87,000 customers had lost power since Friday evening. Electric had been restored to all but 6,221 by Sunday morning, and those customers might have to wait as flooding was preventing crews from getting to downed lines and failed transformers, the utility said.