The National Weather Service called flooding in Cedar Rapids, Iowa, a "historic hydrologic event" Thursday as the swollen river poured over its banks at 500-year flood levels, forcing the evacuation of nearly 4,000 homes.

The National Weather Service issued a flood warning for the Cedar River in east central Iowa Thursday, saying residents should expect "unprecedented river crests" and calling the situation serious. One of the Cedar Rapids, Iowa, levees already has broken.

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"The rest of the levees in the city have not broken down but what the problem is is the water went way up over the top — well over a foot over the top of the levees," Dave Koch, the city's public information officer, told FOX News, adding "it's a 500-year flood and it just overwhelmed us."

The Midwest has been inundated with floods in recent days, with a man dying Thursday in Albert Lea, Minn., after his vehicle fell into a flooded stream. Two others were rescued.

Officials estimated that 100 blocks in Cedar Rapids were under water.

"We're just kind of at God's mercy right now, so hopefully people that never prayed before this, it might be a good time to start," Linn County Sheriff Don Zeller said. "We're going to need a lot of prayers and people are going to need a lot of patience and understanding."

The problems in Cedar Rapids came a day after frantic sandbagging enabled the upstream cities of Cedar Falls and Waterloo to narrowly avoid widespread flooding.

Despite several days spent preparing for the approaching high water, Cedar Rapids couldn't avoid being hit hard. Rescuers had to use boats to reach many of the residents stranded in 3,900 homes.

"There are homes, there are businesses, police department, fire department — we're all under water," Koch said.

In downtown, flood waters neared the top of stop signs and cars were nearly covered in water. People could be seen dragging suitcases up closed highway exit ramps to escape the water.

It wasn't clear just how high the river had risen because a flood gage was swept away by the swirling water.

The surging river caused part of a railroad bridge and about 20 hopper cars loaded with rocks to collapse into the river. The cars had been positioned on the bridge in hopes of weighing it down against the rising water.

"We're in uncharted territory — this is an event beyond what anybody could even imagine," said Brian Pierce, a meteorologist with the National Weather Service in Davenport.

As Cedar Rapids dealt with rising flood waters, other Iowa cities warily watched rivers further swollen by storms overnight into Thursday that brought up to 5 inches of rain across west central Iowa.

The heavy rain moved east during the day, soaking people as they hurried to remove items from businesses as police told them to move to higher ground.

Joe Childers, an official at a U.S. Bank in downtown Cedar Rapids, was in jeans and tennis shoes as he worked to protect items.

"We're trying to keep water out of as many places as we can," he said. "It's pretty amazing. I don't think anyone really expected it this far."

Prisoners had to be moved from the Linn County jail, including some inmates transferred from the Benton County jail in Vinton because of flooding. The sheriff's office also was under water, Sheriff Don Zeller said.

"We've had to move our operations out of the area and to our alternate emergency site," Zeller said. "We are just trying to regroup. When you don't have all of your equipment and you don't have all your facilities to operate out of — we're at a little bit of a disadvantage ... but we're carrying on as normal."

In Des Moines, officials said they were urging residents to evacuate more than 200 homes north of downtown because of concerns that the Des Moines River would top a nearby levee.

Public Works Director Bill Stowe said officials were also watching the Des Moines and Raccoon rivers through downtown Des Moines.

"We're certainly concerned and last night's rain elevated those concerns," Stowe said. "We'll be carefully watching the situation over the next couple of days."

Despite rising water, the city's water treatment plant was operating normally. The plant was knocked out of service in the 1993 floods, cutting off water to Des Moines for 12 days.

Meteorologist Rod Donavon of the National Weather Service said there was a strip of 3 to 5 inches of rain across west central Iowa and another strip of 2 to 3 inches in central Iowa.

"A lot of water fell in the Raccoon River basin, which is of concern as it moves toward the Des Moines metro area," he said

Donavon said he had not seen any new river forecast projections but it will "be a concern."

Gov. Chet Culver has declared 55 of the state's 99 counties as state disaster areas. Nine rivers are at or above historic flood levels.

In Cedar Rapids, evacuations pushed deeper into flood-prone neighborhoods on the city's southeast side Wednesday night. City officials imposed a 9 p.m. to 5 a.m. curfew in evacuated neighborhoods.

Several emergency shelters were opened, and the city had closed all but one of its bridges over the Cedar River.

"I believe that this is God's way of doing things, and I've got insurance, so I'm not worried about it," said Tim Grimm, who was forced to leave his home in the city's Czech Village area.

City Manager Jim Prosser said the river might exceed the capacity of the protections Cedar Rapids had in place to control it.

"Our primary focus now is the life, safety and welfare of the public," he said.

The City Council voted to give city officials emergency powers until the floodwaters had subsided.

Public Works Director Dave Elgin told the City Council on Wednesday to prepare for a long flood — not just a record-setting one.

Iowa City officials have approved a mandatory evacuation ordinance at a special council meeting on Wednesday. The city put the order into effect around 2 a.m. on Thursday for residents in the Normandy Drive area on the city's north side near the Iowa River.

In Coralville, residents along two streets have until 5 p.m. Thursday to evacuate. The city also is asking that residents try to avoid using running water and toilets while it is raining, because the volume of water is overwhelming the water plant.

The Associated Press contributed to this report.