One of the worst affected areas is Cedar Rapids city, where 438 streets have been submerged and nearly 4,000 homes evacuated.
Officials in the city - which is the state's second largest with a population of about 120,000 - warn its drinking water supply is under threat.
The cost of the damage in Cedar Rapids alone has been estimated at $737m (£380m).
City Mayor Brian Fagan said: "It's a bit overwhelming. This is an endurance competition."
The Cedar river crested on Friday night at nearly 32ft (9.75m), 12ft (3.66m) higher than the previous record, set in 1929.
"This is our version of Katrina," Johnson County Emergency Management spokesman Mike Sullivan said in Iowa City, in a reference to the hurricane that caused devastation in New Orleans in 2005.
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