Many streams will see moderate to major flooding through the weekend, the service added, and flooding along the Missouri River will continue into next week.
The storm, which contributed to the deaths of a utility worker in Texas and a Colorado State Patrol officer, dropped heavy rain as it moved east across the central Plains.
Douglas County Commissioner Mary Ann Borgeson says "Things are moving and changing at a rapid pace", and people need to follow instructions.
The high water pushed some waterways to record levels in Nebraska, South Dakota, Iowa and Minnesota, though a cooler and drier forecast for the next two weeks suggested some possibility of relief for those states.
The order came Friday.
The National Weather Service expects the Missouri River to reach 30.1 feet in St. Joseph early next week and hold at near record levels until the middle of next week, when it is expected to begin to slowly recede.
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Barr also made remarks and said President Trump's emergency declaration on the issue is "firmly grounded" in the law. As president, Trump has the constitutional authority under Article I, Section 7 to reject a proposal from Congress.
A flood warning has been issued for the Nith River through New Hamburg and Ayr as flows are expected to peak on Friday afternoon and late Saturday morning, respectively.
Lower Michigan also saw severe thunderstorm warnings, watches, flooding, high winds and hail as the storm trekked across the Midwest. "In some locations it's the worst flooding on record on many of these river gauges". The flood stage at Kansas City is 32 feet. The risk of major flooding at Clarksville in a normal year is 12 percent.
Sarpy County officials urged all residents directly along the Platte and Missouri rivers to evacuate Friday morning as water levels continued to rise. A breached levee led to the rise along the northwest side of town along the Platte River.
The U.S. Army Corps of Engineers, which manages the river, increased releases from Gavins Point Dam in southeastern South Dakota due to limited storage capacity behind the dam for the excess runoff. That prompted the releases, which could worsen flooding downstream. Flood coordinators are advised to monitor conditions along River Drive (south of Caledonia), Sims Lock Road, Grand Sports Road as well as the communities of Cayuga and Port Maitland. The next several days should provide some relief.
The National Weather Service in Omaha Nebraska is now evacuating and shutting down their radar due to a levee failure at the Union Dike, flood waters are now rushing into the warned area.