The National Weather Service in North Platte extended the Flood Warning until Saturday morning for the Elkhorn River near Ewing affecting Holt County.
The Missouri River in St. Joseph now expected to have its second highest crest ever by Tuesday at 30.1 feet.
The Missouri River is expected to reach a record crest at Brownville this weekend.
"Runoff will result in flooding in low lying areas, typically prone to spring flooding", the GRCA said in a statement on Wednesday afternoon.
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.
Historic flooding in the Midwest has compromised a dam in Nebraska, killed at least one man and threatened the closure of a nuclear power plant. The city is now working to bolster levees.
The federal agency justifies its ominous reports based on the build up of snow in the northern stretches of the Mississippi River basin, high levels soil moisture, and the current volume of water already moving through the river and its tributaries. They could be tested this year.
The midweek storm crippled parts of Colorado and Wyoming with blizzard conditions.
Wisconsin's governor declared a state of emergency Friday as flooding worsened, and Iowa's governor expanded an emergency proclamation issued a day earlier.
More than 140,000 farm acres are anticipated to be affected by the flooding. Flooding, hail and strong winds also were reported in parts of the two states.
In Omaha, the National Weather Service office was evacuated due to flooding concerns.
When a flood alert is in place, residents are advised to prepare a bag containing medicines, insurance documents and other important items, and to check for flood warnings.
"Turn around, don't drown when encountering flooded roads".