The National Weather Service said the river had crested in the St. Louis area and the Illinois towns of Grafton and Alton farther north.
Friday's tornado was initially rated as an EF3. But the agency upgraded that ranking after surveying damage and concluding that the storm had winds of 295 mph.
The rain finally cleared out by Saturday morning.
Missourian readers have been sending us their views of rain and flooding in Columbia.
A record of 2.51 inches of rain has exceeded the previous record of 1.57 inches in 1969. More rainfall expected Friday afternoon and evening could push the total higher.
Fire Department warns against trying to cross flooded roads.
Residents enjoyed temperatures in the high 80s on Tuesday.
Balmy, seasonal temperatures Tuesday provided a respite from what's been an unpredictable spring in Columbia.
The National Weather Service has issued a winter weather advisory for western Missouri with the possibility for some sleet and snow early Friday in the Columbia area.
Missouri weather is so unpredictable that different weather models could show different projections, and city governments don't know which ones to use.
Heavy rains that caused some flooding in the last week brought drought relief to the upper Midwest, western Corn Belt and central portions of the Plains.
The campus received more than half an inch of rain Tuesday. A short stop-motion video shows colorful rain boots and umbrellas at MU.
There is a 30 percent chance of snow Tuesday in Columbia with snow already falling in northwest Missouri.
The Mississippi, Missouri and other Midwestern rivers in Missouri and at least five other states have surged since torrential rains drenched the region over the past few days.
The weather service warned that sensitive plants could be damaged by the cold temperatures and frost, something Strawberry Hill Farms owner Steven Sapp is monitoring closely.
Columbia Regional Airport has measured more than 3 inches of rainfall since Sunday. If the river gets above 26 feet, pumping will begin at Hartsburg.
Drivers should avoid flooded roads because the depth and force of the water might not be evident, according to a release from Public Safety Joint Communications.
In the Plains and Midwest, seemingly every community was under some sort of watch or warning.
Heavy rain across the Midwest has eased drought conditions in some areas.
Public Safety Joint Communications activated warning sirens across Boone County shortly after 5:15 p.m. Wednesday in response to a tornado warning issued by the National Weather Service for the southeastern part of the county.