A rare winter flood shut down portions of two interstates on Tuesday, threatened hundreds of homes and caused sewage to flow unfiltered into waterways.

Torrential rains over the past several days pushed already swollen rivers and streams to virtually unheard-of heights in parts of Missouri and Illinois. Record flooding was projected at some Mississippi River towns, and the Meramec River near St. Louis was expected to get to more than three feet above the previous record by late this week.

At least 18 deaths in Missouri and Illinois are blamed on flooding, mostly involving vehicles that drove onto swamped roadways.

The river on Tuesday spilled over the top of the levee at West Alton, Mo., about 30 kilometres north of St. Louis. Mayor William Richter ordered any of the town's approximate 520 residents who had not already left their homes to get out of harm's way.

Missouri Gov. Jay Nixon activated the national guard to assist with security in evacuated areas and to help divert traffic at road closure sites.

In another eastern Missouri town, Union, water from the normally docile Bourbeuse River reached the roofs of a McDonald's, QuikTrip and several other businesses. The river reached an all-time high Tuesday, nearly six metres above flood stage.

Interstate 44 was closed near the central Missouri town of Rolla, and a section of Interstate 70 was shut down in southern Illinois. Hundreds of smaller roads and highways were also closed across the two states, and flood warnings were in effect.

St. Louis in trouble

The River Des Peres is a man-made storm sewer channel that flows through south St. Louis into the Mississippi River, a few kilometres south of the Anheuser-Busch brewery. The channel is deep enough that flooding isn't a concern under normal conditions.

But there is nothing normal about this December flood.

The Mississippi River is expected to reach nearly five metres above flood stage on Thursday at St. Louis, which would be the second-worst flood on record, behind only the devastating 1993 flood.

The high water was blamed on the shutdown of a wastewater treatment plant on Monday just south of St. Louis, causing sewage to go directly into nearby rivers and streams. The Metropolitan Sewer District of St. Louis said the Fenton wastewater treatment plant, which is designed for 27 million litres per day of flow, was treating nearly 96 million litres per day at the time of the malfunction.

One of the two wastewater plants in Springfield, Mo., also failed, allowing partially treated sewage to flow into a river.

Mississippi River in partial shutdown

The U.S. Coast Guard closed a eight-kilometre portion of the Mississippi River near St. Louis due to flooding. Capt. Martin Malloy cited high water levels and fast currents in the river, which is a vital transportation hub for barges that carry agricultural products and other goods.

In central and southern Illinois, flood warnings were in effect a day after a winter storm brought sleet and icy rain. Major flooding was occurring along the Kankakee, Illinois, Sangamon and Vermilion rivers.

An Illinois prison with nearly 3,700 inmates was preparing for possible flooding from the Mississippi River on Tuesday. Illinois Department of Corrections spokeswoman Nicole Wilson says that employees and emergency work crews at the Menard Correctional Center near Chester are filling sandbags and "working around the clock."

The maximum security prison is on lockdown, and visits have been suspended. Officials also anticipate having to bring in hundreds of portable toilets in case the prison's water service is shut down.

Missouri and Illinois weren't the only states dealing with difficult conditions. Heavy rain continued in parts of the South, such as Georgia and eastern Alabama, which has in parts seen more than 35 centimetres of rain since Dec. 21.

Parts of eastern Oklahoma and Arkansas were under flood warnings and flood watches on Tuesday. Up to 30 centimetres of snow was forecast for Iowa and the Great Lakes region, the National Weather Service said.

The severe weather has stranded tens of thousands of travellers during one of the busiest travel periods of the year. As of 9:30 p.m. ET on Tuesday, more than 1,440 flights had been cancelled in the United States and about 8,500 were delayed, according to FlightAware.com.

Severe Weather Missouri

A car is surrounded by flood waters in a trailer park in Pontoon Beach, Ill. on Tuesday. ((Chris Lee/St. Louis Post-Dispatch via AP) )

With files from Reuters