Train passengers faced major disruption as flooding hit rail services.
No trains are running between Derby and Nottingham due to flooding on the tracks at Draycot, and other East Midlands' services have been disrupted.
In the West Midlands, a "vast amount" of services were cancelled or delayed because of floods and landslides.
The prime minister said an emergency meeting about flooding - which has affected 818 properties across England - would be held.
Boris Johnson said troops were "helping deploy over 20,000 sandbags" in South Yorkshire, where hundreds have been forced to leave their homes.
More than 100 schools in the West Midlands have shut and weather warnings are in place across the country, including Oxfordshire.
Heavy rain has forced a major route into Hull to close in both directions between South Cave and Melton, in East Yorkshire, causing travel disruption.
The A63 is the only link between the M62 motorway and the city. Highways England said the closure was "due to increased flooding from water running off the surrounding fields".
Northern Rail warned commuters not to travel between Sheffield, Gainsborough and Lincoln until further notice.
East Midlands Railway (EMR) said Network Rail was working to lower the water level at the flooded track in Draycott and disruptions would continue through Friday.
Wet weather over the next 48 hours could bring heavy flooding to areas already affected by rising waters, the Environment Agency (EA) said.
The Met Office said yellow warnings for rain for South Yorkshire and the East Midlands meant fast flowing or deep floodwater was possible, "causing a danger to life".
It said further homes or businesses could be flooded and some communities "may be cut off by flooded roads", warning of "heavy and persistent" rain until 22:00 GMT.
"Even some amount of rain could cause rivers to rise," Met Office meteorologist Luke Miall said.
Parts of Lincolnshire and the Midlands could also be affected by rain falling on already saturated ground, the EA said.
In South Yorkshire, which has been badly hit, hundreds of people have had to leave their homes in the village of Fishlake and the Army was deployed to help the relief effort around Doncaster.
About 30 residents have been evacuated from a caravan park in Lincolnshire as a precaution.
The Short Ferry Caravan Park near to Bardney is close to the River Barlings Eau, which burst its banks over the weekend flooding more than 1,000 acres of fields.
Schools are shut in Herefordshire, Worcestershire and Warwickshire along with dozens of road closures.
Several motorists have had to be rescued from their cars with river levels expected to peak on Friday.
Rail services in and out of Birmingham stations are being cancelled or delayed by flooding affecting at least eight different routes with a knock-on effect for other train journeys because of congestion at stations and on the tracks.
Anne Hathaway's cottage in Stratford-upon-Avon was closed on Thursday afternoon because surrounding roads were flooded.
It is not known if the venue will reopen on Friday
In Oxfordshire, fire crews rescued a number of people from vehicles stuck in flood water.
Kate Marks, flood duty manager, said: "The Environment Agency has teams working around the clock on the ground erecting temporary barriers and delivering sandbags to areas expecting further rainfall."
There are 130 flood warnings in place across the country, meaning flooding is expected. Sixteen of those have been issued along various parts of the River Don, while seven are for the River Severn including the Tewkesbury and Shrewsbury areas.
The agency has advised people "to stay away from swollen rivers" and not to walk or drive through floodwater as just 30cm (11.8in) of flowing water is enough to move your car.
About 500 homes have been flooded in Doncaster with 1,200 properties evacuated in areas hit by the floods.
Fishlake has been cut off by the floods and the council said the village was not safe and that residents were advised not to return home.
The EA said it was "currently pumping 1.2 tonnes of flood water every second out of Fishlake".
EA field teams, assisted by our partners at @SYFR are currently pumping 1.2 tonnes of #flood water every second out of Fishlake. Keep abreast of the latest flood information at https://t.co/Rgk2ufgQYU pic.twitter.com/jX6yf3PCnl— Environment Agency - Yorkshire & North East (@EnvAgencyYNE) November 14, 2019
Doncaster Council said roads into the area remain closed, adding: "There is still a lot of deep standing water in the area presenting significant safety risks.
"The advice from South Yorkshire Fire and Rescue is that where you cannot see the ground it is unsafe to walk or drive."
The authority said the EA, along with emergency services, were working hard to make the area safe but "the latest estimates suggest a safe return could be up to three weeks away for some residents".
It said nine hubs had been set up in the town for residents to get help on returning to their homes and how to claim financial support.
More than £190,000 has been donated to an appeal to support flood victims in South Yorkshire as well as £50,000 being pledged from the Red Cross for those affected in Yorkshire and the Midlands.
Peter Pridham, a church warden in Fishlake, said residents had been told the risk of further flooding was "being managed and is manageable".
He said: "We are moving from an immediate emergency to a long-term recovery. It's going to take a very long time to return to any normality."
Personnel from the Light Dragoons have laid sandbags in Stainforth, near Doncaster, in an attempt to shore up the village's bridge.
On Wednesday, the prime minister faced criticism over his response to the flooding during a visit to Stainforth.
One resident told Boris Johnson: "I'm not very happy about talking to you so, if you don't mind, I'll just mope on with what I'm doing."
Mr Johnson said he understood the strength of feeling as "you cannot underestimate the anguish that a flood causes".