More flooding is expected to hit parts of England in the early hours of Friday before outbreaks of heavy rain start to ease, according to the Met Office.
The forecaster issued an amber warning for areas of the Midlands and the south of the country, which came into force at 6pm on Thursday and will last for 12 hours.
Yellow rain warnings were already in place for large parts of England and Wales and western parts of Northern Ireland.
Areas affected by the amber warning – including Milton Keynes, Oxfordshire, Cambridgeshire, Leicestershire and the West Midlands – were struck by flash floods as the Met Office warned the regions could see 30-40mm of rainfall within three hours.
Meteorologist Greg Dewhurst told the PA news agency that northern and central parts of England and Wales had been hit the hardest, with rain expected to move further south overnight and into Friday morning.
He said: “There will continue to be localised flooding. A lot of these areas have been hit by rain in the past few weeks which means the ground is already saturated.
“The amber warning is in place until 6am and the wider yellow warning will be lifted at 9am. We’re expecting it to then ease up and become a bit drier.
“But rivers often take time to respond so we’re expecting disruption to continue in central and southern parts throughout the morning. Those planning to travel on Friday should factor this into their journey times.”
As of 11pm, the Environment Agency had 49 flood warnings in place across England, meaning flooding is expected, and 120 flood alerts, meaning flooding is possible.
Recent flooding in areas including Bedfordshire, Northamptonshire and Oxfordshire have brought widespread travel disruption and damage to properties.
According to the Met Office warning, the weather could lead to difficult driving conditions and road closures, homes and businesses are likely to be flooded and there is a “good chance” some communities will be cut off due to floods.
(PA Graphics)
Delays and cancellations to train and bus services and power cuts are also likely while footage shared on social media showed cars battling through partially submerged roads.
Councils and emergency services in Northamptonshire and Hertfordshire confirmed a number of road closures and reassured residents they were working to keep people safe overnight.
Tewkesbury Borough Council, in Gloucestershire, has been handing out sandbags to residents to help protect their homes against flooding.
Parts of the country saw more than the monthly average rainfall on Monday, with flash flooding damaging homes and disrupting travel.
AFC Wimbledon were due to play Newcastle in the third round of the Carabao Cup on Tuesday but it was called off and rescheduled after the Cherry Red Records Stadium was hit by flooding and appeared to have a sinkhole in the pitch.
Firefighters and police worked late into Tuesday night to evacuate residents after flooding at the Billing Aquadrome holiday park.
There were further downpours on Wednesday evening.
Around 385 properties were flooded in Hertfordshire, Bedfordshire, Northamptonshire, Kent and the Home Counties, according to the Environment Agency.
The rain is expected to clear during Friday leaving conditions much colder on Saturday.