On Monday, the South East was the worst hit as flooding in Kent closed all lines through Orpington railway station for several hours, while police shut a section of the M25 overnight after discovering two sinkholes on the central reservation.
The motorway was closed in both directions and Highways England warned it was expected to remain shut throughout most of this morning.
National Rail has also warned that Southern and Thameslink trains will be heavily impacted during the morning commute, with some services delayed or cancelled due to flooding.
Today, northeastern parts of England and the Midlands are expected to bear the brunt of the downpours, with a yellow warning in place until midnight.
Some areas set to see up to 60mm of rain, particularly over the first half of the day.
Another warning covers Devon and Somerset, where similar conditions are expected.
A total of 31 flood alerts - which mean flooding is possible - are in place across the country.
The Environment Agency has issued three flood warnings in southeast England, for the River Wandle in Morden, south London, the Emm Brook in Wokingham and Ravensbourne in Bromley.
The agency said on its website: "River levels have risen as a result of localised thunderstorms. Flooding of property is expected imminently. Please take action."
On Wednesday and Thursday, some parts of the UK could be struck by 60mm to 80mm of rain, and possibly even up to 100mm.
Met Office meteorologist Alex Burkill described the figures as the "worst-case scenarios" but added that people needed to "be aware that we're in for some treacherous weather".
"If you add it all up some places are likely to see over 100mm this week, which is around double the average they would get in the whole of June."