Red “immediate action” flood warnings were issued for parts of south-east London and Essex as parts of the capital were expected to see a month's rain fall in a matter of hours.
The RAC said it had seen a surge in calls for assistance as a result of the weather.
London Fire Brigade (LFB) received hundreds of calls to reports of weather-related incidents, including lightning striking property, flooded homes and businesses and rising waters trapping vehicles.
It comes after rain and muddy conditions caused traffic problems for revellers heading to Glastonbury music festival, with some drivers facing delays of up to 12 hours.
RAC spokesman Simon Williams said: “We have seen a massive uplift in calls for help with hundreds of extra breakdowns in London, Kent and East Anglia as motorists suffer the consequences of flash floods and the knock-on traffic delays.
“Alternative routes have become badly affected by the sheer volume of vehicles as drivers try to avoid the jams, and sadly this has led to yet more breakdowns.
“In the South West the situation around Glastonbury continues to be a challenge and we are working to help those who have broken down en route to the festival.”
In just one hour, 20.5mm of rain fell in Bexley, East London, close to half the June average, with some parts expected to see multiple showers bringing a month's rain on Thursday morning.
The Environment Agency has issued four flood warnings covering rivers in Bromley, Sidcup and Basildon, and 22 flood alerts across parts of the South East.
Showers were expected to ease by Thursday morning before returning with similar intensity from 2pm.
The Met Office issued an amber “be prepared” warning of rain for parts of Kent, Sussex and Surrey effective until 6am on Thursday, while a yellow warning covering the South East is in place until 6am on Friday.
Many of London's roads were affected by localised flooding, including the North Circular which was closed at Waltham Forest.
In Battersea, flood waters rose steadily after heavy rain began to fall after midnight, eventually flowing at knee height into ground floor homes on one street.