A family caught in London floods were forced to break a window before abandoning their car.
It comes as 11 areas in the east, south east and London have been warned by the Met Office to expect heavy rain and storms between 11am and 10pm today, with as many as two inches forecast to fall.
Flights from Gatwick have also been affected and parts of the M25 have been closed.
The Met Office warned: "Heavy showers and thunderstorms are expected to break out today leading to some flooding and disruption.
"Some places will miss these, but where they do occur, 30 to 50 mm of rain could fall in less than an hour and a few places may see in excess of 100 mm in a few hours where storms are slow moving. Lightning and hail will be additional hazards.
"Showers and storms will slowly die out this evening."
In a tweet, Gatwick Airport warned that the weather conditions are likely to cause delays and cancellations to flights. It said: "Air traffic control restrictions are currently in place across the South of England and parts of Europe due to poor weather conditions.
"This will unfortunately cause delays and cancellations to some flights today."
On the M25 two lanes are closed clockwise between J11 and J12 and between J22 and J23.
After weeks of dry conditions the deluge is expected to cause flooding in several areas, with power cuts also feared.
Among the areas affected by the amber alert is London, with residents and commuters warned of possible disruption owing to the conditions.
People in rural areas may also be cut off by the deluge of water after weeks of bright sunshine and high temperatures.
A separate yellow thunderstorm warning remains in place for nearly half the country, with forecasters extending it further north to include southeast Wales
A spokesman added: "The yellow area has been extended northwestwards to cover more of England and moving into southeast Wales, the start time brought forward, and the likelihood of impacts increased."
