Areas in and around the capital had been facing potential flooding during afternoon downpours on Tuesday.
The Met Office has issued new amber thunderstorm warnings for parts of south-eastern England between 4pm and 7pm.
Forecasters warn of water spray, sudden flooding and lightning strikes, which could lead to power cuts, damage to buildings and delays to public transport.
It comes as the UK recorded its hottest day of the year so far, after the temperature reached 32.2C (89.96F) at Heathrow Airport in west London on Tuesday afternoon.
The previous high for the year was 31.6C, which was also recorded at Heathrow on Sunday.
An amber extreme heat warning is also set to last until Friday, with the mercury expected to climb as high as 33C in parts of the country.
The thunderstorms could echo the flooding witnessed last week in London and the South East, which affected several Underground stations.
Dan Stroud, a Met Office forecaster, told the PA news agency: "We have issued some new amber thunderstorm warnings for parts of south-east London, down to parts of Essex and Kent.
"There is also one in place for areas surrounding Cambridgeshire.
"We're seeing some fairly heavy showers developing during the afternoon along with reports of lightning and hail.
"There will be some intense spells of heavy rainfall as the afternoon develops and some slow-moving downpours, some places will see it, others won't at all.
"There may be some localised flooding issues as a fair amount of rain will fall - meaning possible delays to public transport, power cuts and potentially surface flooding."
Mr Stroud said the recent spell of hot weather has drawn in moist air to eastern parts of the country, which is causing the downpours.
He said as much as 40mm-60mm of rain could fall in one hour, with some areas seeing a "substantial" amount.
Commuters may be the worst affected by the downpours, with South Western Railway reporting a track circuit failure at London Waterloo.
The Environment Agency has issued 16 flood alerts for Tuesday - meaning flooding is possible - in parts of London, Nottinghamshire and Derbyshire.
Mr Stroud added: “If you get heavy rain you’ll certainly know about it, but the rest of the country is continuing to bask in dry skies and warm temperatures.
“We’re seeing the warmest temperatures in south-western areas and parts of Wales.”
The Met Office has issued an amber extreme heat warning for parts of Wales, all of south-west England and parts of southern and central England over the next few days.
Public Health England has extended its heat-health warning, which warns people to take measures to stay cool and look out for vulnerable people, until Friday.
Where are the flood alerts in London and south east?
Kingston upon Thames
Richmond upon Thames
Ewell to Kingston upon Thames
Oxshott to Thames Ditton
Silk Stream and the Deans
River Pinn and Woodridings Stream
Lower Lee tributaries
Rivers Beam and Rom
Shuttle and Cray
The government’s Flood Information Service will be updated by 9am on Wednesday or earlier if the situation changes.