A girl who was hit by lightning in Hyde Park is recovering and is now in a stable condition in intensive care.
Roads in north-west London were among those flooded
Two others are also believed to be improving after they were hit during Tuesday's thunderstorms.
A witness said the three 15-year-old cousins were lifted into the air by the force of the strike at 1740 BST.
West London was worst hit by floods and hailstones which caused chaos on roads, trains and the Tube and is still causing disruption at Heathrow Airport.
A London Ambulance Service spokesman said paramedics had risked their lives to treat the girls.
He said: "The storm was still overhead and lightning was still coming down while they were treating the patients."
The girl stopped breathing before the first paramedic arrived, but she is now said to be in a stable condition at St Mary's Hospital in Paddington.
The other two injured girls are said to be "comfortable" after being kept in hospital overnight suffering from minor burns.
A fourth girl who was with them, was not struck but was treated for shock.
Across London, commuters faced a struggle to get home as parts of London Underground's Metropolitan, District, Piccadilly and Central Lines were closed because of floods.
On Wednesday, the Bakerloo Line was still subject to disruption between Queen's Park and Harrow because of last night's flooding.
Problems on the track, which is managed by Network Rail, have also affected Silverlink rail services between Willesden Junction and Wembley.
A lightning strike in Lewisham, south-east London, damaged signal fuses which delayed trains in and out of Charing Cross and London Bridge stations.
And a shopping centre in Staines, west London, was evacuated after heavy rain brought down some shops' ceilings.
London mayor Ken Livingstone said he thought the problems were partially caused by long-term cutbacks in public services.
He told BBC London: "Clearly if you get a whole month's rain in an hour there are going to be problems.
"But the problem's far greater than that. I think the problem may be that a generation ago borough councils regularly cleaned out the drains and the storm drains... far too many now don't do that as regularly as they should and when the rain comes you find the drains are blocked."
He said he would speak to borough councils after the summer break about whether drain cleaning should be increased.