Two east London hospitals have asked patients to stay away after their emergency departments were hit by flooding on Sunday.
Ambulances are being redirected after torrential rain caused severe flooding in homes, roads and stations.
London Fire Brigade says it has taken more than 1,000 flooding-related calls.
It rescued people trapped in cars and is helping those with flooded basements and collapsed ceilings.
A spokesperson for Barts Health NHS Trust which runs both Newham and Whipps Cross hospitals, said: "Patients are asked to attend alternative hospitals where they can. A major incident has been called across the Trust."
Many of the capital's roads closed due to the flooding, including the Blackwall Tunnel, the A12 and parts of the North Circular.
Stepney Green station remains closed although eight other Tube and London Overground stations have reopened.
A yellow thunderstorm warning remains in place for parts of south-east England.
St James's Park in London saw 41.6mm (1.6in) of rain on Sunday, making it the wettest part of the country.
Residents on a street in Woodford, in east London, grabbed buckets, brooms and wooden boards to prevent rising rainwater from flooding their homes.
Restaurant manager Mariya Peeva said her neighbour's bedroom was flooded and that her son helped others to protect their homes from the flooding.
Ms Peeva, 46, told the PA news agency: "My son went to buy some food from the local shop - by the time he came back the whole street and the pavement were already flooded and the water was coming into our front door."
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At the scene: Greg McKenzie, BBC News
The A&E department at Newham Hospital is still closed this morning, with ambulances being diverted to neighbouring hospitals.
As you peer through the doors of the A&E department here, the entire floor is soaked as far as the eye can see.
There are mops left on the floor, security guards are guiding people away.
The hospital says it will still treat the most urgent admissions but is advising people to use other hospitals until it fixes the rainwater damage.
Other parts of the hospital, such as the maternity unit, remain unaffected.
Resident Chris Date tweeted a photo of a bus in Bakers Arms, Walthamstow, saying the flood water was "above the kerb".
"It's impossible to walk on the pavement. To get on that bus the water came up to my shins. This is a canal, not a road," he said.
Cyclist Eddie Elliott, 28, said he had passed the area near Queenstown Road station in Battersea to find the road "totally shut down".
"Having been born and raised in London, I have never seen anything quite like it," he said.
Mr Elliott said the flooding was the worst he had experienced in the city, and described seeing "buses stood broken down in the water".
Standon Calling festival in Hertfordshire was abandoned due to Sunday's flooding.
The Environment Agency has six flood warnings in place. They are for two areas in London, near Beverley Brook at West Barnes and Worcester Park.
The further warnings are for:
- Stour Brook from Haverhill to Sturmer -Suffolk
- Bumpstead Brook through Steeple Bumpstead to New England - Essex
- Monktonmead Brook at St John's - Isle of Wight
- Whitwell, Wroxall, Langbridge and Alverstone on the Eastern Yar - Isle of Wight
A further 19 less severe flood alerts have also been issued, covering most of the capital and parts of surrounding counties.