London Underground said 29 stations had to be closed as crumbling Victorian drains and pumps failed under the strain.
Parts of the District, Circle, Central, Hammersmith and City, and Metropolitan lines ground to a halt. The East London line was suspended from New Cross to Shadwell.
London Underground said it was one of its worst floodings. Last August it warned that unless ageing infrastructure was replaced and pounds 18m spent on urgent remedial work it would be a case of 'no drains - no trains.' Because of government funding restrictions it could only spend pounds 9m on new pumps and repairing drains. This year's budget is pounds 6m, although it believes pounds 17m needs to be spent.
The spokeswoman added: 'Every day we have to pump three million gallons of water out of tunnels and stations.
The city's groundwater is rising and about 77km of track drains made of brick, clay and concrete are vulnerable to fracture.'
A limited repair programme failed to avert the shut down of Richmond, Kew Garden, Gunnersbury, Baker Street, Great Portland Street, Euston Square, Kings Cross, Barbican, Moorgate, Liverpool Street, Aldgate, Marble Arch, Lancaster Gate, Queensway, Holland Park, Shepherd's Bush, White City, Notting Hill Gate, Westminster, South Kensington, Victoria, Kennington, and Temple. There was no District line between Turnham Green and Richmond. Hammersmith and City lines stopped from Baker Street to Aldgate. Central line services were suspended between White City and Marble Arch and District and Circle lines closed at Victoria and Kennington.
The London Weather Centre said two inches of rain had fallen, and the problems arose when the two thunderstorms swathed over the city where water could not disperse.
Forecaster Bob Prichard said: 'There was more rain in 24 hours than in June and July put together. Previous storms seemed to by-pass central London, quite simply it was our turn.' He said that the next few days were due to be dry. Thames Water says it will not reimburse sewage flood victims because it had been caused by exceptional weather.
Hammersmith was badly affected, with 70 reported cases of basement sewage floods - some up to four feet deep. Sewers also burst in Islington at the junction between Clerkenwell and Caledonian Roads.
Thames Water said: 'London has a combined sewerage system, taking both foul and surface water, allowing the sewers to fill up rapidly when exceptional weather conditions occur, and we had exceptional weather last night.'
Hammersmith council, contracted to work on the sewers on behalf of Thames Water, said: 'We've got emergency teams all over the borough at the moment trying to pump out the sewage. We are doing what we can, but the main is over 100 years old and it cannot cope with the rainfall.'
The National Rivers Authority said this storm was of an intensity that would be likely to recur only once in every 40 years. It said 48.3mm of rain fell in Holland Park in less than an hour on Wednesday. In Deptford 47.6mm fell in 16 minutes. Yesterday morning 40mm fell on Deptford in 15 minutes.
London Fire Brigade received more than a thousand telephone calls between 11pm and 2am during the downpour on Wednesday night. Pleas for help continued non-stop from early yesterday. A spokeswoman said:' We've had hundreds of calls about flooding in basements. Also a few burglar alarms have been activated because of the wet.
The RAC said: 'Worst hit areas have been west London and the M25 where drivers have had to put up with severe congestion.' Among roads closed were the A406 North Circular at Willesden and the A40 at Perivale.
9am: High Street Kensington Tube station was awash with bedraggled commuters pouring from abandoned trains and running for buses and taxis, writes Matthew Brace. They harangued guards and demanded complaint forms.
Passengers on a crowded District Line train from Earls Court were trapped in a tunnel for over 35 minutes when signals failed at Gloucester Road.
The atmosphere was sticky, and conversation scant. The slim carriage windows had stuck fast and no amount of frenzied pushing by two determined businessmen would shift them.
Notting Hill Gate was evacuated as water poured through the roof on to platforms. 'It's like Niagara up there, one official said.
One driver shrugged as he stared at the rain rushing off his cab roof. 'This is one of the worst mornings I've had and I've been in this job for more than 20 years. I'm not even sure where this train's going now.
In the ticket hall queues intertwined across wet flagstones. The lines for telephones were 20 people deep and for ticket kiosks twice that.
A guard summed up his morning: 'Chaos, absolute chaos. I've lost count of the number of stations that have been closed. Signals are out all over the place, trains stuck in tunnels - bloody awful.'
Outside a cab driver said: 'You think it's bad here, you want to see it up Liverpool Street. You don't need a car to get out of there - you need a bloody boat.'
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