Monument Station remains closed and has been for much of the day due to flooding as the heavens opened on the day of the EU referendum; engineers are working to fix the problem.
The Circle line still has sever delays after being suspended earlier on, due to a signal failure caused by flooding at Farringdon.
That signal failure is also causing problems on the Hammersmith and City line, as well as the Metropolitan line, which has no service between Baker Street to Aldgate.
The downpour has failed to damped the Waterloo and City line, though there is no service due to a fire alert at Bank.
The District line has no service between Parsons Green and Wimbledon due to flooding at Wimbledon Park and there are severe delays between Edgware Road and Parsons Green.
Service has been suspended on TfL Rail between Liverpool Street and Ilford and there are severe delays on the rest of the line.
The Bakerloo line has no service between Stonebridge Park and Harrow & Wealdstone due to a signal failure at Stonebridge Park, though there is a good service on the rest of the line.
On the London Overground, there no service Surrey Quays to New Cross due to flooding but good service on all other routes.
The London Fire Brigade have received over five hundred 999 calls as the storm hit London. Firefighters have attended more than four hundred incidents and the worst hit areas have been in the east, including Havering, Barking and Dagenham, Bexley, Greenwich and Lewisham.
A TfL spokesperson said:
We apologise to customers whose journeys have been disrupted this morning. A small number of our stations have been closed or part-closed due to flooding, caused by the heavy rain. We’re working to clear the water as quickly as possible so that services can return to normal. Passengers are advised to check the TfL website and our social media feeds for the latest information.