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Passengers are being warned of severe disruption on the rails as flooding and signalling issues continue to cause problems.
Southeastern has tweeted to say commuters trying to get home to Kent can use London Underground and the DLR at no extra charge between London Stations.
The company also says commuters can use the high speed at no extra charge, although St Pancras is very busy.
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Heavy rain is continuing to batter the county, with a yellow warning in force, predicting more heavy, thundery downpours later.
Emergency crews have been out in force helping people affected by flooding, and commuters have been hit with significant delays on the rail network.
Many services have been diverted due to a major signalling problem at Cannon Street caused by torrential rain.
Cannon Street and London Bridge stations were closed for most of the day, but reopened just before 5pm - although delays remain.
Flooded tracks in south west London are also having a knock-on effect.
Southeastern issued an apology for the "significant delays" across the network.
"The torrential rain and heavy thunderstorms overnight have caused significant delay across our network" - Southeastern spokesman
A spokesman said: "We would ask passengers to please bear with us. The very heavy torrential rain and thunderstorms have caused a great deal of issues across our network and these have continued throughout the day.
"We would urge people to please leave extra time for their journeys home tonight and check before they travel."
A spokesperson for Network Rail added: "Our engineers have been out in force today working at locations across the south east with heavy duty equipment to clear flood water and repair damage to lines.
"We are working hard to keep trains running and to get users of the railway home safely tonight.
"We understand that passengers have faced delays and disruption to their journeys today, and advise them to check before they travel before making further journeys, either with their train operator or with National Rail enquiries.
"There is more severe weather forecast this afternoon so further disruption going into the evening peak is possible."
A Met Office expert said scattered thunderstorms are likely to break out from this afternoon and into tonight.
A spokesman said: "Please be aware of possible disruption to travel and localised flooding as well as frequent lightning.
"Where thunderstorms occur torrential rain and frequent lightning are expected, as well as a chance of some hail.
"Thirty milimetres or more of rain could fall in an hour and locally in excess of 50mm is possible in two or three hours."
Overnight, firefighters received several calls about flooding in areas including Eastchurch, Herne Bay, Margate and Cliftonville.
Crews were called to Crown Road in Sittingbourne just before 4am to pump water away from homes.
They also attended Staplehurst Road in Sittingbourne after floods caused a storm drain to lift, leaving a two foot round hole in the road.
The used tools to retrieve the drain cover and secure it back in place.
Part of Herne Bay station has also been flooded this morning.
A photo tweeted by @hernebaybob this morning shows a rail commuter wading through floodwater after heavy downpours caused the underpass the fill.
A lightning map shows severe thunderstorms heading to the county later.
Toby Howe from Kent Highways said: "Overnight we have had additional crews on call.
"We have had tankers on locations to deal with what it's possible overnight, however a lot of the problems are only apparent as we get to daylight."
Eight flood alerts are also in place across the county.
Kent Fire and Rescue Service is warning people to follow safety tips in the event of flooding, including calling 999 if there is a risk to life or serious property or environmental damage.
Residents are advised to know how to turn off gas, electricity and water before water enters the home, and to help neighbours.
Avoid walking or driving in or near flood water and keep children away from flood wate, as there could be hidden dangers like sharp objects, raised manhole covers and pollution.
The storms followed a tranquil evening across the county, with KentOnline readers reporting spectacular sunsets.
A yellow weather warning for heavy rain is in place until 2am tomorrow, but parts of Kent face an amber warning - from 3pm to 11pm.
For more advice, visit the Environment Agency website for flood warnings or call 0845 988 1188.