A train headed to Charing Cross hit a tree on Thursday evening, leaving the tree stuck under the train which is now unable to move.
This has left the line blocked at Mottingham in both directions until at least 9pm, affecting Southeastern services.
Meanwhile, Heathrow travellers are still facing delays on the Piccadilly Line with train cancellations hitting services.
Transport for London was reporting minor delays between Acton Town and Heathrow as of 8.45pm on Thursday.
On top of all this, a signalling fault at London Waterloo is also causing disruption.
The fault means trains are unable to use Platforms 1 to 4 at the station until further notice, meaning some services may be cancelled, delayed or revised.
The problem re-occurred on Wednesday afternoon and National Rail has warned the disruption will last until the end of the day.
