Following the derailment at Selhurst and the signal failure at London Blackfriars and Norwood Junction, GTR took the decision to issue a “do not travel” alert.
Passengers were urged to avoid using the network “if at all possible” in order to manage demand for the services.
The derailed train blocked the depot, preventing other trains from leaving. Images taken showed the train remained upright and there were no confirmed injuries.
BBC London has been told that the derailed train will be moved on Wednesday night.
A spokesperson for Thameslink said there would be 134 trains out of position overnight, and drivers would have to begin Thursday’s service in different locations.
This could lead to some disruption in the Thursday morning rush hour. Passengers were advised to check before they travel.
National Rail Enquiries said the signalling fault meant fewer rail lines were available for use and trains running on the available lines had to run at slower speeds than normal on Wednesday.