Virgin Trains is advising customers not to travel between Scotland and England, after a fallen tree closed the west coast main line north of Carlisle.
The rail operator said ongoing disruption on the east coast main line made it impossible for passengers to use the route as an alternative.
Network Rail said it had engineers on site attempting to repair the damage.
The problems on the east coast main line were caused by damage to overhead lines and a fatality near Newcastle.
Passengers on one train leaving Edinburgh Waverley reported a four-hour delay and overcrowded carriages.
Virgin Trains said the services on the west coast main line were delayed as a result of the fallen tree between Carlisle and Lockerbie.
It was reported to Network Rail at 10:00 and engineers spent the day cutting back vegetation and repairing overhead wires which were damaged.
The disruption also led to long queues at Carlisle station.
A spokesman for Virgin Trains said: “The closure of our route to Scotland is causing significant disruption and we want to apologise to all our customers affected by this.
“We’re doing our best to help people complete their journeys but would advise anyone who has not set off on their journey to either wait until the disruption has cleared, travel tomorrow or get a refund.”
It came as the Met Office issued an amber warning for heavy rain which could cause flooding and transport disruption to south east Scotland.