Rail passengers have endured a second day of disruption, this time caused by severe winds and flooding rather than power outages.

After travellers recovered from delays of up to 12 hours on Friday following the National Grid failure, weather caused chaos in the national rail network, ports and roads.

The most high-profile victim was the west coast mainline between Scotland and England, closed after a foot of water submerged tracks between Carlisle and Lockerbie. Earlier, Network Rail imposed speed restrictions on many routes, particularly in coastal areas, where winds reached 60mph and several uprooted trees blocked lines.

Passengers trying to cross the English Channel were delayed by up to five hours by the high winds. Ferries queued outside the port of Dover until tug boats could guide them in. In central London, gusts felled a massive tree in Russell Square, blocking a road and diverting bus routes.

Weather warnings were issued for much of the UK with forecasts of thunderstorms in Scotland and Northern Ireland and strong winds across Wales and most of England.

As the latest disruption unfolded, travellers stranded in trains outside London on Friday for more than eight hours spoke of their frustration. At King’s Cross station, closed on Friday evening to avoid overcrowding, passengers exchanged horror stories from the day before.

Joshua Carr, a stage manager, told the Observer he had been trapped on a train from Edinburgh to King’s Cross for nine “painful” hours. “We didn’t move for three hours and didn’t arrive until 1:45am,” he said.

A freelance journalist travelling to London from Scotland described being stuck for more than 12 hours after the train left Edinburgh. Dayna McAlpine said her London North Eastern Railway train, stationary for hours outside King’s Cross, quickly ran out of provisions: “We ran out of food around 7pm – parents were going up and down the train carriages looking for food for their children.”

As rail bosses struggled to get the network running, a watchdog urged rail passengers to claim compensation. David Sidebottom, director of independent transport user group Transport Focus, said: “Passengers who heeded advice not to travel should claim delay-repay compensation to get their money back, including those using a season ticket.”

Across most of the country, the weather is likely to be more settled today with showers and some patches of sunshine breaking through.