East Coast Trains were running a restricted service between York and Darlington at the end of a day of flooding throughout the North East.
Signalling problems and points failures, caused by water on the line north of Northallerton, meant the service between York and Darlington had to be suspended earlier.
By the evening, some services were running again between Newcastle and Edinburgh.
One of the two tracks was back in operation, allowing East Coast to operate an hourly service in each direction. An amended timetable is operating between Newcastle and Edinburgh.
East Coast passengers with tickets for Tuesday, September 25, can travel without restriction on Wednesday, September 26.
It is hoped that there will be further improvement to services tomorrow, and travellers are advised to check before making their journey, and delaying any journeys if possible.