Northern has issued a ‘do not travel’ notice on the Manchester Victoria to Chester route, through Warrington Bank Quay.
This is due to train crew shortages, the operator says.
A spokesman said: “Due to train crew shortages across west and central depots, the following routes are ‘do not travel’ routes, and replacement road transport will not be provided.
“These are Manchester Piccadilly to Stoke-on-Trent, Manchester Victoria to Chester via Warrington Bank Quay, and Manchester Victoria in general.
“Ticket acceptance has been arranged on Transport for Wales services from Manchester to Chester and Crewe, and TransPennine Express services from Liverpool to Manchester.
“We encourage everyone to plan ahead and check journeys before travelling, particularly last trains of the day, which may be earlier than usual and may be cancelled at short notice.
“If you do travel, please leave yourself plenty of time to do so, and do not rely on last services.
“Trains currently showing may not run. Our control teams are working to update the train plan, but you should check closer to the time of travel.”
Meanwhile, most services will not run to Liverpool Lime Street station today as Network Rail carries out ‘essential work’ in the area.
Signals are being replaced in Edge Hill and on Runcorn Viaduct, and track will be renewed in Mossley Hill.
Because of the complicated layout of the track in the area, most lines into Liverpool Lime Street station need to be closed to allow the work to be carried out safely.
Liverpool Lime Street station will be open for retail, rail replacement services and access to the Merseyrail network, which is unaffected.
Passengers are advised to check National Rail Enquiries or with their train operator to plan their specific journey ahead of time.
Hayley McMahon, project manager at Network Rail, said: “We are very sorry to passengers whose journeys will be affected by the work.
“The signalling upgrade is necessary to allow trains to run safely and reliably into Liverpool for years to come.
“I would advise all passengers to plan their journey in advance as timetables will be amended.”