Passengers have been told that disruption is set to continue into tomorrow after the River Don burst its banks across the region.
Northern is advising customers to check carefully before travelling this afternoon as flood water continues to cause problems on a small number of routes across the north of England.
Customers are being advised not to travel on some routes until further notice after inspections took place earlier today.
Despite improving weather in many areas this morning there remains potential for disruption to services throughout the day on Friday and, possibly into the weekend.
Northern customers are advised to allow extra time for travel and to check ahead.
A Northern spokesperson said: "The Friday afternoon peak will still see disruption on several routes and disruption is likely for the rest of the day in some areas.
"We are still advising customers on a small number of routes in South Yorkshire - not to travel as flooding is making rail and road travel extremely difficult.
"Colleagues at Network Rail have inspected the tracks and working hard to return them to normal working, but at present we have no estimate as to when we will be able to operate services on the affected routes."
The spokesperson added: "Northern would like to thank customers for their understanding and patience as we continue to try to run as many services as possible."
Customers are advised not to travel on the following routes until further notice:
Sheffield - Lincoln/Gainsborough, there is currently no estimate for when the line will re-open (ticket acceptance is in place on East Midlands Railway between Lincoln - Nottingham/Newark/Doncaster and on LNER between Newark Northgate - Doncaster and Retford - Doncaster)
Sheffield - Leeds via Moorthorpe, route is expected to be closed until Saturday 9 November
Sheffield - Goole
Sheffield - Doncaster, route is expected to be closed until Saturday 9 November
There are also problems still affecting other lines in the North:
Flooding has been reported at Garforth with speed restrictions in place on the line towards Leeds. The line towards York is open an operating as normal.
Doncaster - Scunthorpe will not call at Kirk Sandall due to flooding.
Flooding on the Calder Valley (between Todmorden and Hebden Bridge) has subsided with services now running at normal speed between Manchester Victoria and Leeds. Residual disruption is expected until the end of day.
Flooding on the Penistone line has now cleared meaning services are, once again, operating between Huddersfield and Sheffield. The Hope Valley line is also fully open.
Flooding has also subsided at Adwick meaning services are now running between Leeds and Doncaster. Northern ticket holders will be able to use LNER services on this route.
For up-to-the-minute train running information please check National Rail Enquiries.