Commuters have faced a struggle to get into work this morning.
Train operators are warning passengers not to travel on a number of routes through Yorkshire and the North West.
This includes lines from Sheffield to destinations such as Leeds via Moorthorpe, Lincoln, Doncaster and Goole.
Trains are also unable to run on routes such as Manchester Piccadilly-Cleethorpes, Leeds-Doncaster and Hebden Bridge-Rochdale.
Rail replacement bus services are not being provided due to road closures and unsafe driving conditions.
Rail firm Northern warned that disruption could continue into the weekend despite the weather improving in many areas.
A spokesman said: “We are still advising customers on several routes not to travel as flooding is making rail and road travel extremely difficult.
“Colleagues at Network Rail are inspecting the tracks and working hard to return them to normal, but at present we have no estimate as to when we will be able to operate services on the affected routes.”
He added that Northern will “try to run as many services as possible”.