A yellow rain warning has been issued by the Met office for South and West Yorkshire.
Train operator Northern has also warned customers in South Yorkshire to expect disruption into rush hour on Monday.
Inspections on routes still affected by flooding have taken place this morning with reports there is still a "significant amount of work required" before the tracks are cleared for trains.
Northern said it is working closely with colleagues at Network Rail to return normal working to the railway as soon as possible, but conditions remain challenging.
Until further notice customers are still being advised not to travel on some routes in South Yorkshire.
Northern customers across the network are advised to allow extra time for travel and to check ahead as there remains potential for disruption to services and timetables may be amended on some routes.
Doncaster - Scunthorpe, due to flood water at Kirk Sandall the line remains closed with no estimate as to when the route will re-open.
Sheffield - Goole, flooding continues to cause issues and there is no current estimate for when the route will re-open. Northern customers may travel on TPE services between Leeds and Hull, using Northern services between Leeds and Doncaster.
Sheffield - Doncaster, due to severe flooding at Rotherham and between Mexborough and Conisbrough disruption is expected to continue. Further work and testing will be carried out on Sunday with services unlikely to be reinstated before Monday morning.
Sheffield - Leeds via Moorthorpe, flooding at Rotherham Central means services will not call at Rotherham until further notice. The line at Rotherham will be closed until at least Tuesday.
For up-to-the-minute train running information please check National Rail Enquiries.