Train services between Doncaster and Hull are affected after heavy rainfall hit parts of the region over the weekend.
Northern rail said services to Hull would terminate at Doncaster and restart at Goole, with disruption expected to last all day.
A bus service is in operation between Doncaster and Goole.
The Environment Agency said seven flood warnings were currently in place along the River Don.
A further warning, meaning flooding is expected and action is required, remains in place for the River Trent at Beckingham Marsh.
On Sunday, the Environment Agency said levels on the River Don reached 15.5ft (4.73m) with usual levels up to 11.8ft (3.6m).
South Yorkshire Police said roads were also closed in some parts of Doncaster.