The A646 Burnley Road between Hebden Bridge and Todmorden was shut when the River Calder burst its bank at Callis Bridge, Hebden Bridge.
And there were also problems on M62 as conditions made driving hazardous.
A number of other roads have been affected by the heavy rainfall but at this stage they remain open.
Calderdale Council's street cleansing and construction teams are out clearing culverts and gullies blocked by leaves to alleviate the problem.
Train journeys through Hebden Bridge and Todmorden have also been hit because of flooding in the Smithy Bridge area, Littleborough.
Journeys may be delayed by up to 45 minutes.
The A646 Halifax Road is shut between the mini roundabout in Todmorden town centre and the turning circle at Hebden Bridge.
Calderdale Council closed the road at 7.10am.
Police received reports of flooding in Charlestown near the Woodman Pub at 6.30am, with people saying they had seen dustbins floating in the water and cars having trouble driving through.
A car was reported stranded in the Woodhouse Road area of Todmorden at 7.20am.
Earlier this morning the Environment Agency has the entire upper River Calder catchment are at Flood Watch status - in which road flooding and flooding of low lying land is expected. As of 8.10am these had not been extended to Flood Warning, in which homes may be affected.