Traffic is moving slowly in both directions on the A639 near Rothwell due to flooding. A crash on the A61 Wakefield Road is also affecting traffic travelling both ways.
Flooding has also hit traffic on the A644 Wakefield Road near Huddersfield, between the A62 Cooper Bridge Road and the M62 motorway.
A flood on the A6178, Rotherham, has closed the road in both directions near the Magna Science Adventure Centre.
The A616 in South Yorkshire is closed in both directions between Flouch and Stocksbridge due to flooding. South Yorkshire Police and Highways England are working to clear the road.
Flooding has also been reported on the A61 Westwood New Road, South Yorkshire.
In York, traffic lights failed on the A19 at Bootham, and on the A64 heading out of the city towards North Yorkshire, the AA reported.
In North Yorkshire, the A66 has been closed in both directions between the A1M at Scotch Corner and A67, Bowes, after a crash.
The A66 is also closed between the junctions for the A685, Brough, and the A67, Bowes. Highways England said drivers should use the A69 or M62 as an alternative route.
Strong winds have also been slowing traffic on the M62 near Howden, East Yorkshire.