The Met Office has also issued a yellow rain warning for West Yorkshire, in effect from 9am on Wednesday to 6am on Thursday.
Flooding of a few homes and businesses is possible, bus and train services will probably affected and spray and flooding on roads probably making journey times longer.
The flood alert near Wetherby is in place due to high river levels on the lower River Nidd around Skip Bridge.
Levels are expected to remain high throughout Wednesday.
Flooding to low-lying land and roads is possible.
People living nearby are advised to avoid using low-lying footpaths near local watercourses and avoid driving through floodwater.