Train services to Leeds, Bradford and Skipton have been suspended because of flooding on the line at Cononley.
Earlier flooding at Hellifield had closed the line between Skipton and Hellifield, affecting the services to Carlisle and Morecambe.
Northern says no alternative road transport is being provided because of the flooding, and passengers are advised not to travel.
Storm Ciara has also brought problems to many roads, with the A6068 flooded north of Cowling as well as the A65 at Chelker, Keighley Road in Skipton near to McDonalds, and Skipton Road in Keighley close to Greenhead Lane.
Bus services are affected as a result. The 62 and the 66 are diverting via the A629 Keighley to Steeton bypass to avoid the flooding at Beechcliffe. The 62 will continue to serve Steeton Top and Airedale Hospital.
A number of houses in Silsden have also been without power and Silsden Beck remains subject to a Flood Warning, meaning residents and businesses close to the beck should take action to protect their property and possessions.