Trains between Ilkley, Skipton and Bradford Forster Square were expected to remain closed all day while Network Rail teams pumped water from the railway line.
The line has now reopened and the tracks have been checked for any damage.
Northern has confirmed the line is safe for trains to pass, however a full service is not expected to run until at least 5pm.
Passengers are advised to check before they travel.
Matt Rice, Route Director for Network Rail’s North and East Route, said “Storm Ciara has caused widespread disruption across the country and our teams have been working nonstop to keep passengers moving safely.
“We are pleased to confirm that the line has now reopened at Kirkstall following severe flooding. Whilst the line has reopened, a full service isn’t expected until later this afternoon, so we encourage all passengers to check their journeys before travelling.
“We would like to thank passengers for their patience, as we work with train operators to get a full service running as soon as possible.”