Services running through the station will be cancelled, delayed by up to 60 minutes or revised.
The flooding in a tunnel near Shipley is causing the chaos.
Northern are reporting that services towards Skipton and Bradford Forster Square cannot travel beyond Leeds.
The flooding is also expected to cause delays on services running between Leeds - Morecambe and Carlisle.
Services running between Leeds and Ilkley in both directions of travel are still currently able to operate but may be delayed or cancelled.