Services running through the station will be cancelled, delayed by up to 60 minutes or revised.
All lines are blocked between Leeds and Wakefield Westgate.
Further disruption has been caused due to a boat colliding with a bridge between Leeds and Huddersfield.
Several bridges, including foot bridges, over the River Aire have also been closed due to concern for safety after a large pontoon broke free from its moorings.
People are asked to avoid the area.
The following LNER services have been cancelled:
16:45 Leeds to Kings Cross due 19:27.
17:16 Leeds to Kings Cross due 19:48.
17:47 Leeds to Kings Cross due 20:27.
18:15 Leeds to Kings Cross due 20:41.
Tickets for cancelled services will be valid on services across tomorrow and Tuesday (February 21 & 22).
Northern meanwhile 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 may also be delayed or cancelled.
Disruption is expected until the end of the day.
Support the YEP and become a subscriber today. Enjoy unlimited access to local news and the latest on Leeds United. With a digital subscription, you see fewer ads, enjoy faster load times, and get access to exclusive newsletters and content. Click here to subscribe.