Services out of Leeds to Ilkley and Skipton were halted on Sunday night after flooding on the line at Kirkstall.
No services ran on Monday morning and Northern rail says it will be “at least” 3pm before any trains can run - signalling chaos for the afternoon rush hour.
National Rail later tweeted that the disruption would last “until end of service”.
Problems were compounded when Northern Rail announced on Monday it would not lay on replacement bus services - despite promising a bus for passengers on Sunday - forcing travellers into their cars and regular buses.
Commuters who tried to divert to the Harrogate rail line found the road blocked at Pool-in-Wharfedale.
There was standing room only on many rush hour buses this morning as they made their way through often gridlocked main routes.
YOUR TRAVEL OPTIONS
• A service is running from Bradford Forster Square to Ilkley and Skipton. It is possible to take a train from Leeds to Bradford Interchange and then walk for ten minutes across Bradford Forster Square station.
• The Leeds-Harrogate line is running. Closest stations to those affected are at Horsforth and Weeton.
• Take the bus: Normal services are operating, subject to flooding on local roads.
Northern Rail has made no mention of refunds for season ticket holders.