Several routes were affected, with the deluge blocking the route between Wigan Wallgate and Southport after a landslip near Burscough Bridge.
Journeys between Bolton and Preston and Bolton and Clitheroe were also badly hit.
Northern updated the following services at 6.30pm:
Wigan to Kirkby – flooding at Up Holland has subsided and trains are now running, though delays and cancellations are possible.
Wigan to Southport – a landslip has caused the complete closure of the line, this will continue to affect services between Southport and Alderley Edge, and Southport and Stalybridge.
Chorley to Adlington – previous flooding at Yarrow viaduct has subsided and services are now operating, though delays and cancellations are possible.
Flood water started to rise in the area this morning and as levels rose above the tracks, it became impossible to run services on the affected routes.
Chris Jackson, Regional Director at Northern, said: “Unfortunately, because of the rising flood water, we were unable to run our usual services on several routes which had – and continues to have – a significant impact on our customers.
“Colleagues from Network Rail have worked hard to reduce the water levels and return rail services to the route.
“As that work continues, I am again calling on our customers to please be patient. Where we can’t run trains we will operate buses to keep people on the move, but these will add extra time to usual journeys.”
Delay Repay compensation is available for any customers whose journeys are delayed by 15 minutes or longer this afternoon.
To make a claim visit the Northern website and follow the links to Delay Repay.
Commuters are advised to check their journey at: