Train services from Blackpool North to Preston have been cancelled due to floodwater on the tracks near Poulton - and people have been warned that even more cancellations could be on the way.
Delays and short notice cancellations are expected to continue for the rest of the day due to heavy rain impacting on Northern's ability to operate.
Localised flooding is likely to create problems on a number of routes - although in some cases the flood waters may subside quickly, the company said.
Northern customers are advised to allow extra time for travel and to check ahead for all rail travel in the North West.
Flooding at Culcheth Farm, between Newton-le-Willows and Manchester, means trains are running at reduced speeds in that area.
There are also lineside equipment issues between Summit and Dean Royd tunnels towards Manchester Victoria which may cause delays.