Torrential downpours have caused localised flooding and train delays, as well as prompting the fire service to issue a warning to drivers.
Northern Rail said there had been disruption on some of their lines due to the severe weather, with flooding between Liverpool Lime Street and Stalybridge/Manchester Victoria meaning trains are being disrupted.
Their spokesperson said: "Trains will be delayed by up to 10 minutes, cancelled or revised. We anticipate disruption will continue until 15:30.
"Trains between Liverpool Lime Street and Scarborough services will start and terminate at Manchester Victoria.
"Customers are advised to travel on the next TransPennine Express or Northern between Manchester Victoria and Liverpool Lime Street."
Merseyside Fire and Rescue Service has advised motorists to take great care on the roads due to poor driving conditions.
Tweeting to members of the public ahead of school run time and the evening rush hour, they said: "It's very wet across #Merseyside this afternoon with a number of reports of flooding. If you're driving, give yourself extra time.
"Be safe & mindful of conditions: Slow down. Increase distances. Turn on your lights. Avoid driving through flood water where possible."
They told the ECHO that they have already been called out to rescue a car that became trapped in flood water on Leach Lane in St Helens shortly before 2pm.
Flood water had collected under the bridge and the car had got into difficulties, but had been helped free by other members of the public by the time the fire service arrived.
The emergency service wants commuters to be mindful of the conditions as the Met Office has predicted the rain to continue throughout the day well into the evening.
Yesterday they issued a yellow weather warning for parts of Wirral, which remains in place.
However, it is expected to dry up by tomorrow and become milder with sunny intervals.
