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More trains have been cancelled this morning due to overnight flooding in Wirral.
Merseyrail said water had to be pumped away from the tracks at Hooton last night, but heavy rain overnight has affected Chester and Ellesmere Port services again.
The company has published an amended timetable.
It means rail replacement buses are running to Rock Ferry, resulting in delays and cancellations into Liverpool.
Standing water is also causing problems on many of the region's roads.
Parkgate Road in Chester remains closed due to a flood and it is also causing problems on the M53.
Merseyrail has warned passengers to expect delays of at least 15 minutes to all services.
A number of Merseyrail services have also been brought to a standstill by Storm Ali.
Rail services are suspended between Hooton and Chester and West Kirby and Birkenhead North because of fallen trees.
Rail replacement buses will shortly be in operation.
On the Northern line, services on between Ormskirk and Maghull are suspended because of a tree on the line in Aughton Park.
Merseyrail has also put ticket acceptance is in place for passengers travelling between Liverpool South Parkway and Liverpool Lime Street via Merseyrail services because of issues with mainline services.