More than half of services on Merseyrail and Northern will be cancelled, while Southern said it aimed to run most of its 2,200 trains.
Deserted stations, empty trains and heavy traffic marked the beginning of a 24-hour rail strike over the role of train guards on Monday morning.
Southern rail, which has seen profits hit by the ongoing action, was earlier this year forced to apologise to customers who had suffered months of severe disruption and inconvenience.
A Southern spokesperson said: "We've made it clear to the RMT that we'll meet with them if they confirm they will not call any further industrial action".
The RMT strike on Southern was the 30th since a row over the role of conductors flared nearly a year ago.
Northern said it planned to run around 300 extra rail replacement bus services to help keep the north of England on the move during planned industrial action on Monday, which also centres on the potential introduction of driver only operation.
There is lots of time to talk and agree how we modernise the way we provide customer service.
Rail workers and unions argue that the move to DOO trains presents a safety risk to passengers, and will ultimately be used by management to reduce staff numbers and bring costs down.
The trade union has said that there is no need for a dispute as they have reached an agreement with train firm, Transpennine Express, which has kept the guarantee of a guard on every service and hopes that other train firms will follow suit.
Some of the 200 guards with Merseyrail say they are anxious that they could lose their jobs, but Merseyrail insisted no-one would be made redundant and their jobs would be moved to a different area by adding new drivers positions and around 60 new on-board customer service positions.
"It is disappointing that the RMT are disrupting passengers across the country", said rail minister Paul Maynard said.
As part of our proposals we are prepared to offer guarantees on jobs and pay to our people.
An RMT spokesman told The Yorkshire Post: "The situation will be reviewed by the executive of the union and they will decide what the next course of action will be".