Members of the Rail, Maritime and Transport union at Southern Railway, Merseyrail and Arriva Trains North were said to be "solidly supporting" the 24-hour walkout in separate disputes over staffing and driver-only trains.
Merseyrail was worst hit after drivers refused to cross picket lines, leading to 20% of services running, half as many as planned.
Andy Heath, of Merseyrail, said: "It is unfortunate that many drivers took the decision not to work today.
"This is bad news for the travelling public within the Liverpool city region and the local economy, both of which will suffer as a result of today's strike."
Northern said its plan to run 980 services, or around 40% of its normal timetable, worked well.
Paul Barnfield, regional director at Northern, said a few more morning rush hour trains ran than originally planned, adding that very few would be in service after after 5pm.
"On behalf of Northern I would like to thank our customers for working with us today and altering their travel plans. I would also like to thank all of our people who have worked so hard to run our trains today."
Northern and Merseyrail are introducing new, driver-operated trains in the coming years to replace ageing rolling stock.
The RMT, which is opposed to driver-only trains, said it had been a "highly successful" day, with support from its members and the public.
"We are pressing hard for talks with all three companies to try to reach a negotiated settlement," said a spokesman.
The RMT strike on Southern was the 30th since a row over the role of conductors flared almost a year ago.
Southern said it ran almost 90% of its normal service, in line with expectations, adding that more than half of conductors and on-board supervisors reported for work.