Average rail ticket prices have risen by 3.4% across the UK, in the biggest increase to fares since 2013.
Protests are planned at some 40 stations, as many commuters see their season tickets go up by more than £100.
Campaigners warned that many people were “being priced out of getting to work”.
The Department for Transport said price rises were capped in line with inflation.
Commuter routes that are now more expensive include Liverpool to Manchester (up £108 to £3,152), Maidenhead to London (up £104 to £3,092) and Elgin to Inverness (up £100 to £2,904).
Fare increases to regulated fares are calculated using the previous July’s Retail Prices Index (RPI) measure of inflation.
Around half of all tickets fall under this category.
Paul Plummer, chief executive of industry trade body the Rail Delivery Group, said the fare changes would provide cash for better services and investment, including the Thameslink and Great Northern rail upgrades.
“For every pound paid in fares, 97p goes directly back to operating and improving services,” he said.
But Bruce Williamson, of campaign group Railfuture, has called for the lower Consumer Price Index (CPI) inflation measure to be used for regulated fare increases.
Mr Williamson argued that if CPI had been used rather than RPI since 2004, rail fares would be 17% lower.
He said people were being priced out of getting to work, with British rail fares among “the most expensive in Europe”.
Commuter Sarah Beer, from Lingfield in Surrey, said her rail commute to London of nearly £4,000 a year was an “extortionate amount of money”.
“It is like watching the Great Train Robbery all over again,” she told BBC Radio 4’s Today programme.
“What I cannot grasp, in this day and age, is that all we ask for is a reliable train service.”
On the first working day of 2018, many commuters took to social media with their reactions to the increases.
Stephen Joseph, chief executive of the Campaign for Better Transport (CBT), accused the government of choosing to “snub rail passengers” while fuel duty continued to be frozen.
“The extra money that season ticket holders will have to fork out this year is almost as much as drivers will save,” Mr Joseph said.
“That doesn’t seem fair to us.”
Meanwhile the National Union of Rail, Maritime and Transport Workers (RMT) said the need for public ownership of the railways had “never been more popular or necessary”.
A spokesman for the Department for Transport said it was investing in the “biggest modernisation of our railways since the Victorian times”.
He said: “This includes the first trains running though London on the Crossrail project, an entirely new Thameslink rail service, and continuing work on the transformative Great North Rail Project.”
Mark Carne, chief executive of Network Rail, said passengers would see a “huge change” in the coming year due to investment in rail networks.
“We all share the desire to try to keep fares as low as possible,” he told BBC Breakfast. “My job is to run the network as efficiently as possible.”
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