Average rail ticket prices have risen by 3.4% across the UK, in the biggest increase to fares since 2013.
Protests are under way at around 40 stations, as many commuters see their season tickets go up by more than £100.
Campaigners warned that many people were being “priced off” UK railways, while Labour described the network as “fractured, expensive and complex”.
The Department for Transport announced that price rises were capped in line with inflation and improved the network.
Commuter routes that are now more expensive include Liverpool to Manchester which has gone up by £108 to £3,152, Maidenhead to London which has gone up £104 to £3,092 and Elgin to Inverness which has increased by £100 to £2,904.
Fare increases to regulated fares – which comprise about half of all tickets – are calculated using the previous July’s Retail Prices Index (RPI) measure of inflation.
The financial burden of running the rail system has increasingly fallen on passenger since 2007, after the government decided taxpayers as a whole should pay less via subsidies.
Fares used to account for about half the cost of running our trains, whereas now it is about 70%.
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.
“None of us obviously want to pay higher fares,” he told BBC Radio 4’s Today programme, adding: “Fares are actually underpinning massively required investment.”