Darren Shirley, chief executive of the Campaign for Better Transport, said passengers "suffered atrocious service in 2018".
He added the latest fare increase will "only add to their misery".
Mr Shirley continued: "The Government's decision to press ahead with this fare rise despite a year of delays, cancellations and overcrowding shows a total disregard for passengers and may leave many wondering what they are paying for.
"The review of the railways currently under way must prioritise passengers' needs and recommend a fundamental reform of the fares system and how fares are set."
Bruce Williamson, of campaign group Railfuture, claimed passengers are being given "another kick in the wallet" following a "terrible year" on the railway.
He said: "Since 2004, rail fares have raced ahead of people's incomes whilst the cost of motoring has remained static, partly thanks to the Government's continuing freeze on fuel duty.
"Petrol is now cheaper than it was in 2011, when the last fuel duty increase kicked in.
"In that time, rail fares have gone up 28%. Are they trying to drive us off the railways?
"Why are hard-working commuters being punished for the 'crime' of trying to get the train to work? It really is war against the train passenger."
Labour's shadow transport secretary Andy McDonald said: "Today's rail fare increases are an affront to everyone who has had to endure years of chaos on Britain's railways.
"Falling standards and rising fares are a national disgrace. The Government must now step in to freeze fares on the worst performing routes.
"Labour will bring our railways back into public ownership so they are run in the interests of passengers, not private profit."
Labour's chairwoman of the Commons' Transport Select Committee Lilian Greenwood described the price hike as "a real kick in the teeth".
She added: "A fares system in which there is such a disconnect between quality of service and price is quite clearly broken.
"Most people have experienced years of wage stagnation or real-terms reductions in their pay and are struggling to make ends meet.
"A 3.1% increase in train fares therefore seems doubly unjust. For some long-distance commuters, the annual cost of getting to work could increase by more than £100."
In London, Mayor Sadiq Khan said he was freezing fares Transport for London (TfL) is responsible for.
"Our TfL fares freeze is in contrast to the private rail companies hiking up fares again, despite the litany of cancellations, delays and overcrowding on services like Southern and South Western Railway," he said.
"Given the continuing woeful services on suburban rail routes, the increase in rail fares of 8.8% over the last three years is simply a disgrace."
Robert Nisbet, regional director of industry body the Rail Delivery Group, said: "We understand that nobody wants to pay more for their journey to work but money from fares is underpinning record investment to build the better railway customers want and the country's economy needs.
"We want more people to benefit from the opportunities travelling by train opens up which is why we are pleased that the industry's 26-30 Railcard will go on sale today and we will support the government decision to reduce fares for 16 and 17 year olds.
"Everyone wants an easier to use range of fares which is why we will soon be unveiling the results of our consultation with proposals to government on overhauling outdated regulations that underpin the existing system."