Click here for a list of each train company's fare rises
The lowest increase, at 2%, is on Hull Trains.
Inflation is currently running at 2.7%.
Rail Passengers Council spokeswoman Caroline Jones said: "Most passengers would say that they don't want to pay more for the same service now.
"What they want to see is that the investment going in is put into getting the trains running on time, because that's the one thing passengers really want to see.
"And if that's then happening, then they won't mind paying a bit more for a better service."
The fare hikes were originally announced in December.
George Muir, Director General of the Association of Train Operating Companies (ATOC), said: "Fares have to rise to pay for the huge investment which the rail industry is currently making in the railways - which is the fastest growing in Europe."
He said the money would pay for "new trains, better passenger facilities, improved customer information and more security at stations".
Regulated fares - set by the Strategic Rail Authority and including season and saver tickets - will rise on average by 4%.
Unregulated fares - determined by individual rail companies - such as cheap day returns, long distance open tickets and advance purchases will increase by varying amounts, but also averaging around 4%.
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