See the full list of train company fare rises
Island Line prices will go up by 5.3% while there will be no increase for Hull Trains and Heathrow Express passengers.
Unregulated fares, which account for 60% of tickets sold, will go up by varying amounts depending on train operator, with an average rise of 4.7%.
There are also big increases planned for the two dedicated airport services, the Gatwick Express and Heathrow Express, which will both see rises of 7.3%.
Passenger Focus, the independent rail consumer watchdog, said the new fares would hit those who were unable to book tickets in advance.
Anthony Smith, Passenger Focus chief executive, said: "Inflation-busting price hikes on top of already high fares will make for an unhappy passenger New Year.
"If you now want to travel longer-distance in the peak and don't know exactly when you are coming back you will pay very, very dearly.
"If passengers want flexibility or have no choice about when to travel they now face off-putting prices.
Brian Cooke, chairman of passenger group London Travel Watch, said: "While we accept fares have to rise sometimes, any price rise above inflation is regrettable and will seem a lot to passengers in and around London who are increasingly faced with crowded platforms and trains."
Shadow transport secretary Chris Grayling said: "This is very unwelcome news for passengers and will only underline the fact that things are really not right on our railways."
Liberal Democrat transport spokesman Alistair Carmichael said: "Passengers will be exasperated by these fare increases, whilst levels of overcrowding on their trains continue to get worse."
Atoc director general George Muir said: "While no-one likes to pay more for their travel, we need the revenue to pay for the ongoing improvements to the railways that passengers expect - and overall satisfaction levels are now at an all time high of 80%.
"Train operators will continue to raise their game, delivering further improvements to the railway and enhancing the travel experience of passengers."