People returning to work in the new year will have to pay up to 4.3% more for many mainline train journeys, while Tube and bus fares have also gone up.
A single journey paid in cash on the Tube will now cost at least £4, while bus passengers will have to fork out £2 for peak-time travel.
Passengers using a prepaid Oyster card have been spared the fare hike.
The rises, which came into effect on Monday, have been described as "exorbitant" by passenger groups.
On many main lines it is the fourth successive year in which ticket prices have risen by more than inflation.
Tickets for the Heathrow and Gatwick Express train services have risen by 7.3%.
Oyster fares that have not risen in price include a single journey on the Tube, which is still £1.50, and peak-time bus fares, which remain at £1.
But an annual Oyster card season ticket for travel in all six underground zones in London will rise 4.88% to £1,720 when the fare changes come into force.
Mayor Ken Livingstone said: "The headlines about big cash fare increases today show the savings are now to be found on Oyster with many Oyster fares now half the cost of the cash alternative."
But Roger Evans, London Assembly's Conservative transport spokesman, said the fares on Oyster had risen by nearly 9% "by stealth".
Earlier Brian Cooke, chairman of passenger watchdog body London TravelWatch, said the "exorbitant" fares will "hit infrequent visitors and tourists".
Mr Livingstone added the increase was needed to fund massive investments to develop new rail links and improve services which meant "three years of 10% fares increases".
"The savings and efficiencies made by Transport for London mean that the third, planned 10% increase in fares for this year has been significantly cut back," he said.