The fare increases will allow increased investment in the railways, says Transport Secretary Grant Shapps.
The increase is below the Retail Price Index (an older measurement of inflation that is used to calculate rises in the cost of living and wages).
However, it will still push some fares up significantly, with many commuters facing an increase of more than £100 for annual passes.
This comes after Resolver saw over 6,000 complaints made about rail services in 2019.
The majority of complaints were about disrupted journeys, with nearly 1,500 people contacting Resolver after their trains were delayed or cancelled.
This may be set to change in 2020, however.
Mr Shapps has said that the Government is committed to “putting passengers first” and is taking steps to tackle the “fragmented” rail system.
Some rail operators face losing their franchise as a result of poor service. Mr Shapps has identified Northern as being of concern, with one in 16 trains cancelled in the four weeks to 7 December 2019.