More than four million trains have been rescheduled – and day one has not passed without hiccups.
Some passengers were left frustrated and confused by cancelled services.
Great Northern, which runs trains northeast out of London to places including Cambridge and Peterborough, said on its Twitter feed: “A reduced Great Northern service is expected until the end of the day.
“A short-term amended timetable is in place across the Great Northern network. This is resulting in a reduced service operating with trains being cancelled or revised.
“Disruption is expected until the end of the day.”
Passengers complained to the firm on social media saying they had been told services had been cancelled due to an “operational incident”.
The UK’s busiest franchise – Govia Thameslink Railway (GTR), which consists of Southern, Thameslink, Great Northern and Gatwick Express – will see changes for every service and the addition of 400 trains every day.
The new GTR timetable has been designed to extend stop times at busier stations and increase turnaround times at destination stations.
A GTR spokesman said: “We are introducing the biggest change to rail timetables in a generation and, as we have been informing passengers, we expect some disruption to services in the initial stages.
“This is a significant logistical challenge as we make rolling incremental changes across more than 3,000 daily services.
“We apologise to customers for any inconvenience caused during the initial stages of the timetable change.
“The improvements we are making will lead to a significant boost in capacity with a 13 per cent increase in services across the GTR network immediately.”
The introduction of new trains and services follows billions of pounds of investment and the number of alterations is seven times larger than normal.
The changes are designed to increase overall frequencies and reliability.
However, there has been criticism as some passengers will find their regular journeys are no longer possible.
It is expected there will be some disruption as trains and crews are redeployed over the coming weeks.
Many of the timetable changes are a result of the £7bn invested in the Thameslink programme in the South East.
This includes the rebuilding London Bridge Station, new trains and improvements to tracks.
Commuter belt areas such as Hertfordshire, Bedfordshire, Kent, East Sussex and Surrey, where many pay several thousands of pounds for annual season tickets to London, will be affected.
Emily Ketchin, founder of campaign group Harpenden Thameslink Commuters, said the operator was “slashing key Harpenden services by a third”.
GTR said it carried out the biggest consultation of its kind and received 28,000 responses to its plans.
The operator said it would be able to carry an extra 50,000 passengers travelling to London in the morning peak each day.
There will also be 80 more stations that will have direct services to the centre of the capital.
GTR chief executive Charles Horton said: “We are introducing the biggest ever change to rail timetables to significantly boost capacity on the UK’s most congested network.”
The Rail, Maritime and Transport (RMT) union described the new timetable as a “disgusting insult” to disabled passengers.
It said the latest instruction from GTR tells staff not to attempt to place people of reduced mobility on a train if there is a possibility of delaying the service.
A GTR spokesman said “we place a priority on making our services accessible to all” but he said it cannot hold trains when people arrive at a station without enough time to board.
A shortage of diesel rolling stock and delays to electrification work between Manchester and Bolton will mean many of Northern’s planned improvements have been deferred.
TransPennine Express (TPE) will now be the sole operator between Manchester and Huddersfield off-peak which will add extra capacity but trains will only stop at every other station to save time.
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Some passengers from Levenshulme and Heaton Chapel see trains go from four trains an hour into Manchester cut to three off-peak, with a gap between services of up to 49 minutes.
Anthony Smith, chief executive of passenger watchdog Transport Focus, said: “Having plenty of staff on the ground from the start and during the initial transition, when changes bed down, will be critical.”