A number of services were delayed or cancelled when the new timetable was introduced on Sunday, with the disruption continuing into Monday.
Thameslink operator, Govia-Thameslink Railway (GTR), said the new arrangements represented the “biggest change to rail timetables in a generation”.
A spokesperson said passengers should expect “some disruption” in the early stages of implementation but “despite some cancellations”, passengers would benefit from an immediate increase in capacity.
The Rail, Maritime and Transport Union, though, branded Monday’s disruption “Meltdown Monday” and said it was emblematic of the “privatised chaos” on Britain’s railways.
The upgraded £7bn Thameslink route runs south from Bedford and serves a number of key international travel hubs.
These include Luton airport, St Pancras International station and Gatwick airport, with GTR also responsible for Gatwick Express services, as well as Asford International station via connection.
Both Luton and Gatwick took to social media to warn passengers of the impending changes, which were put out to consultation last year.
Said Luton: “The new Great Northern, Thameslink, and Southern timetable starts tomorrow [Sunday]. There have been significant changes so please check before you travel.”
The Thameslink network now extends to around 3,600 daily services throughout the south of England.
Its new timetable sought to add around 400 more trains to the network every day, extend stops at busy stations and increase turnaround times.
Improvements set to benefit travellers include a new half-hourly cross-London service from Gatwick Airport via Redhill to London Bridge, Blackfriars, Farringdon, City Thameslink station, St Pancras International and Luton Airport Parkway.