Commuters faced travel misery on Thursday morning after a fault hit some South Western Railway services between Waterloo and Vauxhall, as well as Battersea.
Separately a signalling fault was disrupting journeys from Marylebone.
The track circuit failure at Queenstown Road in south London meant some lines towards Waterloo were blocked, a busy commuter route, while lines were also blocked between Waterloo and Vauxhall.
Passengers have been advised that London-bound services will not stop at the Queenstown Road until 2pm, while the Waterloo disruption is expected to last until 12pm.
In other travel woes, a fault with the signalling system is causing disruption to journeys running to / from London Marylebone.
Chiltern Railways, which runs the route from Marylebone to commuter destinations such as Aylesbury and Oxford, said trains may be cancelled or delayed up to 30 minutes until 9.30am.
On the London Overground, passengers were also experiencing disruption, as a points failure at Stratford meant fewer services can run to and from the station to Clapham Junction and Richmond.
TfL advised some services may be cancelled and there was a severe delay on the line. Disruption is expected until 10am.
There was however a good service operating on all other lines.
It comes two days after services running through London Bridge were severely disrupted due to a cable trackside fire.
The outage severely affected Southern, Thameslink and London Overground services in south and south-east London.
