Commuters have faced major disruption to train services through Monday into the evening rush hour.
National Rail says disruption to trains in the Denmark Hill area will continue until 5pm when the service is expected to recover.
All trains via Denmark Hill had been halted since 5am due to a signalling fault, but lines have since reopened.
Some trains may still be cancelled or revised, National Rail has warned.
On the TfL network, the Circle line is suspended due to a fire alert at Moorgate.
The same incident is causing severe delays on the Hammersmith & City line trains, while a separate fire alert at Willesden Green is causing severe delays on parts of the Jubilee line and the entire Metropolitan line.
The Metropolitan line is also suspended between Baker Street and Aldgate.
Earlier a multi-vehicle crash on the M1 northbound caused delays between junction one at Brent Cross and junction five for Watford.
Follow the latest updates below...
Live updates
Incident cleared at Denmark Hill
National Rail has confirmed the incident has now cleared and services should be back to normal.
Disruption expected until 5pm
The fault at Denmark Hill has been resolved and disruption is now only expected until 5pm, an improvement on the 8:30pm stated earlier.
Thameslink trains are operating as usual.
Southeastern and London Overground services are operating with some delays.
Windrush line operating with minor delays
Due to the earlier signalling fault at Denmark Hill, the Windrush line is now operating with minor delays between Clapham Junction and Surrey Quays.
There is a good service on the rest of the line.
Circle line suspended
The Circle line is entirely suspended while TfL respond to a fire alert at Moorgate.
The Hammersmith & City line is subject to severe delays in both directions.
Freight train blocks service to Victoria
While the Southeastern service scrambles back to its feet, a freight train was reportedly stranded near the tracks of the incident in Denmark Hill, causing further delays.
Southeastern has confirmed the freight train has now moved, so both lines can resume running via Denmark Hill.
Series of fire alerts cause disruption on London Underground
As we head into rush-hour, a series of fire alerts at multiple stations have caused disruption on several London Underground lines.
There is no service anticlockwise on the Circle line and no service westbound between Hammersmith and Barking on the Hammersmith and City line due to a fire alert at Moorgate.
There are severe delays on eastbound on the H&C line and clockwise on the Circle line.
An earlier fire alert at Willesden Green has caused minor delays on the entire Jubilee line and severe delays on the Metropolitan line.
The Metropolitan line is also part suspended between Baker Street and Aldgate.
Signalling system has been fixed, say Southeastern Railways
Southeastern Railways have said the signalling system at Denmark Hill has now been fixed, after a fault was first identified at around 5am this morning.
In a post on X, the operator said the first trains will be the 15:03 service to Gravesend from London Victoria and the 14:15 service from Gillingham to London Victoria.
Disruption to last until 8:30pm
The major disruption to trains via Denmark Hill will last until 8:30pm.
Routes on the Windrush line on the London Overground network will not run between Clapham Junction and Surrey Quays.
Southeastern routes to and from London Victoria are also impacted, including services from Gravesend , Orpington, Swanley, Dartford, and Gillingham.
Thameslink services are also affected between Sevenoaks/Orpington / Beckenham Junction and London Blackfriars, and between Brighton and Bedford, and between Sutton and Kentish Town / St Albans City, and also between Orpington and Luton.
Passengers are being advised to check before travelling.
Good service on all other lines
TfL is reporting a good service on all lines, except the Windrush line.
The Windrush line on the London Overground network has been suspended between Clapham Junction and Surrey Quays since around 5am this morning.
The rest of the line is operating as usual.
Trains via Denmark Hill remain cancelled
Trains via Denmark Hill are still cancelled or experiencing huge delays.
The incident was first reported at around 5am this morning and is not expected to be resolved until around 3pm.