The low-speed derailment of an empty train caused the cancellation of numerous services running through the terminal.
It also meant no trains could leave the depot onto running lines to begin their schedules.
Disruption is expected until 11am, South Western Railway said.
A file image of a South Western Railway train
Andrew Matthews/PA
The following services have been affected:
between Waterloo and Windsor and Reading
all services from and to Waterloo via Richmond and Kingston
between Waterloo and Dorking and Guildford and Woking
South Western Railway said problems were also "exacerbated by several train faults in the London Waterloo, Raynes Park and Twickenham areas as well as some passengers being taken ill on other services".
"We are very sorry for any delay that this may cause to your journey," it said.
