National Rail says the delays are caused by a person having been hit by a train at Wimbledon earlier today. Although all lines have now reopened there are still delays of up to 40 minutes while services recover.
Alterations and cancellations to trains between London Waterloo and Staines are also occurring because of trains and train crew being out of place because of this earlier disruption.
In addition to the delays, trains between London Waterloo and Salisbury / Exeter are currently starting from and terminating at Basingstoke. The first train to run normally from London will be the 17:20 London Waterloo to Exeter St Davids service.
There are delays of up to an hour on South West Trains through Wimbledon after a person was hit by a train. Two out of four lines have been closed by the fatality.
South West Trains are promising that commuter services will be "normal" in the morning, following hours of delays due to engineering work.
In a statement, the company said: "Safety is our absolute priority. We have no choice but to make sure these repairs are carried out before we can restore train services on these lines."
Trains on some of the country's busiest routes were cancelled or delayed tonight because of emergency engineering work and signalling problems, causing travel chaos for thousands of passengers.
South West Trains services to and from London Waterloo were hit at the height of the evening rush hour, on one of the hottest days of the year.The disruption was caused by emergency engineering work outside Waterloo, and signalling problems near Haslemere in Surrey.
A spokeswoman for South West Trains said:
"We would like to apologise for the disruption our customers will face on their journeys home tonight.
As a result of emergency engineering work to fix a track defect, we are unable to use four platforms at Waterloo which is having a serious impact on the services we can deliver.
Because of that we will have to run an amended timetable for the rest of the day.
Safety is our absolute priority. We have no choice but to make sure these repairs are carried out before we can restore train services. We expect to run a normal service from tomorrow morning. We would like to apologise again to our customers for this and thank them for their patience"