Delays continue until at least 9am on First Great Western services between Bristol Temple Meads/Weston-super-Mare/London Paddington and Portsmouth Harbour and on Cross Country services between Bath Spa and Glasgow.
It follows an earlier incident on the line near Keynsham and is adding up to 60 minutes to journeys.
A train traveling from London Paddington became stuck in floodwater at Pound Pill in Corsham in the early hours of this morning. 90 passengers were on the train, which came to a halt in a cutting where water was up to a metre deep in places.
All the passengers were rescued from the train by 0600 this morning.
The train is still blocking the track causing major disruption to rail services in the region.
Services to and from Bristol Temple Meads are unable to call at Chippenham. Trains are being diverted via an alternative route, adding around 45 minutes to journey times.
The Swindon to Kemble rail line has re-opened as a double track for the first time in nearly 50 years.
It's taken 18 months to install the extra line at a cost of £45 million.
But there won't be any extra trains on the route until at least 2017.
Network Rail say that trains are still not stopping at Bath Spa station because they are carrying out safety checks on a bridge which carries the mainline over Sydney Gardens.
Network Rail has confirmed it has the money to pay for a £700 million pound package of improvements to train services around Bristol.
It includes station upgrades at Temple Meads and Bristol Parkway, and building extra tracks at Filton. There will be capacity for more than 3000 extra seats for passengers during the rush hour.
The main railway line between Taunton and Tiverton is to be closed for three weeks in the new year for repairs.
Network Rail is to spend £15 million upgrading the line and repairing a Victorian tunnel. Replacement coach services are planned along with extra car parking.
The closure is due to start on January the 18th and will last until February the 10th.
Work has started on a £45 million pound project to dual a length of railway track between Swindon and Kemble stations.
There's only been a single track since the 1960's, limiting the number of trains which can use the twelve-mile stretch.
Ken Goodwin reports:
Work has started on a 45 million pound project to double a twelve mile length of track between Swindon and Kemble stations.
There has been just a single railtrack between the two stations since the late 1960s, when one of the tracks was removed to save money.
Network rail says the work should be finished by march and will mean up to four trains per hour will be able to run in each direction.
Work starts today on adding a second track to the railway line between Swindon and the Gloucestershire village of Kemble. The work will reinstate a track that was removed in the 1960s and increase the frequency of trains through the Cotswolds to the Midlands.
A level crossing where a man from Warminster and a man from Wells died is expected to be replaced with a bridge.
They were among seven who died after a train derailed in Berkshire in 2004. Network Rail is expected to announce the replacement at Ufton Nervet as part of a rail electrification scheme.