Around half of services to London out of Brighton have been cancelled because of major flooding at Patcham, near Preston Park.
Tim Shoveller, Managing Director of SWT has written to all passengers to explain what the rail operator is doing to keep services running.
Like most rail companies across the ITV News Meridian region, Cross Country trains are also affected by the severe weather conditions.
First Great Western (FGW) and Network Rail plan to restore the majority of services into and out of London Paddington from Monday.
Network Rail's engineering and maintenance teams have been working to try and solve the problems caused by the flooding at Maidenhead that had affected the normal signalling system reducing service to just 20% of normal capacity.
Through a series of innovative engineering solutions, from start of service on Monday, in excess of 75% of normal services will be running.
Saturated ground could lead to flooding around Croydon, Hambledon, Basingstoke and Lower Farringdon in Hampshire.
Peter Willison, of the Environment Agency (EA), told a Whitehall briefing: "We are likely to see more severe flood warnings along the south coast representing the risk from very strong and big waves.
"The rainfall that we will see today, that will bring river levels back up on the Thames and we expect levels on slow responding rivers like the Thames, like the Severn, to stay high for a number of days to come.
The Met Office predicted a return to the worst of the winter weather with almost every pocket of the UK experiencing downpours, winds or snow, much of it falling on already-saturated ground.
Windsor, Maidenhead, parts of Surrey and communities in Buckinghamshire, West Berkshire and Reading are at risk from the River Thames, which has seen levels rise to 60-year highs, and significant flooding is expected.
Severe gales, large waves and high sea levels are threatening coastal flooding on the Dorset coast, while the south coast from Cornwall to East Sussex is also at an increased risk, the Environment Agency said.
A triple threat from the elements, with warnings in place for heavy rainfall, gale-force winds and snow, will pile on the problems for areas already struggling in the wake of record wet weather and a string of wild winter storms.
More than 1,000 homes have been evacuated in the Thames Valley and the West Country, and others have been left without electricity.
Ongoing flooding could continue to affect homes, businesses and land for at least another week, the Environment Agency said.
The agency has 23 severe flood warnings - meaning risk to life - in force along the River Thames, the Severn at Gloucester, on the Somerset Levels and on the south coast, and hundreds more flood warnings and alerts across England and Wales.
Services between Newcastle and Reading/Southampton will terminate/start at Birmingham.
Services between Manchester and Bournemouth will run in two portions:Manchester-Oxford, and Didcot Parkway-Bournemouth.
First Great Western will be providing alternative transport between Oxford and Didcot Parkway that can be used by CrossCountry customers.
Passengers holding Advance tickets may travel on earlier or later trains as necessary. CrossCountry tickets may also be used for travel on Chiltern Railways, First Great Western and South West Trains services where required.
South Eastern say the landslips between Robertsbridge and Battle, and at Stonegate, are causing disruption on the line between Tonbridge and Hastings.
The line between Wadhurst and Battle is closed, meaning no trains can run between these stations. This is to allow Network Rail engineers to fix the damage caused by the landslips. The line is not expected to reopen before Monday 17 February.
The big concern for Network Rail and the rail companies is if more flooding take place, closing the line around Oxford. Network Rail expects it to affect services between Oxford and Didcot, with the possibility of disruption to the Henley and Marlow branch lines.
Engineers have been working trackside near Oxford removing sensitive equipment to prepare the railway for possible flooding. Network Rail say engineers have been out across the South and South East repairing and monitoring the railway.
Following a drop in floodwater at Athelney the railway line between Exeter and London Paddington, via Newbury, is due to reopen on Monday 10th February.
– First Great Western
First Great Western has announced that customers affected by the floods in the South West will not be charged the £10 administration fee and will be eligible for a full refund.
South West Trains have updated their plans for rail services on Thursday. They plan to run normal services to operate on routes, run test trains to overnight to ensure the tracks are clear and to provide information on all services for early commuters.
Following the strong winds and torrential rain South West Trains expects to run a normal service throughout the day on Thursday. Forecasters are predicting heavy rain overnight but the winds have dropped.
Full service information can be found on South West Train's website here. A spokesperson for the South West Trains-Network Rail Alliance said:
– South West Trains spokesperson
“Over the last 24 hours we have had additional staff working across the network to ensure that tracks were cleared as quickly as possible with minimum disruption to planned services. We're sorry for any inconvenience caused by the weather and thank passengers for their patience.