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.
In a deal announced by the Government today, First Capital Connect (FCC) will continue its franchise until September when a new Thameslink, Southern and Great Northern (TSGN) franchise will start.
Yesterday, a Which? table placed FCC 17th out of 19 train companies for passenger satisfaction, with FCC also scoring the equal-last number of points for train cleanliness.
The new deal for FCC covers services between London, Bedford, Brighton and Kings Lynn.
Starting in September, TSGN will be the largest franchise on the network and will take in the £6.5 billion Thameslink improvement programme which includes new electric trains.
– Transport Secretary Patrick McLoughlin
The new contract with FCC represents the best deal for passengers and taxpayers. It ensures the continuity of the existing service and guarantees the completion of the ongoing Thameslink Programme."
Rail services in the Thames Valley were badly disrupted again tonight because of another signal failure caused by flooding at Maidenhead. Dozens of services have been cancelled or delayed.
First Great Western say the issue which started at around 5pm has now just been resolved but delays will continue for the rest of the evening. Around half of all trains were cancelled or delayed during the rush hour.
It comes as Network Rail warn passengers delays could continue for two months because of rising water levels.
Following severe flooding in Datchet, the rail line between Staines and Windsor and Eton Riverside has now reopened.
The first trains ran smoothly this morning into London Waterloo, with normal train services resuming.
Buses have been put on standby just in case.
Buses have replaced trains between Romsey and Eastleigh due to a fallen tree.
The tree is blocking the line between Romsey and Chandlers Ford.
Replacement road transport services are conveying passengers between Eastleigh and Romsey in both directions until further notice.
Buses are departing Eastleigh at 10 past the hour each hour and Romsey on the hour, every hour.
No trains ran on Sunday between Leamington Spa and Banbury due to a landslip. Chiltern Railways advised customers north of Banbury to use Virgin Trains between London Euston and Birmingham New Street.
Chiltern Trains plan to run a normal timetable on Monday, 17 February but will need to pass the area at a reduced speed.
FGW is planning to run a near normal service on high speed routes into and out of London on Monday with the exception of the route closures at Dawlish, and between Bridgwater and Taunton. Buses will run on those routes that are closed.
Local services will also be running between Reading and London on Monday, although because of the flooding affecting signalling equipment near Maidenhead, there will be a small number of trains that we won't be able to run.
Mark Hopwood, First Great Western managing director, said:
– Mark Hopwood, First Great Western
This is great news for our passengers, who have faced a very difficult period of travel. We are finalising a new amended timetable, which we will publish through our online systems later today. To help customers who postponed journeys last week, ticket restrictions remain lifted until Monday. Customers are strongly advised to check our website before setting off in the morning."