First Great Western, CrossCountry, and South West Trains, are all reporting major delays on routes.
Disruption has been caused between Oxford and Didcot Parkway due to flooding.
As a result CrossCountry services will not be running on this stretch of line with a replacement service in place.
Network Rail say they are doing all they can to fix the tracks but admit more storms may bring more problems.
Robin Gisby of Network Rail told Sky News: “It’s not just the flooding, it’s the groundwater.
“The water table, not just where you see floods but Hampshire, Sussex, Surrey, all the way round through Kent and elsewhere, it’s the highest it’s ever been for sometime.
“So a lot of our embankments, a lot of our track, is heavily waterlogged at the moment”