All trains between London and the Midlands and the south west were cancelled on Saturday morning as Network Rail engineers battled to control flood waters.
As of 1pm rail companies across the south and south west advised that journeys on many routes remained subject to "severe delays" and that customers are strongly advised not to travel unless the journey is absolutely essential.
Chiltern Railways, CrossCountry, First Great Western, Southern, Virgin Trains and Wrexham & Shropshire trains were all badly affected.
First Great Western, serving routes between London and the south west said customers were strongly advised not to travel. It suffered flooding between Swindon and Bristol Parkway, Newbury and Westbury and all services between London Paddington and South West England (Taunton / Exeter St Davids / Plymouth / Penzance) were currently suspended.
Virgin Trains, serving routes between London and the north west, suffered badly from flooding between Rugby and Birmingham New Street.
On Saturday morning all services between London and Birmingham were cancelled. These resumed at lunchtime, but still face massive delays of up to two hours. Services will be running at reduced speed on various parts of the route, and services will also be diverted between Milton Keynes Central and Rugby via Northampton, causing journey times to be extended by up to 50 minutes.
Devon and Somerset was worst hit by storms overnight, and Devon & Somerset Fire & Rescue Service has warned motorists to avoid driving into floodwater after receiving up to 300 calls during the night and fire crews performing up to 20 rescues of people from vehicles and properties affected by flooding.
Fire officers are now warning people that there is still a lot of static and moving water and blocked roads. It advised people should drive with caution and should not attempt to drive through floodwater.
The town of Ilminster is particularly badly affected by flooding with some houses under 1m of water and the roads leading into the town are also badly flooded.
Other towns in Somerset which have been badly affected by flooding include Castle Cary, Wincanton, Yeovil and Martock.