There are delays of up to 40 minutes on First Great Western services between Swindon and Portsmouth Harbour due to a fallen tree on the line between Fareham and Southampton Central.
It's also also affecting Southern and South West services. Trains will divert to Portsmouth & Southsea and Bognor Regis accordingly.
Some trains will divert through Eastleigh due to a tree on the line at Burlesdon.
There's disruption on South West Trains between Basingstoke and Woking due to flooding at Farnborough.
Trains are unable to call between Winchfield and Brookwood.
The firm says there is no estimate for when a normal service will resume.
Be aware of driving/walking/riding into large puddles of standing water. Apart from the obvious getting wet there are hidden dangers #flood
Listening to force radio, units being dispatched to assist people who've driven into flood water. Please drive carefully
A Flood Alert has been issued by the Environment Agency for the Upper River Wey.
Flooding is possible for the Upper River Wey including Alton, Farnham, Bordon, Frensham, Tilford, Godalming, Guildford and Peasmarsh .
The River and Flooding forecast is as follows: Levels on the Upper River Wey have been rising quickly in response to the heavy rainfall today.
Levels are expected to continue to rise today and flooding of low lying land and roads is expected this afternoon, especially in the Alton area.
However, property flooding is not currently expected.
The weather prospects are for outbreaks of rain which will be heavy at times.
This will clear in the afternoon when the weather will become dry.
Wednesday lunchtime weather for the west of the regionRead the full story ›
Heavy rain is causing disruption across the south. There are reports of flooding and fallen trees.
Bitterne Road near the junction on Somerset Avenue flooded. Passable but only just. http://t.co/NFlE068z3d
Southampton MP Royston Smith tweeted these images of flooding in his constituency.
It's a washout for Hampshire cricket club today.
Disruption on South West Trains at Ashtead due to fallen tree on the line. Wood choppers are on their way to remove the tree.
Trains to Dorking and Guildford (via Leatherhead) are affected. Until further notice lines are blocked.
There is no estimate when a normal service is likely to resume