The AA said it recovered 100 vehicles from flood water, mostly across Surrey and Essex, following torrential overnight rain.
Darron Burness, head of the AA's flood rescue team, said: "It's gone a bit mad today with a massive surge in flood call-outs following the heavy overnight rain.
"Some of the people we went out to this morning got stuck after their cars were swamped by passing lorries. If you risk driving into flood water, you're a sitting duck as the air intake on most cars is pretty low, which makes them very vulnerable.
"Rather than taking a detour, these drivers will be making a rather embarrassing call to their insurer this morning and many will have their pride and joy written off. As well as swamping cars, the bow waves of passing vehicles can flood property too, forcing water into people's homes."
Network Rail engineers are currently at Balcombe Tunnel, pumping water away to allow a limited train service to begin.
Passengers are, however, being warned to check before they travel as further heavy rain is due in the area.
Two other lines remain blocked in the county, with the East Grinstead line flooded at Lingfield and Dormans and the Redhill-Tonbridge route blocked at Nuffield.
Network Rail's route managing director for Sussex, Tim Robinson said, "It has been a difficult start to the day and we apologise to passengers for their disrupted journeys today.
"We are working hard to get the lines clear again as soon as possible."
Sussex Police are advising motorists to be aware of the conditions on the roads today as heavy rain fell over night, bringing major flooding issues to West and Mid Sussex.
The A23 is currently closed between Bolney and Pease Pottage, leading to extensive tailbacks.
Although diversions have been set up, many other roads in the area have been badly affected or closed by flooding.
- The A24 at Broadbridge Heath, Findon and Dial Post
- The A29 at Bury Hill, near Pulborough
- The A281 at Henfield
- The A27 east of Chichester
The Environment Agency is warning that an area from Westerham to Sevenoaks is at risk of flooding following heavy rain last night.
River levels in the River Darent are rising rapidly and property flooding is expected this morning.
Properties in Westerham, Brasted and Sundridge are considered most at risk.
The Environment Agency says it expects river levels to keep rising until early afternoon.