The rain - up to an inch in six hours in some parts - fell on ground already saturated by double the normal December rainfall totals. More showers are expected today with a band of heavier rain tomorrow.
A lifeboat and four coastguard dinghies were deployed five miles inland at Barnham, West Sussex, to help the fire brigade rescue people from floods up to eight feet deep. Cars were floating down the road, the fire brigade said.
Many minor roads were impassable in the West Country, and on the south coast where the A27 between Sussex and Hampshire was blocked.
Train services between London and Brighton were halted because of a flood in a tunnel near Burgess Hill, while the line in Devon was blocked by floods near Newton Abbot.
At Lymington, Hampshire, a train was partly derailed when it struck an oak tree that fell across the rails.
The National Rivers Authority issued alerts on rivers along the south coast. Council workers in Portsmouth and Weymouth handed out thousands of sandbags.
Emergency services on the Isle of Wight reported some of the worst flooding in memory. The local radio station had to shut down after its offices were flooded.
In Cornwall, flash floods up to seven feet deep swept through Polperro.