Parts of Wiltshire are on severe flood alert as the Environment Agency said the present severe danger could last for a week.
With a further three days of heavy rain predicted, warnings were issued for 22 rivers across the country.
Fears were raised after the worst storm for a decade caused a trail of death and destruction across southern Britain and rivers swelled when a month's rain fell in a day.
In the West Country the River Avon was threatening to burst its banks near Bradford-on-Avon while the whole of the south east of England was still in danger.
The Environment Agency's director of water management Geoff Mance said: "The flooding is not over. The big rivers are still rising and we have heavy rain forecast for the tomorrow evening so we will see further flooding this week."
An Environment Agency spokeswoman said the main worry today (Tuesday) was the Avon through Wiltshire, which is on severe alert between Melksham and Bathford.
She said the main concern was the village of Bradford-on-Avon: "The picture is looking better as river levels begin to drop but there are still a lot of properties in danger."
Wiltshire Constabulary has set up a bad weather office at its headquarters in Devizes to deal with problems around the county.
The storm left six people dead, two others missing and a multi-million pound clear-up operation after 90mph winds battered much of the country.
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