Environment Agency officials issued seven flood warnings in North Yorkshire and the East Riding, telling homes and businesses to expect flooding.
Less serious flood watch alerts were also in place in 12 further areas, where low-lying land was at risk from rising water levels.
The worst-affected parts of the region were near York, at Buttercrambe Mill and Naburn Lock, and along the East Coast, where warnings were issued for Scarborough, Sandsend and Kilnsea.
Places on flood watch included sites between Whitby, Filey and Staithes, and areas near the Don, the Derwent and the Hull.
In York, a flood watch was in place for riverside walkways by the Ouse at South Esplanade, King's Staith and Queen's Staith, where three cars were partially submerged in water yesterday.
Robert Holmes, landlord of the Kings Arms pub in King's Staith, which was badly affected by a deluge in 2000, said the river broke its banks about eight hours before officials warned of potential flooding in the area.
"The river started going up over the banks at about 9pm on Friday," he said, "but it wasn't until about four or five o'clock on Saturday morning that the Environment Agency issued a flood watch, by which time these cars near the Queens Hotel were really flooded."
The worst of the weather was in the South, and a severe flood warning – the agency's most serious alert – was issued for parts of Cambridgeshire.
It applied to an area around Bury Brook, between Kings Ripton and Ramsey, where 99 properties were at risk.
Residents were allowed to stay in their homes but urged to move valuables upstairs.
Killer storms hit Europe: Page 13.
Weather forecast: Back Page.