Flood alerts remain in place for 14 areas off the East Anglian coast, the Environment Agency (EA) said.
HM Coastguard Lowestoft issued a warning overnight after Oulton Broad flooded parts of Nicholas Everitt Park on Monday.
Warnings remain for Southwold in Suffolk and much of the waterways on The Broads.
Minor flooding to coastal roads and footpaths was likely on Tuesday evening and Wednesday morning, the EA said.
The high waters of the Rivers Bure, Waveney and Yare "were caused primarily by gale-to-storm-force winds in the North Sea".
"These generated large waves and saw elevated tidal levels off the coast of East Anglia," said an EA spokesman.
"High water levels at low tide restrict the drainage of water from the Broads, again resulting in elevated water levels on the Broadland rivers."
Weatherquest forecaster Dan Holley agreed that strong winds and unusually high tides meant some rivers could not drain "as efficiently as they normally do during low tide".
"Strong northerly winds from the Arctic, responsible for the current cold spell, and the associated long fetch have resulted in a significant swell running down the North Sea.
"Tidal elevations around parts of the Norfolk, Suffolk and Essex coast have been over one metre (3.3ft) above normal during the past couple of days," he said.
Strong winds will persist through Wednesday, but will gradually ease and turn more westerly by Thursday, when conditions should gradually start to improve, according to the forecaster.