An estimated 1,000 properties are at risk in Kendal and about 600 in Egremont after river levels rose.
Overnight rain was not as heavy as expected said the Environment Agency, but its 12 severe flood warnings for Cumbria and Lancashire remain in place on Sunday.
People in parts of Kendal and Egremont have been advised to leave and stay with their family or friends.
Police in Cumbria have warned drivers to avoid unnecessary journeys.
BBC reporter Andy Gill, in Grasmere, said many roads in the area had minor flooding.
A severe flood warning indicates a danger to life. Lower level flood warnings and alerts have been issued for large parts of northern England and Wales.
Further heavy rain is expected across Cumbria, other parts of north-west England and south-west Scotland on Sunday.
That rain will fall on already saturated ground, which increases the flood risk.
Reception centres opened at Kendal Town Hall and West Lakes Academy in Egremont throughout Saturday night, but Dave Hughes, chairman of Kendal Mountain Rescue, said not everyone had been willing to leave their homes.
"Some people decided to stay at home. You can understand that people may be reluctant to leave their beds," he said.
Hundreds of homes are under threat of flooding in two Cumbrian towns.