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.

The 33-year-old Australian ended his second spell at Fir Park this summer.
"Things have changed a little in terms of the Australia (move) in that it has not turned into what I exactly want," McDonald told BBC Scotland.
"I think everyone thought I'd made my mind up and pretty much I'm open to all offers."
McDonald was with Well from 2004-2007 before he joined Celtic and enjoyed three successful years at Parkhead.
Following spells at Middlesbrough and Millwall he returned to Fir Park in 2015, but his hopes of a switch to an Australian side this summer have yet to materialise.
"It was well documented at the end of the season that I was maybe looking to go home," McDonald added.
"Things haven't gone the way I would have liked in that area at the minute, so that's still ongoing.
"You get a couple of crazy ones (offers) here and there abroad. Locally, I haven't looked into it too much as yet."
Hundreds of homes are under threat of flooding in two Cumbrian towns.
[NEXT_CONCEPT]
Scott McDonald's proposed move to Australia has stalled and the former Motherwell striker says he will consider offers in Scotland.