The latest storm came ashore Saturday night and was expected to force several rivers over their banks as it saturates the region Sunday, National Weather Service forecasters said.
With rivers and streams already running high, the weather service issued flood warnings for both the Napa and Russian rivers, two rivers north of San Francisco with a history of flooding.
"Some roads will become inundated and some of the agricultural areas will take on some water," said Mark Strudley, a hydrologist with the weather service.
The Napa River was expected to flood near St. Helena and Napa around noon on Sunday, while the Russian River was expected to flood near Guerneville early Monday morning, Strudley said.
The Napa River overwhelmed downtown Napa in 2005, flooding or destroying about 1,000 homes and forcing thousands of residents to leave the area.
With that in mind, residents worked to fill 700 bags with 10 tons of sand, city official Danny Lerma said.
"When you see it happen, you always remember, and you say, 'I'm going to be better prepared,'" Lerma told KGO-TV. "And that's what they're doing right now."
Farther north, forecasters said the Truckee River near Lake Tahoe was expected to crest above flood level by Sunday morning. The threat of flooding prompted officials in Truckee, a small town of about 16,000, to set up an evacuation center.
A flash flood watch was also in effect for a wide area of Northern California through Sunday evening.
Just across the border in Nevada, a state of emergency was declared in Reno, Sparks and Washoe County due to the expected flooding.
The weather also prompted cancellations of Christmas parades and tree lightings in Sparks and Truckee.
Officials were also warning people to be careful along beaches.
A high surf advisory was issued by the weather service, with swells expected to be 14 to 16 feet along the Northern California coast. In Southern California, high surf was predicted in Los Angeles, Orange and San Diego counties.
In San Diego, the Ocean Beach Municipal Pier was closed because of big waves and high tides.
At the peak of Friday's storm, some flooding was reported and thousands of people in Northern California were without power.
The stormy weather may be behind a crash that involved several cars on Interstate 280 outside of San Francisco on Saturday morning, as well as the death of a Pacific Gas & Electric worker in West Sacramento who was killed after his truck crashed into a traffic signal pole during the stormy weather Friday.