National Weather Service meteorologist Tom Dang says the wet weather system dropped more than a half inch of rain in Sacramento on Saturday.
In the Shasta Lake area, up to six inches of rain fell since Friday.
Funnel clouds were spotted in Tehama and Glenn counties, prompting the weather service to issue a tornado warning. Dang says there's been no word on whether they touched down.
On Wednesday, a twister near Roseville damaged more than a dozen homes.
Meanwhile, heavy snow fell in the Sierra Nevada above 3500 to 4000 feet.
About three-quarters of an inch of rain fell in San Francisco, and about two inches were recorded on top of Mount Tamalpais.