Sheets of pouring rain made for treacherous driving. One person was injured in an accident on Highway 101 that blocked all lanes near San Rafael, the California Highway Patrol said.
PHOTOS: Strong winds, rain move through Bay Area
The storm caused damage in San Pablo after a fallen tree hit two homes, crushed a car and caused power outages.
In Palo Alto, a tree fell over three cars in front of the Woodland Park Apartments on Bayshore Road.
The heart of the storm blew through San Francisco at 9 a.m.
A flash flood left the intersection at Alemany and Bayshore boulevards underwater. "I saw it when I was driving up and I saw a tow truck trying to get a car out. I said: 'Oh my God that's a lot of water,"' Regina Mulligan said.
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Several drivers misjudged the high water on an on-ramp to Highway 101 as they got stuck. Tow truck drivers were busy rescuing drivers throughout the morning. "Cars kept driving in, you know I kept telling them not to and they kept driving in," a tow truck driver said.
In Daly City, there was flooding on the bottom floor of an apartment building located on 88th Street. "And then all of the sudden, we started yelling, 'move your cars, move your cars,'" Raleigh Pabalate said.
The building is located at the bottom of a hill, so storm drains got overwhelmed.
The same flooding happened last year, so officials posted a note ahead of the storm, telling residents to avoid parking in the garage.
PG&E said it's working to restore power to residents in the Bay Area. At the height of the storm, PG&E said there was nearly 15,000 outages.
Forecasters said scattered showers are expected until midnight in parts of the Bay Area, so officials are reminding residents to drive slow, saying there is debris and flooding on the freeways.
After a lull Saturday, the system moved into parched Northern California overnight packing precipitation, strong winds, lightening and some hail.
The latest storm will dump slightly less rain in the state than the previous systems - with the Bay Area and the San Joaquin Valley expected to get up to about half an inch, National Weather Service meteorologist Nathan Owen said. "We'll see a very similar storm to what we had the last round with less rain, but we're expecting a good bit of wind for this system," he said.
The National Weather Service issued a strong wind advisory for the Bay Area that will stay in effect through Sunday night, saying wind with gusts of 40 to 50 mph are forecast for the area.
The weather service warned that dry trees could topple and bring down power lines.
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Central California could also see winds gusting up to 55 mph and higher peaks in the Sierra Nevada could see up to two feet of snow, the weather service said.
In Southern California, chains were required Saturday on several roads leading to the Bear Mountain and Snow Summit resorts after several inches of snow fell on the San Bernardino Mountains.
A storm Friday dropped 6 inches at higher elevations and brought rain, hail and thunderstorms elsewhere.
The National Weather Service said daytime temperatures in the mountains will stay in the 30s through the weekend and that more snow is expected before Monday.
The Southern California coast remains under a high surf advisory through Sunday, with unpredictable waves topping 10 feet.
Forecasters have said a strong El Nino weather system could drench California and other parts of the West in the coming months. However, Johnny Burg, a meteorologist with the National Weather Service in Seattle, said he didn't believe the latest Northwest storms were related to El Nino, a warming in the Pacific Ocean that can alter weather worldwide.
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The Associated Press contributed to this story.