It was the third storm system to hit the area in less than a week. The storm dropped as much as an inch of rain an hour in some area.
In Oakland, the storm flooded streets and toppled dozens of trees.
High winds were also a problem. An overturned big rig closed the eastbound lanes of the Richmond-San Rafael Bridge.
Forecasters had issued flood warnings for the Napa and Russian rivers, two rivers north of San Francisco with a history of flooding, as well as the Truckee River, near Lake Tahoe. But by Sunday afternoon, they had canceled the warning for the Russian River.
More than 8,000 sandbags and about 150 tons of sand were distributed in Napa before the storm, but after the heaviest rain moved out, the city appeared to avoid any major damage.
The storm knocked out power to thousands of people around the Bay area.