Numerous people in the Lake Berryessa area spotted a classically formed funnel cloud over the reservoir on Wednesday afternoon.
The National Weather Service said the whirling cloud, which occurred shortly before 2:30 p.m., was classified as a water spout since it apparently formed over water.
There were no reports that the water spout did any damage, said Weather Service meteorologist Larry Smith.
Smith said atmospheric conditions over rural Napa County on Wednesday afternoon were conducive to water spouts. A cold front had swept through, creating unstable air, he said.
The National Weather Service first learned of the water spout when a Sacramento TV station put up a video on Twitter, Smith said.