The warning was issued around 1:40 p.m. and was in effect through around 7:45 p.m., according to the National Weather Service.
The warning applied to the area to the west of Laguna De Santa Rosa, western Rohnert Park, the lower portions of Mark West and Windsor creeks and eastern Petaluma.
A flash flood warning means flooding is already happening or is imminent, according to forecasters.
The warning comes as Sonoma County and the Bay Area are pelted with heavy rain, causing flooding in creeks, streams, underpasses and other low-lying spots.
National Weather Service officials are advising people in the area not to try to cross quickly flowing water or water of unknown depth and to be especially cautious at night when it's harder to spot flooded areas.
If flash flooding occurs, people are advised to move quickly to higher ground and leave any low-lying areas subject to flooding.
As of 6:30 p.m. there are 1,580 customers without power in the North Bay, 375 without power in the Peninsula, 121 without power in the South Bay, 31 without power in the East Bay, 31 without power along the coast and 30 customers without power in San Francisco.
Bay Area storm causes accidents, topples trees, floods roads
The conditions on Highway 101 in both north and southbound directions were wet, rainy and visibly a challenging mess for drivers. The rain that started on Thursday hasn't taken a break. With the heaviest totals predicted for the North Bay, parts of Sonoma County are already feeling the punch.
In parts of Sonoma County the rainfall measured around 12 inches.
On Fort Ross Road in Sonoma County, the two-lane road was reduced to just one as half the roadway fell away. A pick-up truck also got swept away as the mud fell down the hillside.
At the intersection of Highway 121 and Highway 12 in Schellville the creek overflowed into the area and ran into the intersection. Cars could not get through and had to find other detours for much of Saturday.
More than 50 flights have been cancelled and dozens more are delayed at San Francisco International Airport today as heavy rain continues to blanket the area, airport personnel are reporting.
Rainy conditions have prompted the cancellation of 59 flights to and from the airport, and dozens of delays ranging from 30 to 90 minutes, according to airport duty manager Joe Walsh.
The inclement weather prompted the Federal Aviation Administration to call for a ground delay program at the airport that is expected to last through midnight.
Travelers are encouraged to check with their airlines before heading to the airport.
The Bay City News and Associated Press contributed to this story.