Airport duty manager Bob Rotiski said the delays could lengthen and are expected to last throughout the day.
At Mineta San Jose International Airport, spokesman David Vossbrink reported strong winds and lots of rain but good visibility and no major delays.
Flights usually take off and land to the north due to prevailing winds, but this morning's weather has caused airports to direct planes to the south instead, he said.
"During stormy conditions, winds turn around and come from the south," he said.
The airport is advising passengers to check with their airlines for any weather-related schedule changes.
No delays were reported at Oakland International Airport.
United Airlines has issued a weather travel waiver for flights passing through Oakland, San Jose, San Francisco and Sacramento airports today. The waiver makes it easier for passengers to reschedule flights without a fee.