The Santa Cruz County warning includes the cities of Santa Cruz, Watsonville, Scotts Valley, Boulder Creek and Ben Lomond.
"Rainfall rates of a half inch to 1 inch per hour are common. As the strong front moves through the region this afternoon expect widespread flash flooding," the weather service warning stated.
The Monterey County warning includes the cities of Seaside, Salinas, Monterey, Marina, Soledad, Prunedale, Greenfield, Gonzales, Castroville as well as the Del Monte Forest and Carmel Valley Village areas.
The flash flood warning will remain in effect until 4:15 p.m.
Residents in the area should be aware that flooding could be imminent and take appropriate precautions such as moving to higher ground, according to the weather service.
Monterey County Office of Emergency Services spokesman Dave Leist said that because the reservoirs in the area are all below 50 percent capacity there is a lot of runoff storage capacity.
"We're not really anticipating any major flooding. (The warning) is basically for drivers. Don't drive into flooded areas," Leist said.
Six inches of water is enough to move a car and drivers should drive away from any flooded bridges or intersections, Leist said.