The National Weather Service issued a severe thunderstorm warning and a flash flood warning for Julian as well as areas near Alpine, Potrero and Interstate 8 between Pine Valley and Boulevard.
A powerful storm system was bringing 60 mph wind gusts and penny-sized hail.
At the time the warnings were issued just before 3:30 p.m., the storm was located near Highway 78 between Banner and S2 and moving west at 5 mph.
Another storm was located just west of Julian, the NWS said.
Just before 4 p.m., the severe thunderstorm warning was extended through 4:45 p.m.
The areas that could be impacted included Alpine, I-8 between Pine Valley and Boulevard, Lake Morena, Potrero, Campo, Tecate, Barrett Lake, Skye Valley, Japatul Valley and Dulzura. The storm was slowly moving to the northwest.
As the warnings were issued, two inches of rain had already been recorded in the area, the NWS said.
The heavy rain could cause flash flooding or cause damage to roofs and trees. Residents nearby were urged to move indoors and to the lowest floor of a building.
The summer downpours were caused by a high-pressure system over the southwest that was pushing tropical moisture to the San Diego region, creating hot and muggy conditions.
Temperatures were expected to reach into the mid-90s in areas like Alpine, Poway and Escondido with the coastal communities like Oceanside and San Diego hovering near 80 degrees.