A severe thunderstorm warning has been issued for the area of Pine Valley and Mount Laguna.
The storm was nearly stationary just before 2 p.m., according to the National Weather Service.
There was flooding reported along Sunrise Highway.
Damage from hail and winds is possible in communities like Mount Laguna, I-8 Between Pine Valley And Boulevard, Pine Valley, Hwy S1 Between Lake Cuyamaca and Mount Laguna.
As of 2:20 p.m., the storm was 2 miles northeast of Julian and moving northeast at 10 mph.
San Diego has not seen relief from the mugginess as a flow of monsoonal moisture hovers over the region.
"There is a slight chance that those storms could sweep into our inland valleys; much lower chance though of them trying to head to the coast," NBC 7 Meteorologist Sheena Parveen said.
The NWS said at least isolated flash flooding is expected. Residents should be prepared to take action should Flash Flood Warnings be issued.
Meanwhile, the inland valleys to the coast will be under a heat advisory until 8 p.m. The heat index, which combines temperatures and relative humidity to give a "feels-like" temperature, was predicted to be in the 90s.
The NWS said during the hours of the heat advisory, dehydration, heat cramps and heat exhaustion are possible. People are urged to drink plenty of water, to stay out of the sun and to check on others. San Diego County has dozens of "cool zones" where people can go to escape the heat.
A similar weather pattern brought late afternoon showers, dark clouds and lightning strikes to some parts of the county on Wendesday.
More than an inch of rain fell in Pine Valley, and about a third of an inch had doused Alpine, Escondido and Mt. Woodson by 4:30 p.m.
The NWS reported 396 cloud-to-ground lightning strikes in the county by 6 p.m. There were 22 reported in Riverside County, one of which sparked a fire near Murrieta that had ballooned to 1,000 acres by 9 p.m. and forced evacuations.
Southern California's muggy weather is due to a blast of monsoonal moisture from the Gulf Coast. That monsoonal moisture was also bringing stormy weather to the eastern parts of the county.
Conditions were expected to improve by the weekend; though temperatures would remain hot, humidity levels were expected to decrease significantly, finally bringing some relief to the region.