The hundreds of earthquakes included a magnitude-4.9 tremor Wednesday afternoon, according to the U.S. Geological Survey.
There were 28 quakes alone from 11 p.m. Wednesday through 10 a.m. Thursday ranging in magnitudes of 2.5 to 3.6.
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The swarm is centered beneath agricultural fields south of the Salton Sea, about 2.5 miles northeast of the small town of Westmorland.
"When you have a lot of earthquakes, you tend to have a lot of earthquakes," seismologist Dr. Lucy Jones said. "But it doesn't make it more likely for it to trigger somewhere else. This doesn't make us worry about the San Andreas fault; its too far away."
However, the shaking was also felt in San Diego and Riverside counties, but so far there are no reports of major damage there
Dr. Jones says the zone is a common source of swarms, and this is one of the largest ever.
Notable past seismic activity in the region includes a 1981 swarm that included a magnitude 5.8 quake and a 2012 swarm that produced a magnitude 5.4 quake, the USGS said in a statement.
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Past swarms have remained active for up to 20 days, but the average is about a week, the USGS said.
The USGS said during this earthquake swarm, the probability of larger earthquakes in that area is significantly greater than usual.
The state on Thursday coincidentally launched a "Don't Get Caught Off Guard" campaign to raise awareness of California's earthquake warning system which detects the start of a quake and sends alerts so that people can protect themselves before shaking arrives.
The annual Great California ShakeOut, in which millions of people practice the "drop, cover, hold on" response to earthquakes, is scheduled for Oct. 15.
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The Associated Press contributed to this report.