An unusual torrent of rain and flash flooding hit the San Diego area on Monday, shutting down highways, swamping roads and leaving some residents to watch helplessly as water swept away their cars or wreaked havoc on their homes.

The deluge caught many off guard, as up to three inches fell in the span of three hours, according to the National Weather Service. By early afternoon, the agency noted that the San Diego River was actively flooding, with water levels still rising.

As reports of damage surfaced, Todd Gloria, the mayor of San Diego, declared a state of emergency and urged residents to avoid any unnecessary travel. Mr. Gloria said the city was coordinating efforts with local, state and federal agencies to ensure a comprehensive response. Displaced residents were directed to an evacuation center set up by the American Red Cross.

Officials found themselves fielding numerous rescue calls in an area that received more rain on Monday than it did during the much feared Tropical Storm Hilary last August.

“By all indications, this will shake out as one of the top 10 wettest days for the airport here out of all the climate records going back to the 1800s,” said Brian Adams, a meteorologist with the National Weather Service in San Diego. “It’s been a day, yeah.”

In the Mountain View neighborhood of San Diego, which was hit particularly hard, many residents spent the day attempting to sweep water out of their garages, an act that did not feel as futile as addressing the mud that had flowed into their homes. The water, judging by the telltale brown lines on the exterior walls of residences, had been several feet high. Inside, a thick sludge covered carpets.

“The whole house is, like, under mud,” Lara Lockwood, 43, said as she anxiously took in the scene outside the home she has owned for eight years. The patio table had been flung to the front of her garage. The yard had become an impassable marsh. The wooden fence had been ripped apart. And her cat, Bagheera, was missing.

“I wasn’t expecting anything like this,” said Ms. Lockwood, an interior designer. She planned to take several days off work. “It is very overwhelming. I don’t even know where to start.”

Her neighbor, Jarvis Landers, 65, worried about his flooded cars. A forklift operator and a shipping and receiving clerk, Mr. Landers has lived in the neighborhood for decades and worried that a nearby drainage ditch was plugged up by debris because it had not been properly cleaned out before the storm.

Across the region, drivers found themselves navigating clogged roadways or, worse, forced to abandon their cars altogether. Sections of major freeways looked more like rivers. In some areas, vehicles had been swept askew by floodwaters.

On Interstate 15, lanes were shut down after a semi truck turned over. Cleanup crews were also scooping up mud that had flowed onto the highway.

Some schools in the region closed early because of flooding or loss of power, while those at others were advised to shelter in place. About 14,500 San Diego Gas & Electric customers had lost electricity as of Monday afternoon, according to PowerOutage.us.

“We have had power outages, loss of communication and flooding at some sites,” the National School District in San Diego County said on X.

After two homeless shelters flooded, the city of San Diego scrambled to transport people to public gymnasiums. The San Diego Central Library also closed after its parking garage flooded, while the San Diego Police Department announced that both of the front counters at its downtown headquarters would be closed for the day. Sandbags were offered at recreation centers across the city.

“We are very spoiled here in San Diego,” said Argelia Ventura, the manager at Maggie’s Cafe in the Barrio Logan neighborhood. “We knew rain was coming but it was surprising that it was that heavy.”

Ms. Ventura, 46, watched the downpour through the restaurant’s giant windows and knew that it would diminish the lunch rush that arrives for chile relleno omelets and chilaquiles. Only about 10 tables had been filled by the afternoon. One family scurried in only because their apartment had flooded.

“It does hurt a lot, because usually we are going day to day,” Ms. Ventura said. She planned to close early.

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