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Waves up to 15 feet pounded the central California coast on Thursday as the latest in a series of storms — driven by an El Niño system equaling the strongest on record — brought high surf and coastal flood warnings to the state's beaches and mudslides inland.

"Over the last few days, it's been high, but I think we're going to see our highest surf over the next couple of days," Emily Thornton, a meteorologist for the National Weather Service, told NBC News.

The surf was expected to erode beaches, damage some coastal structures and raise the risk of ocean drowning, the weather service said.

The third day of storms affected by El Niño conditions in the Pacific brought showers and isolated thunderstorms to California — a relative respite from storms that drenched the state Wednesday, flooding roads and sending mud sliding down parts of the state affected by wildfires and drought.

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San Diego County was especially hard hit, as heavy rain collapsed the roof of a Goodwill store in Escondido overnight and caused a mudslide Thursday morning in a residential neighborhood in Rancho San Diego, shutting down traffic.

"There's not much vegetation left up there because of the drought and stuff, so it's like a slip-and-slide," Tony Lewellen told NBC San Diego after 4 inches of mud made its way into his family's Rancho San Diego house. "It just runs down the mountain."

No one was injured when the roof caved in at the Goodwill store and donation center in Escondido, police said. The store was closed Thursday pending repairs.

In San Luis Obispo County, rescuers pulled a surfer from dangerous waves near Morro Rock on Thursday afternoon. NBC station KSBY reported that the man was OK.

Fire crews in Tucson, Arizona, meanwhile, rescued two people and dog from a vehicle in a flooded road Thursday afternoon. No one was injured, the Tucson Fire Department said.

Moving into Friday, conditions will clear and the state will have a chance to begin to dry, Thornton said. The next chance for light rain is expected Saturday.

Related: Flashback: When El Niño Struck in 1997

This year's El Niño is tied with the strongest on record. The 1997 and 1998 weather systems brought record rainfall in California and Peru, heat waves in Australia and fires in Indonesia.

But not all El Niños are the same, said Dale Eck, director of the Global Forecast Center at The Weather Channel.

"What we have seen this year so far has not been what you would call the classic weather pattern with a strong El Niño," Eck said.

"They're not getting 10 to 15 inches of rain," Eck said, comparing this year's weather to the 1997 and 1998 El Niños. "We're now seeing a series of storms that are dumping 1 to 3 inches in California."

This level of rain could spell good news for the drought-afflicted state, he said, as the winter storms were building up the snow pack in the Sierra and San Gabriel mountains.

"What's more important than the rain falling in Los Angeles and San Francisco is the snow pack building up in the Sierras," he said. "They are adding feet of snow."