Rain from a major atmospheric river storm moved into Southern California early Thursday, causing flooding and several road closures during the morning commute and concerns about greater disruptions as the rain continues.

The moisture-heavy system continued to forge a trail of wet, windy weather across the state, dumping significant rain and snow across Northern California on Wednesday — including some historic rainfall amounts — and causing minor roadway flooding, downed trees and some power outages.

While showers continue across the state, the storms’ strength has turned toward the Southland, with the heaviest rainfall expected through noon.

Early Thursday, the National Weather Service issued a flood advisory for much of Los Angeles County and eastern Ventura County through 8 a.m., warning of likely flooding in low-lying and poor-drainage areas.

As of 5:30 a.m., weather officials said the rainfall in L.A. County had “caused widespread urban, roadway and small stream flooding.”

Rainfall totals had already reached an average of 1 to 2.5 inches across much of L.A. County, with some places already over 3 inches — and more rain still to come.

In Ventura County, officials warned that almost all roads were slick if not flooded; in Santa Monica, flooding closed a stretch of the Pacific Coast Highway at the McClure Tunnel; and in Huntington Beach, a three-mile stretch of the Pacific Coast Highway was also shut down by flooding.

In Costa Mesa, Orange County firefighters rescued a man who became trapped in fast-moving waters in a storm channel.

“We were expecting some heavy rain, but it’s going to be short-lived,” Mike Wofford, a National Weather Service meteorologist in Oxnard, said Thursday morning. “L.A. is going to be seeing the end of the rain here in the next couple hours.”

A cold front also moved in with the atmospheric river, bringing high winds across the region, with some gusts already recorded above 60 mph. Officials warned of possible downed trees and power outages.

A winter storm warning is also in effect for the mountains of Los Angeles, Riverside and San Bernardino counties through late Thursday, with the highest elevations expected to get up to 18 inches of snow. A dusting to a few inches of powder is possible as low as 4,500 feet, as temperatures cool off and snow is possible in lower elevations by Friday morning. Forecasters warn that “travel may be difficult to impossible” in the mountains, including along the 5 Freeway corridor. Early Thursday, transportation officials said tire chains would be required for drivers in the mountain communities.

High surf was expected to bring waves up to 12 feet along the beaches of Ventura, Los Angeles, Orange and San Diego counties, and rip currents will make any ocean activities dangerous, the weather service warned.

This system is the first of back-to-back, major atmospheric river storms, which state officials worry could be the start of an extended weather pattern that could cause mounting problems.

This first front is aligning with forecasters’ projections of a fast-moving storm, which officials hoped would help minimize damage from the otherwise powerful system. But another atmospheric river barreling across the Pacific toward Southern California is looking much slower, forecasters warn, which could further challenge the region.

“That one’s definitely looking bigger,” Wofford said. “We’ll probably see similar high-intensity rains, but for a longer duration.”

South and east of Los Angeles — parts of San Bernardino, Riverside, Orange and San Diego counties — remain under a flood watch through late Thursday, with excessive rainfall likely to cause ponding on roadways, flooding in low-lying areas and along some waterways.

Ryan Kittell, a meteorologist with the National Weather Service in Oxnard, said some areas could see up to 1 inch of rain per hour Thursday morning, a rate that is sure to cause flooding.

San Diego, which was still reeling from last week’s historic rains that caused devastating flash floods, was bracing for probable flooding again near Fashion Valley along the San Diego River, where the latest river forecasts showed flood stage would be surpassed by evening.

Heavy snowfall was also forecast in the southern Sierra, with as much as 4 feet possible, depending on elevation. Forecasters warned that in the foothills, where snow gives way to rain, flooding and mudslides could be likely.

And there won’t be much of a break until the next system moves in.

The latest predictions show that Sunday will likely bring the start of that second system, expected to dump 3 to 5 inches of rain, with up to 10 inches possible in the mountains and foothills — totals that could bring “damaging flooding,” Kittell said.

“The potential is growing for a very significant storm,” he said.

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