The National Weather Service downgraded the former hurricane to a tropical depression but not before California Governor Gavin Newsom declared a state of emergency for much of the state's south, with flash flood warnings until at least 3am local time on Monday.
Mountain and desert areas more accustomed to drought could get 12 to 25cm of rain, as much as the deserts typically see in a year, forecasters said.
The storm passed northward through Mexico's Baja California peninsula, where Pacific hurricanes are expected. It killed at least one person in Mexico amid reports of flash flooding in the peninsula, sweeping away some roads.
Images on social media showed raging torrents gushing down city streets that turned into rivers.
Hilary crossed the border on Sunday afternoon, hitting San Diego county with its first tropical storm ever recorded and becoming the first to pelt Los Angeles county since 1939, triggering serious flooding.
San Bernardino county, to the east of Los Angeles, ordered evacuations of towns in the mountains and valleys where social media images showed torrents of water, mud, rocks and trees.
In more populated Ventura county northwest of Los Angeles, the National Weather Service warned of life-threatening flooding as up to 5cm of rain fell within two hours.
US President Joe Biden ordered federal agencies to move personnel and supplies into the region after local officials prepared for days.
But Los Angeles Mayor Karen Bass still worried that people could let down their guard if Hilary left them initially unharmed but later bands of the storm swung back around to surprise those who were not prepared.
"We know that it could get much worse," Bass told a news briefing on Sunday. "My concern is that people will be a little dismissive and go out when we need people to stay at home, to stay safe."
Officials said Los Angeles county's 75,000 homeless people were especially vulnerable, as were hillside canyons and areas recently denuded by wildfires.
As a precaution, the two largest school districts in the state, in Los Angeles and San Diego, cancelled classes on Monday.
The storm stunned people in the nearby town of Rancho Mirage, where water and debris rushed over closed roads and stranded at least one utility in water that rose nearly to the top of its bed.
"It's quite amazing. I've never seen anything like this," said Sean Julian, 54, a resident of the town. "I'm seeing a lot more trees down. And there's a big tree that just fell over there, and I probably shouldn't be out here."Â
