As the waters receded from the swamped homes, schools and businesses in San Jose on Wednesday, thousands of residents in the nation’s 10th largest city remained pitched into a state of uncertainty and sadness in the wake of a “100-year event” flood.

A day after emergency responders rescued more than 400 by boat when Coyote Creek spilled over its banks, public officials and water resource managers admitted they were ill prepared for the sweeping natural disaster.

“If the first time that a resident is aware that they need to get out of a home is when they see a firefighter in a boat, then clearly something went wrong,” San Jose Mayor Sam Liccardo said at a news conference on Wednesday. “We are assessing what it is that led to that failure.”

Officials said residents in an estimated 14,000 households were under mandatory evacuation orders and 36,000 homes in total have been affected by the flood. The devastation mirrored major flooding in January 1997 when the Guadalupe River swelled into San Jose’s neighborhoods amid widespread floods around the state.

The hardest-hit areas this week were the Rocksprings and Brookwood Terrace neighborhoods on either side of Interstate 280, and three mobile home parks farther north on Oakland Road. Six schools — including San Jose and Cristo Rey high schools, Rocketship Discovery Prep, and McKinley, Olinder and Empire Gardens elementary schools — were all within the evacuation zone.

“I think it’s fair to say when we saw the Rocksprings occurrence that we were dealing with a storm event that was on the order of a 100-year event,” said David Sykes, San Jose’s assistant city manager.

The scope of the flood’s destruction became more apparent at sunrise Wednesday after a chaotic 24 hours that involved one of the city’s largest-ever water rescue efforts. Members of San Jose’s Urban Search and Rescue Task Force went door-to-door by boat, pulling hundreds of stranded people from the waist-high filthy water.

Overnight shelters were opened at James Lick and Evergreen Valley high schools in San Jose. No one was injured in the flood, but when people would be cleared to return home remained unknown due to hazardous pollutants that seeped into the floodwater.

“It is not safe for people to go into the water and into their homes,” Liccardo said. “Bluntly, the water is receding, but we are far from out of this.”

Many residents, though, went home anyway to begin sorting through their water-soaked belongings.

In the evacuation area near San Antonio and 21st streets, residents wearing flip-flops or knee-high rubber boots were shoveling water out of their driveways.

Lawn chairs, garbage cans and toppled outdoor kids’ toys were scattered throughout front yards. Cars were left abandoned in the middle of flooded streets.

“What can we do?” 42-year-old Victor Chen said worriedly outside his home on 21st Street. “What do we have to do to keep everyone safe?”

Chen, his two children, ages 8 and 10, and his wife evacuated around 7 p.m. Tuesday — hours after the Fire Department drove by announcing the mandatory order.

“It’s really tough to see. A home is all we worked for, and our family is all here,” he said. “And we had to leave it behind when the water was rising.”

The family’s garage, dining room and one of the children’s bedrooms were flooded. Toys, extra mattresses, a TV, bikes and clothing were all ruined.

The flood happened when a powerful rainstorm on Monday sent water surging out of Anderson Lake, 20 miles away in Morgan Hill.

An especially wet winter pushed the reservoir to capacity for the first time in 11 years. On Saturday, water began surging out of its spillway and down the 30-mile stretch of Coyote Creek, running through San Jose, a city of more than 1 million people, to San Francisco Bay

Even though it was forecast to flood, the amount of water that came rushing down Coyote Creek the day after Monday’s storm caught many by surprise.

“We’re going to be learning from this as we go forward and making adjustments for the future,” said David Vossbrink, a spokesman for the city of San Jose.

But some experts said flooding was almost a guarantee and should have been anticipated.

“Anderson was already full,” said Jan Null, a meteorologist with Golden Gate Weather Services. “And another 3-4 inches of water came into the watershed. I was not surprised by the flooding. I was surprised by the response to the flooding.”

The creek peaked Tuesday afternoon at 13.6 feet, according to a monitoring site in Edenvale. That was well over its 10-foot flood stage and was the highest it has ever been recorded.

Water resource officials had anticipated the creek would reach about 12 feet Tuesday — a level that would flood parts of San Jose, including the Rocksprings neighborhood, according to the National Oceanic and Atmospheric Administration’s river forecast center.

But San Jose officials took few steps to warn those in the threatened area. Santa Clara County Water District officials said they put out alerts on social media and through Nextdoor, a private social network for neighborhoods.

San Jose city officials said there were some alerts that went out on the county’s online emergency notification system that residents must sign up for. There were no door knocks before the river was forecast to flood.

“The fundamental cause of this is over spillage at Anderson Dam,” Liccardo said. “It is a unique event. There’s no question that there were elements of this that were very foreseeable.”

Any future storms on par with Monday’s atmospheric river may bring about more flooding, forecasters said. Rain that was on track to hit the Bay Area over the weekend was not expected to flood Coyote Creek, according to the National Weather Service.

“The best we can do now is monitor the reservoir and warn people ahead of time,” said Gina Adriano, a spokeswoman with the Santa Clara County Water District. “For the next storms, I think it’s a matter of early messaging. But it’s really the power of Mother Nature that we’re up against, and I don’t think that’s a battle anyone can win.”

Adriano said the district has been releasing the maximum 420 cubic feet of water per second out of the base of Anderson Dam since Jan. 9.

The 49-inch-diameter release pipe is the only way to get water out of the reservoir before it rises to the spillway and overflows. Once that happens, dam operators can only watch.

During heavy rain storms, thousands of cubic feet of water per second rushed into the reservoir through the surrounding watershed.

Knowing what caused the flood provided little consolation to the thousands of evacuees — many resentful about the lack of warnings by the city.

“Nobody came by and gave us a warning,” said Jason Loureiro, whose basement unit on 24th Street and Shortridge Avenue was underwater. “They should have given us a heads-up. We would’ve gotten sandbags and prepared the whole area.”

Loureiro said he was “more sad if anything,” adding that he has to “start all over pretty much."

Hien Nguyen, 70, looked at her apartment on Welch Avenue on Wednesday morning with nothing but a fanny pack and the clothes on her back.

“l couldn’t get anything. One (pair of) slacks. One blouse,” she said, throwing up her hands in resignation.

She said her grandson, who lives in the unit behind her, attends DeAnza College but his books, laptop and backpack were stuck inside. His BMW was parked in the garage, and is likely inundated with water.

“After this, we have to throw away everything,” she said.

San Jose city officials created a community relief fund for the victims that can be found through a link at sjmayor.org.

Jenna Lyons, Sarah Ravani and Evan Sernoffsky are San Francisco Chronicle staff writers. Email: jlyons@sfchronicle.com, sravani@sfchronicle.com, esernoffsky@sfchronicle.com Twitter: @jennaJourno, @SarRavani, @EvanSernoffsky