By Thursday the sun was out, and the sky was a brilliant blue.

The wreckage from the night before was everywhere.

Remnants of Hurricane Ida, which left at least 43 people dead as the storm roared through New York and New Jersey, scattered cars and shut down the New York subway system; it downed trees, flooded basements and submerged some dense city neighborhoods in chest-high water. The smell of seawater permeated New Jersey towns far from the Atlantic coast.

The storm dumped a record 3.15 inches of rain in just one hour in Central Park, topping the previous high of 1.94 inches in an hour set just 11 days earlier during Hurricane Henri.

The storm’s severity caught officials off guard. “We did not know that between 8:50 p.m. and 9:50 p.m. last night that the heavens would literally open up and bring Niagara Falls-level water to the streets of New York,” said Gov. Kathy C. Hochul, who declared a state of emergency in New York City on Thursday, in just her second week in office. “Could that have been anticipated? I want to find out.”

Residents who had taken precautions against Henri said they felt blindsided by the wrath and suddenness of Ida.

“I just don’t understand how it happened,” said Secoyah Brown, 30, owner of the shop Whisk & Whiskey in Gowanus, Brooklyn, where three feet of water surged into her basement. At the height of the Wednesday storm, she opened the store to 10 neighbors who needed temporary shelter.

As emergency storm alerts flashed on smartphones with alarming regularity, Ms. Brown spent the night in the shop, wondering what else the storm might bring. “I slept here, to take care of my baby,” she said, referring to her store, which opened two months ago. “It’s very, very stressful. We just got past Henri and now this.”

In Passaic, N.J., Mayor Hector Lora posted on Facebook that 60 residents who were evacuated on Wednesday evening were returned home. But there were still people unaccounted for, and cars abandoned throughout the city. Plus the threat of more flooding to come from the Passaic River as the waters crest.

The mayor said officials were still assessing whether flooding would continue to be a concern. “But as of right now in our downtown area,” he said, “we’ve been able to send people back home.”

Travelers were stuck at airports, where more than 500 flights were canceled and some people hunkered down overnight; they were stranded on highways that suddenly became impassable rivers; thousands were marooned at the Billie Jean King National Tennis Center in Queens, site of the United States Open, where rain gushed through the domed roof of one stadium, suspending play. At Arthur Ashe Stadium, where Diego Schwartzman was playing Kevin Anderson in the second round of the tournament, spectators learned that the subway was not running and that many of the streets around the tennis center were closed.

Subways snarled; some tennis fans made it as far as Times Square, only to be stuck there when all service was suspended. Video on Twitter showed a wall of water cascading onto a subway platform at 28th Street in Manhattan as riders waited for a train.

In Bushwick, Brooklyn, Hannah Harrington on Thursday picked her way through streets littered with cars abandoned and turned sideways by the floodwaters as she returned home from a failed attempt to leave the city.

Live Updates: New York Flooding

Ms. Harrington, 34, a writer and legal assistant, was on her way to La Guardia Airport when she learned that her flight to Florida had been canceled.

Still, she counted herself fortunate. Her first-floor apartment did not take on water on Wednesday night, although the building’s basement flooded.

A basement-level day care facility across the street was rendered uninhabitable. “The trash had apparently swept into their building,” Ms. Harrington said. “It’s crazy.”

In Elizabeth, N.J., water from the Elizabeth River surged 8 to 10 feet, flooding homes and carrying raw sewage, forcing the evacuation of all 600 residents of the Oaks at Westminster apartment complex, where at least four people died.

John Pinto, who turns 82 on Friday, had to abandon his car when it stalled in the rising floodwaters at around 10:30 p.m. on Wednesday. The water outside was already up to his chest. He said he sought help at the Elizabeth firehouse located right across the street from the Oak complex but found it empty — cleared out by firefighters hoping to save their engines from the flood.

Eventually someone gave him a lift home.

“I thought it was my last day,” he said. When he returned with his son Tony to retrieve his car, they found it ruined.

James Rotondo, 62, arrived at his shop, Goldberg’s Famous Deli, in Millburn, N.J., at 4 a.m. to find that the Rahway River had rushed over the stone walls and into the back of his building. The lock to the store was filled with so much mud that his key did not work.

Once inside, he found a freezer that the water had carried from the back to the storefront. A refrigerator was upended, and his heavy counter was turned around. The water line was four feet, and the town immediately got him a pump to get water out of his basement.

Nearby, the rushing waters pulled a black S.U.V. and two dumpsters into the river.

“It’s upsetting,” Mr. Rotondo said. “It’s frustrating. Unreal.”

Yet by Thursday afternoon the subway system and the commuter trains were nearly back to normal, Governor Hochul said.

Her predecessor, Andrew M. Cuomo, had sought to make himself into a national hero during the coronavirus crisis, before resigning last month over multiple charges of sexual misconduct. Ida is Ms. Hochul’s first major crisis.

She intended to learn why state and city officials were not better prepared.

“I am going to intensely ask those questions,” she said, “get the answers, and when I get them I will share them with the public, because every crisis is an opportunity to learn and to improve and be more prepared for the next one.”

Reporting was contributed by Kevin Armstrong, Precious Fondren, Matthew Goldstein, Lauren Hard, Sean Piccoli and Nate Schweber.

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