Outdoor restaurant tables and chairs could be seen bobbing in the waters, and tourists were forced to clamber through the windows of high-end hotels as the water rose to about six feet before 11 p.m. on Tuesday.
As dawn broke on Wednesday, the authorities began to survey the damage.
“I’ve seen things in San Marco I thought I’d never see,” Mayor Luigi Brugnaro of Venice told the Italian station Radio24. “It is a very difficult situation,” he added.
In a post on Twitter, the mayor blamed climate change for the city’s troubles and called for the rapid completion of a long-delayed barrier system.
Later, speaking at a news conference alongside national and local officials, the mayor said that the damage had been significant. “We’re talking hundreds of millions of euros,” he said.
The flooding was the second highest in the city’s history, after the disastrous flood of 1966, which peaked at 6.3 feet. Last year, as severe weather in Italy killed 11 people, ferocious winds drove the high tide in Venice to more than five feet above average sea level.
Residents and tourists could be seen wading through water in rain boots. The water invaded the ground floors of many historic palazzos, stores, restaurants and hotels. At least three vaporetti, Venice’s public transportation boats, sank, Italian media reported. One floated over the banks that line the city’s canals, ending up perilously close to buildings.
Famous tourist spots like St. Mark’s Square were under several feet of water by Wednesday. The crypt of St. Mark’s Basilica was flooded by more than three feet of water, the Italian news agency ANSA reported. Almost exactly a year ago, after a violent storm had swept the city, concerns were raised about the basilica’s ability to withstand the effects of the changing climate, the growing number of days in which the city was under water, and the onslaught of tourists.
By Wednesday morning, the historic piazza was expected to be under five feet of water.
“Venice is on its knees,” the mayor said in a post on Twitter on Wednesday with photos showing him walking through the basilica with the city’s principal prelate, the patriarch of Venice, Francesco Moraglia.
At the news conference the mayor said that while wandering through the city, “I found people in tears because they had lost everything. If we don’t want the city to be abandoned, we have to give certain answers. It’s not just about quantifying the damages, but about the future of this city.”
The patriarch of Venice echoed his sentiments.
“Going around the city we found desperate people, who said that a year ago they were in the same situation,” Msgr. Moraglia said. He added that the Diocese of Venice and Caritas, the Catholic charity, would provide lodgings for people who had been left homeless, giving priority to “fragile people in difficulty.”
“I hope the message passes that the city has been wounded, and that it can’t be wounded each year in the same way,” the patriarch said.
The newspaper Il Gazzettino, under a banner headline, “Acqua Alta. Fear and Anger in Venice,” described the city’s residents as “barricaded in their homes.” The home page of the city’s website bore no good news. More high water was expected in the coming days.
Italian news outlets reported that at least one man had died by electrocution while trying to pump water from his home in Pellestrina, an island that borders on the Venetian lagoon and forms a barrier against the Adriatic Sea.
Mr. Brugnaro said the situation in Pellestrina was critical because the water had overwhelmed sea walls.
“We can’t get the pumps to work because they are underwater,” the mayor said.
Luca Zaia, the president of the Veneto Region, said that Prime Minister Giuseppe Conte would arrive in the city shortly and spend the night.
Venice has also long struggled with overtourism, as officials have tried to prevent colossal cruise ships from docking on the city’s main canal after a series of accidents involving vessels that came in too fast.
In June, a cruise liner plowed into a smaller tour ship and a wharf on a canal in Venice, injuring four people and reigniting arguments about the dangers of allowing huge vessels to pass through the fragile lagoon city.
Italy has also invested billions of euros in a flood-protection system known by the acronym MOSE, but its offshore underwater dams have yet to be completed.
Though Venetian residents have gotten used to wading through flooded streets, strong winds on Tuesday coincided with the high tide, submerging the city.
“Acqua alta has always been normal,” said Lorenzo Bonometto, an expert on lagoon ecology. But the combined high tide and strong winds made the result “an exceptional event,” he said.
The frequency of acqua alta has become more troubling, experts say, and is linked to rising seawater levels, not only in Venice, but also around the world.
Sea levels are rising “at a faster rate” than experts had expected, and that is having a greater impact on the lagoon city, Mr. Bonometto said.
While flooding is a complex phenomenon with many causes, the effects of climate change on sea-level rise, and the intense rainfall that comes with the greater capacity of a warming atmosphere to hold more moisture, are increasingly recognized as factors that can boost natural variation in weather patterns.
There is also the added fact that Venice is sinking.
Luigi Cavaleri, an engineer at the Institute of Marine Sciences in Venice said the city’s subsidence and the rising sea levels meant that Venice was sinking at a rate of one-fifth of an inch a year. That means that the city will be submerged by water more frequently.
Mr. Cavaleri said last year’s storm was a much more serious event, but noted, “Floods will continue.”
Had the flood system been operational, he said, “the city might have been spared. Hopefully, it will be for the next flood.”
Mr. Brugnaro, the mayor, said a completed MOSE project could have averted the disaster — it is scheduled to be operative from 2022 — but that flood barriers were just one element of a complex system. And other elements necessary for the health of the lagoon, such as for the navigability of the canal, were still incomplete.
“We need resources and clear ideas,” he said. “For now, MOSE is a ghost. We want to see it finished.”