Mayor Luigi Brugnaro ordered the iconic St Mark's Square closed on Friday as the latest sea surge struck with strong storms and winds battering the region.
It reached a high of 1.54 metres (five feet) just before midday — lower than Tuesday's peak but still dangerous.
“I'm forced to close the square to avoid health risks for citizens… a disaster,” Brugnaro said.
In the afternoon the square reopened as water levels receded.
But civil protection authorities issued a weather “red alert” for the Venice region on Saturday, warning of violent winds.
Churches, shops and homes in the UNESCO city have been inundated by unusually intense “acqua alta”, or high water, which on Tuesday hit their highest level in half a century.
“We've destroyed Venice, we're talking about one billion (euros) in damage and that's just from the other day, not today,” Brugnaro said.
The crisis has prompted the government to release 20 million euros ($22 million) in funds to tackle the devastation.
“It's shocking to see this, having water up to your knees,” Mexican tourist Oscar Calzada, 19, told AFP Friday.
Surveying the damage, Culture Minister Dario Franceschini warned the task of repairing the city would be huge.
More than 50 churches had suffered damage, he said.
“Seeing these places first-hand gives the sense of a much greater disaster than TV images show,” Franceschini said.
Hotel reservations cancelled
Prime Minister Giuseppe Conte declared a state of emergency for the city on Thursday.
Residents whose houses have been hit are eligible for up to 5,000 euros in immediate government aid, while restaurant and shop owners can receive up to 20,000 euros and apply for more later.
Mayor Brugnaro on Friday also announced the opening of a fund where people in Italy and around the world could contribute to the historic city's repair.
One tourist, Italian Nicole Righetti, said she would be willing to pitch in.
“It would be a shame to no longer be able to see these places, and I think everyone should give,” Righettii said.
Some Venetians, used to the inconvenience of their city's rising waters, nevertheless expressed frustration.
“All the stock in the basement is lost,” lamented Luciano, a worker at a shop along St. Mark's Square.
He said he remembered well the infamous “acqua alta” of 1966, when the water rose to a level of 1.94 metres, the highest-ever since records began in 1923.
“These so frequent high waters have never happened before… this time there's so much more damage than in the past,” he said.
Hotels reported cancelled reservations, some as far ahead as December, following the widespread diffusion of images of Venice underwater.
Climate change warning
Tuesday's high waters submerged around 80 percent of the city, officials said.
Many, including Venice's mayor, have blamed the disaster on global warming and warned that the country prone to natural disasters must wake up to the risks posed by ever more volatile seasons.
The Serenissima, as the floating city is called, is home to 50,000 residents but receives 36 million global visitors each year.
A massive infrastructure project called MOSE has been under way since 2003 to protect the city, but it has been plagued by cost overruns, corruption scandals and delays.