Venice closed St. Mark's Square before the expected third major flood in less than a week as rain showered the rest of Italy and warnings were issued in Florence and Pisa.
Venice forecasts "familiar alto" or high water, with 160 cm (over 5 feet) for Sunday, lower than 187 cm on Tuesday – the highest level in half a century – but still dangerous.
"Maximum attention for today's tide," tweeted City Mayor Luigi Bruniaro, who has estimated damages to date from over 1
"St. Mark's Square is closed. Safety first, he said, when seawater began to swamp the already devastated historic city, where authorities declared a state of emergency.
To the south, Tuscany President Enrico Rossi tweeted a warning about the "flood wave" of Arno and said the boards were installed on the swollen banks of the Pisa river "as a precaution".
Italian media show that paratroopers are helping to strengthen the Pisa river defenses, with authorities monitoring the same river in Florence after a torrential rain rises dramatically overnight.
Arno flooded the devastated Renaissance jewel of Florence in 1966, killing about 100 people and destroying thousands of priceless works of art. Florence civil protection departments advised citizens not to stay near the banks of the Arno River.
The renewed threat of extremely intense high tides in Venice came after a short break on Saturday.
Emergency workers removed temporary lanes from St. Mark's Square and the water began to rise on Sunday, with only police and soldiers visible at noon.
The main tourist site was already closed on Friday for a few hours as heavy storms and winds invaded the region, leaving it submerged by sea waves.
Churches, shops and homes, a UNESCO World Heritage Site, are also flooded in the city.
Since 2003, a large-scale infrastructure project called Mose has been implemented to protect the city, but a multi-billion euro project has been put in place. from cost overruns, corruption scandals and delays.
"We didn't expect high waters to be so high," says Guido Fulgenzi, who planned to open his cafe at St. Mark's Square this week.
"We pay the prices [for the Mose project not being completed]," he said, swooping around in his flooded kitchen, pointing to a high watermark on Tuesday on the wall.
The crisis has prompted the government
Culture Minister Dario Francescini warned of the task of repairing a city where more than 50 churches have suffered damage will be huge.
Residents whose homes have been affected are eligible for up to € 5,000 in immediate state aid, while restaurant and shop owners can receive up to € 20,000 and apply for it later.
Most of the city's ATMs are no longer working because of the water, which makes life even more difficult for tourists and Venetians.
Older residents who remember the infamous Alta known since 1966, when the water rose to 1.94 m, say they have not seen the flood so often before.  Canceled hotels canceled reservations, some far ahead in December, after the widespread imaging of Venice underwater.
High waters on Tuesday flooded about 80% of the city, officials said.
Many, including the Mayor of Venice, blame the global warming disaster and warned that a country prone to natural disasters should wake up to the risks posed by increasingly volatile seasons.
Serenissima, as it is called a floating city, is home to 50,000 inhabitants but receives 36 million visitors each year.