The water level has only reached above 150 centimeters five times since records began, most famously in 1966, when it hit 194 centimeters and devastated the historic city center.
A volunteer firefighter who was helping with the emergency response in San Martino in Badia in the country's north is also reported to have died.
Three-quarters of the Italian city, beloved by British tourists, is now underwater, with even elevated sidewalks being inundated in certain areas.
On Sunday, as floodwaters rose, the Venice Marathon was taking place.
St Mark's Square, which had to be closed on Monday due to the floods, reopened on Tuesday as cafe and restaurant owners began bailing out their businesses in the hopes of attracting customers.
The UK Foreign and Commonwealth Office (FCO) has now updated their travel advice to the region. "You should follow the advice of local authorities".
Croatia's Adriatic coast has also been battered by gale-force winds and heavy rains that have flooded streets, cut off power and ensnared road and maritime traffic.
Tourists and locals alike have been photographed wading through waist-high water.
Experts say there are three main reasons for high water in the city: the rising floor in the lagoon caused by incoming silt; the undermining of the islands by the extraction of methane gas in the sea off Venice; and the overall increase in sea levels caused by global warming. The project, nicknamed Moses, is long overdue, beset by cost overruns and corruption scandals.
Officials also closed major tourist attractions, including the Colosseum and Roman Forum.
Two young people died south of Rome when a tree hit the vehicle they were travelling in, while another person was killed and several injured in the nearby town of Terracina after howling winds brought down scores of slender, tall pine trees. There's a possibility being expressed that flooding this week could reach the levels of floods that Italy last experienced some 22 years ago, when the Arno river flooded the city of Florence, killing hundred people and destroying millions of rare artworks and books.
"The exceptional wave of bad weather leaves us with a dramatic toll: nine dead, four serious injuries and one person missing, " said Interior Minister Matteo Salvini.