On Tuesday, water levels topped only briefly the 80 centimeters that floods St. Mark's Square, one of the city's lowest points.
Almost all of northern Italy was on alert due to the violent storms with wind gusts up to 100 kilometres per hour and the rainfall in some places equivalent to the amount of rain that falls over several months.
Here are some of the most dramatic pictures from the overwhelming flood.
The public transport company closed the water taxi service due to the emergency, with connections remaining active only to the outlying islands.
Heavy winds raised the water levels by more than five feet, causing the worst flooding in a decade.
Venice's central St Mark's Square was closed on Monday afternoon, after the water level reached "acqua alta" (high water) of 156cm (5.1ft).
Venice, which is famous for its canals, is frequently overwhelmed by water in the period from October to December, but the recent flooding has seriously affected the area.
At least three quarters of Venice was under water while large parts of Italy experienced flooding, reported AP.
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Shops owners were pictured on social media using water pumps to protect their livelihoods.
Others, including tourists, donned thigh-high wellies or took off their shoes to wade through the water.
In the province of Frosinone, south of Rome, two people died after a tree fell on their auto, while in the southern region of Calabria, a man was reported missing.
Flooding at high tide has become much more common in Venice because of climate change - a problem that will continue to worsen as seas rise thanks to increasing temperatures and melting ice sheets. That happens, on average, four times a year in Venice.
Around 101 people were killed by the 1966 flood of the Arno and millions of masterpieces of art and rare books were also destroyed.
The Interior Ministry urged officials in storm-struck regions, about half of the country, to consider closing schools and offices for a second day Tuesday.
The national Civil Protection Agency issued multiple weather warnings as storms swept across of the country, Reuters reported.