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Tourists had to put plastic bags over their legs and residents donned rubber boots as water rose to knee-high levels in many parts of the city.
Water levels rose above 55 inches into Thursday morning (local time) and were expected to remain above critical levels "for about 15 hours," local authorities said.
It was the highest tide level since December 2010.
Venice starts flooding when waters rise about 43 inches. When the 55-inch mark is reached, 58 percent of the city is under water.
On Thursday, the famous St Mark's Square was 24 inches under water. Tide levels were expected to return to more normal levels on Friday.
Chioggia, a town on the southern edge of the Venice lagoon, was the worst hit. Tides there reached a peak of 65 inches, the third-highest level since 1966, when the area was devastated by a huge flood.
Venice, which is built on hundreds of small islands, often experiences high water in autumn and winter causing floods to the city's narrow alleyways and squares, including the famous St Mark's.
To tackle the problem, Italian authorities are building a complicated dam system, the MOSE, which is meant to insulate the city from tide levels above 43 inches.
But MOSE has been beset by cost overruns, delays, and opposition from environmental groups. The project is now expected to cost more than $US7.8 billion and become fully operational in 2016.