Tourists in Venice put plastic bags over their legs and residents wore rubber boots as water rose to knee-high levels in many parts of the lagoon city on Thursday.
Movable barriers that would rise from the sea bed to protect Venice from high tides have been in the works for years but will not be operational before 2014.
The median level of the Adriatic Sea swelled to about 1.4 metres above normal – the highest in nearly two years – sending water from the lagoon into St. Mark's Square and many narrow alleyways.
Wooden catwalks which are usually used to allow pedestrian passage over flooded areas were removed after the water rose above them, rendering them useless.
In some places, it was impossible to distinguish where canals ended and sidewalks began.
Much of Italy has been hit by heavy rain and strong winds over the past week. Flooding is common this time of year and Thursday's level, which reached a peak of 140 centimetres, was still below the 160 centimetres recorded four years ago in the worst flooding in decades.
Still, some shops and ground-floor apartments were flooded.