The floods have left people in low-lying parts of Venice, including the popular tourist site of St Mark's Square, wading through knee-deep water.
Tourists and residents struggled to get across the city over raised walkways set up by workers as sirens and loudspeaker announcements reinforced the alert.
Under a new system, warnings and updates were also being sent out by text message.
The Centro Maree predicted earlier that floodwater would fall back to normal levels by 1800 GMT, but said another surge was expected in the small hours of Tuesday.
The entire city, which was founded on a collection of marshy islands in the 5th century and is criss-crossed by canals, suffers from periodic flooding caused by high tides.
The government has begun a multi-billion dollar floodgate project aimed at stopping rising sea levels destroying the city.