The city, which suffered its worst flooding in 50 years on Tuesday, will face a high tide at around 160 cm (5.25 feet) at 1200 GMT, the city's centre for forecasting tides said.
Authorities in Florence and Pisa were also closely monitoring the Arno river, whose water levels rose rapidly in the night due to heavy rain.
The mayor of Venice, Luigi Brugnaro, said on Saturday that the city was preparing for another "tough day". However, he said the situation was expected to be less dramatic than Tuesday when the flooding left squares, shops, homes and hotels inundated.
Brugnaro, who has been appointed special commissioner to deal with the emergency, estimated damages from the flooding in the city since Tuesday at around 1 billion euros ($1.10 billion).
On Tuesday the tide peaked at 187 cm (6.14 ft) at 10.50 p.m. (2150 GMT), just short of the record 194 cm set in 1966. In normal conditions, tides of 80-90 cm are generally seen as high but manageable.
Italy's longest river, the Po, which runs across northern Italy passing through Turin, was also being monitored on Sunday after its level rose by a metre and a half in the last 24 hours due to heavy rain.