Residents and tourists were left to wade on Sunday, with 70 percent of the city flooded, including pathways along Venice's fabled canals.
Authorities said a strong southerly wind had piled up water in the lagoon. By late afternoon Sunday the level had receded slightly to 1.4 meters (4.6 feet) above normal.
Venice is built on hundreds of small islands. To tackle high water in the future, a complicated dam system is being built to become operational in 2016.
The 6 billion euro ($7.8 billion) project - known by its Italian acronym, MOSE, for experimental electromechanical module - has been beset by cost overruns and criticism from environmental groups.
Heavy rainfall and floods were reported in many parts of northern Italy on Sunday. In Toscana, 200 residents had to flee their homes. In the province Massa Carrara, 230 millimeters (9 inches) of rainfall was recorded in just four hours.
ipj/mkg (AFP, dpa, dapd)