People wearing thigh high boots cross flooded St. Mark's square by the Doge's palace.
Prime Minister Giuseppe Conte described the flooding as "a blow to the heart of our country".
This week's flooding was second only to the waters that inundated the city in 1966.
He later tweeted that the cabinet approved an emergency fund of 20 million euros ($22 million) that will be used to financially support the city and the population.
Several museums remained closed to the public on Thursday. It comes as Venetians woke to alarms demonstrating that the tide would stay high in the coming days.More news: Pentagon chief open to military adjustment in Korean Peninsula
More than 85% of Venice was flooded, authorities said. Water levels have turned the square into a glorified pool, and indeed, one man was seen swimming near St. Mark's Basilica.
"Beyond propaganda and deceptive reading, we are voting (for) a regional budget that spent 965 million euros over the past three years in the fight against air pollution, smog which is a determining factor in climate change", he said in a statement.
Another wave of high water followed on Wednesday.
But the high waters, or acqua alta, have caused many tourists to leave the city, and many small business owners are appealing to them to return.
The economy of Venice relies nearly entirely on tourism. The real reason for Venice's plight is whichever idiot who decided all those years ago to build the city on a series of swampy islands at the edge of a lagoon.
There is nothing weird about Venice flooding at this time of year.
According to the BBC, the tide monitoring centre recorded water levels at 1,87 metres.More news: Meet puppy with tail on its head rescued from the streets
The project is an integrated system consisting of rows of mobile gates installed at the Lido, Malamocco, and Chioggia inlets that are able to isolate the Venetian Lagoon temporarily from the Adriatic Sea during acqua alta high tides.
A newlywed couple walks across a flooded square on 14 November, 2019 in Venice.
Work on the project began back in 2003 and has already cost billions of euros. However it has faced many corruption and bribery allegations. Subsequently, Brugnaro blamed the flooding on climate change.
The Italian city of Venice deals with the aftermath of one of the worst floods in its history. However, if we look at the top 10 tides, five have occurred in the past 20 years and the most recent was only last year.
While we should try to avoid attributing a single event to climate change, the increased frequency of these exceptional tides is obviously a big concern.
Called Moses, the moveable under-sea barriers are meant to limit flooding of the lagoon city, caused by southerly winds that push the tide into Venice.
Climate change is exacerbating the situation as melting ice, snow and glaciers around the world are raising sea levels.More news: Spotify is now testing the display of real-time lyrics during song playback
Together with other measures, such as coastal reinforcement, the raising of quaysides, and the paving and improvement of the lagoon, MOSE is created to protect Venice and the lagoon from tides of up to 3 metres (9.8 ft).