According to the artist, it is a symbol of how the values of modernity have been swamped by technology.
Several recent elections have been plagued by scandals, with digital manipulation from third parties appearing to influence the election of Trump in America and Britain's vote to leave the European Union.
"The rise of new digital technologies together with the smartphone has allowed the emergence of a new situation," Havsteen-Mikkelsen told Dezeen.
"Every user has become his or her own media-platform, thereby allowing the targeting of specific information through the development of psychometric algorithms."
Cambridge Analytica is a now-defunct British political consulting company that reportedly reverse engineered data mined from Facebook to help Trump and the Leave Campaign attract voters.
The Russian government is also accused of interfering in the 2016 presidential elections by using social media platforms to impersonate US citizens, undermining Hillary Clinton and promoting Trump.
"I think the Russians and Cambridge Analytica have been cunning enough to see the potentials of psychometric profiles to influence and manipulate voters via the internet," said the artist.
"Through this meddling, a certain sense of democracy has 'sunk'."
Swiss-French architect Le Corbusier established the modernist movement in architecture, and Villa Savoye is one of his most famous works.
Built in Poissy, France, in 1931, it was the manifestation of his purist ideals that rejected unnecessary ornamentation in favour of clean white lines and open plan interiors.
The architect often praised the design of ocean liners and incorporated their design elements in his work, so sinking of one of his most iconic buildings into a body of water is a poignant allegory.
A barge built by Le Corbusier as a homeless shelter in 1910 actually sank in Paris earlier this year after the Seine flooded. Plans are underway to re-float the boat and continue restoring it so it can become a museum.
Le Corbusier himself drowned in the Mediterranean off the southern coast of France in 1965.
For Havsteen-Mikkelsen, who has been painting and sketching the Villa Savoye for a decade, Le Corbusier's masterpiece embodies the essential values of modernism.
"It encapsulated a sense and use of critical reason as a way of creating a better world," he explained.
Critical thinking, he believes, is what is needed most to fight the proliferation of disinformation via technology.
"The foundation of modernity has been seriously challenged," Havsteen-Mikkelsen said.
"The election of Trump and Brexit are symptoms of a larger malaise inherent to our globalised world. Modernity is still there – but it needs to be rescued, excavated, and re-built in a new form."
Flooded Modernism is made from white-painted wood and plywood with plexiglass windows and blocks of styrofoam added for buoyancy.
The free to view festival runs until 2 September 2018, after which the 5,000 kilogram installation will be towed back to the quayside and dismantled.
In London a group of activists flew a giant balloon shaped like Trump as a nappy-wearing, phone-clutching baby near the Houses of Parliament in protest against the US President's visit to the UK.
Photos courtesy of the artist and the Floating Art Festival.