Around 90 firefighters are working to stem the flow of water, and have warned that the clean-up could last all day.
It is feared that gas, electricity and heating pipes could have been damaged by the flood.
The Brünnerstrasse and Floridsdorfer Hauptstrasse have been closed off between Weisselgasse and the Floridsdorfer Spitz, and some smaller roads in the area are also closed.
Public transport has also been affected. The 25 tram is only running between Aspern and Kagran. The 26 tram is operating on two routes - between Kagran and Hausfeldstrasse and between Nordbrücke and Strebersdorf. The 31 tram is only running between Floridsdorf market and Stammersdorf, and between Schottenring and Leopold Ferstl Gasse.
The 28A and 29A bus routes have been diverted. Drivers have been warned to avoid the Floridsdorf area if they can.