The town was founded in 1158 as a linear settlement. Hirschstetten was often flooded due to its proximity to the then-unregulated Danube. In 1809, during the Battle of Aspern-Essling in the War of the Fifth Coalition against Napoleon, the town was partly destroyed. Hirschstetten grew in size in the 1870s after the Danube regulation and the creation of the Marchegger Ostbahn railway line.

In 1904, Hirschstetten was merged into Floridsdorf, the 21st district of Vienna. In 1938, the neighbourhood became part of the 22nd district of Groß-Enzersdorf, part of the new Greater Vienna. In 1945, the town was almost completely destroyed in a bombing attack. In 1954, the 22nd district was reduced, and renamed Donaustadt.