Species composition of desmid algae and their habitat preferences in water bodies of Ekaterinburg city were studied during the 2013–2017. Thirty-seven species and subspecific taxa which belong to 12 genera and 2 families were identified, of which 17 species are new for the eastern macroslope of the Middle Urals. Canonical correspondence analysis, which was performed to reveal habitat preferences, demonstrates that the majority of analyzed species prefer quarry lakes, ponds and overgrown lake shores, contrary to fens and rivers.