To strengthen the ties between the Bohemian and German nobility, her father married her off to the Babenberg margrave Leopold IV of Austria on 28 September 1138.

The Bohemian-Austrian alliance was confirmed, when Leopold's younger sister Gertrude married Soběslav's nephew, Duke Vladislaus II of Bohemia, two years later.

In 1139, one year after Maria's marriage, the Hohenstaufen king Conrad III of Germany, having deposed the Welf duke Henry the Proud, enfeoffed the Duchy of Bavaria to the Babenberg dynasty, ruling the Margraviate of Austria since 976.

Margrave Leopold was Conrad's half-brother by their mother Agnes of Waiblingen; the king may also had helped to arrange the dynastical ties with the Bohemian Přemyslids.

As the marriage produced no heirs for Leopold, Austria and Bavaria were inherited by his elder brother, Duke Henry II.