He was the youngest son of Albert I, Prince of Anhalt-Zerbst, by his second wife Agnes, daughter of Conrad, Margrave of Brandenburg-Stendal.
When both brothers reached adulthood, they ruled the principality of Anhalt-Zerbst jointly.
Her paternal grandmother Agnes of Habsburg was a daughter of Rudolph I, Holy Roman Emperor.
The spouses were distantly related: Elisabeth's great-grandfather Albert I, Duke of Saxony, was a brother of Henry I, Count of Anhalt, Waldemar's great-great-grandfather.
They had six children: In 1365 Waldemar married for a second time to Beatrice (d. 1387), legitimized daughter of Obizzo III d'Este, Lord of Ferrara and Modena by his second wife and former mistress Lippa Ariosto.