Willem Hondius was one of seven children of Hendrik Hondius the Elder (1573–ca 1649) and Sara Jansdochter. A connection with the Hondius family of cartographers in Amsterdam is possible but has not been established. In 1636 Willem visited Gdańsk (Danzig) in Royal Prussia.
In 1641 he moved there from The Hague for good.
Hondius was supported at the royal court of King Władysław IV Waza. The King awarded him the title of Chalcographus privilegialus (privileged engraver) and Chalcographus Regius (Royal engraver).
In August 1651, in the wake of the Khmelnytsky Uprising, Hondius joined the army of Janusz Radziwiłł conquering Kiev. The first ever portrait of the famous Cossack leader Bohdan Khmelnytsky was engraved during this campaign.
Nothing is known of Hondius after 1652, though he may have lived until 1658.