Born into a seafaring family from Biscay, Zubiaur started his naval career in 1568 plying between the ports of Bilbao and Flanders, where he worked under the command of the Grand Duke of Alba.

After getting promoted to General for his naval achievements in the Low Countries, during the Brittany campaign he won several battles against the English for Philip II of Spain, the most famous of them during the relief of Blaye.

During the 4th Spanish Armada, this time sent to Ireland, Zubiaur made landfall at Castlehaven in December after being driven back by contrary winds.

In 1604, inspired by the works of engineer Peter Morice in London, he built an advanced waterwheel system for the irrigation in Valladolid, similar to the Artificio de Juanelo.

During the ensuing battle, Zubiaur was wounded and lost two ships and 400 men, but he managed to save the fleet and find shelter at Dover, under the protection of the English artillery, now allied to Spain.