The Dwejra Tower was built in 1652 during the magistracy of Grand Master Giovanni Paolo Lascaris, and was funded by the University of Gozo.

It is one of the Lascaris towers, which was meant to act as a watchtower and guard the surrounding areas from corsair landings.

In 1744, Grand Master Pinto made going to the Fungus Rock illegal because a plant, popularly known as the Maltese fungus, growing on the rock's flat top was believed to have medicinal powers, and Dwejra Tower was used as a lookout to prevent anyone climbing on the islet.

It was again used in World War II as an observation post, and on the 27th March 1943, Captain Frank Debono and Carmelo Zahra, who were stationed there, rescued an RAF pilot who had crash-landed his Mark Vb Spitfire on the cliffs overlooking the bay.

It was passed on loan to Din l-Art Ħelwa in a state of complete dilapidation.