The earliest reference to a shipyard in Pisa is in the early 1200s when the city shipyard was built to the west immediately outside the walls. This shipyard was intended for both shipbuilding and repairs to serving galleys. In about mid-century, fortifications were built around this area close to the city walls.

In those days, a channel joined the dockyard to the river; it was probably situated near the southwestern corner of the fortifications, and entered “obliquely” into an internal basin surrounded by a round-arched sheds, the only remaining trace of which are the seven arches that can be seen incorporated into the stretch of 13th century city walls on the south. Towards the end of the century, several fortified towers were erected.

A number of changes appear to have been made in the 14th century: the city walls were raised in height, the 13th century sheds demolished and the southern defensive wall moved northwards. The canal was moved to a more central position and new sheds, with gothic arches, were built for the galleys. These are the five aisles of ruins still seen today on the western side of this area.