The Roman city of Pollentia was founded on the north-eastern coast of Mallorca (Balearic archipelago) after the Roman conquest of the island in 123 BCE. There is evidence that the city had two harbours, a small harbour located to the north, whereas the main harbour was located to the south of Pollentia. Our study focuses on the southern harbour, on a coastal plain in proximity to the ancient city. Four sedimentary cores were taken and bio-sedimentological analysis was performed. Here, we describe the palaeogeographical changes in this area, evolving from an open lagoon environment between ca. 3200 and ca. 500 cal. years BCE to a semi-enclosed lagoon during Roman times. Progressively, the lagoon became silted and was isolated from the sea by the development of a large sand spit, probably during the second half of the first millennium CE. We also discuss the water depth, linked to the palaeosea level, which is important in defining the possible ancient harbour location.