The progradation of the Medjerda delta has been the subject of many studies since the 19th century. The scale and the rapidity of this phenomenon interested researchers in various fields early on, such as geomorphology, geology, palaeogeography, history, archaeology, or geoarchaeology. Indeed, the delta prograded by around 10 km over 3 millennia. At the time of its foundation supposedly at the end of the 12th century BC, the Phoenician city of Utica was located on a promontory bathed by the sea, but the sediments carried by the Medjerda progressively sealed the bay, leaving the tip of the Utica promontory now 10 km inland. This area is therefore an exception to the general pattern along the Tunisian coast, since as over the same period everywhere else there is a regression of the coastline, owing to a sea level rise of several decimeters. Based on multi-proxy analyses of two coring transects, this paper aims to reconstruct the palaeoenvironments and the palaeogeography of the Medjerda delta’s progradation since the mid-Holocene, some aspects of which are described in ancient sources. The results highlight in particular an episode of high-intensity flooding around the 4th century AD, which is consistent with episodes of high floods and an increase in sedimentation rates recorded in the watershed at the end of the Roman period. The gradual abandonment of the city of Utica can certainly be related to the activity of the Medjerda River, but our results show that it is because of an increase of fluvial sediment contribution in connection with an erosive crisis in the headwaters, and not because of the change of course of the river, which had occurred long before.