A multiproxy analysis (sedimentology, geochemistry and pollen) of sediments recovered in the Butrint lagoon (Albania) allows us to reconstruct the environmental changes that occurred in the area during the 1st millennium AD. In this paper, we compare these analytical results with the evidence provided by archaeological investigations carried out at the site of the Roman city of Butrint (surrounded by these lagoon waters) and in the city's hinterlands. From this, we can say that different periods of farming and siltation (AD 400–600 and 700–900) were accompanied by increased run-off and wetter conditions in the region. This coincided with the territorial and economic expansion of the Byzantine empire, suggesting the key role of trade in the profound land use changes experienced in Butrint.