The lake sediment record was used to reconstruct past vegetation dynamics and human impacts from the middle Neolithic (6500 cal. B.P.) to the Middle Ages (1500 cal. B.P.) around Lac d'Antre in the southern Jura mountains of France. This lake was surrounded by the Gallo-Roman sanctuary of Villards d'He'ria, which has been widely investigated by archaeologists and enables a comparison between palaeoenvironmental proxies and archaeological data. Pollen and microscopic charcoal analyses were conducted on a 500 cm sediment core with eleven radiocarbon dates providing the chronological control. In a mixed oak woodland context, the successive development of Taxus, Fagus and Abies were mainly caused by climatic variations during the Neolithic, in which there was weak human impact. The first significant signs of human activity were detected during the Bronze Age from 3900 cal. B.P., followed by an increase of human pressure and woodland clearances during the Iron Age, from 2700 cal. B.P. The occupation of the Gallo-Roman sanctuary was continuous with the Iron Age occupation. All the analysed palaeoenvironmental data indicate that the strongest human impact occurred during the Gallo-Roman period, which matches the occupation of Villards d'He'ria previously dated by archaeologists from 2000 to 1700 cal. B.P., 1st to 3rd century A.D. Moreover, there appears to have been a new period of human settlement close to the lake at the beginning of the Middle Ages. The low charcoal accumulation rate (CHAR) recorded during the Bronze and Iron Ages suggests that fire was not the main agent used to clear the dense woods to create new cultivated fields and pastures. High CHAR values recorded during the Roman period may represent fire use for domestic and agro-pastoral activities.