Rapid environmental changes along the Mediterranean coasts influenced the sedimentary dynamics, shoreline position and human settlements in deltaic areas over the last millennia. An innovative and multiproxy approach using geostatistical modelling was developed to estimate geomorphic evolution and sediment fluxes in deltaic areas, while palaeoecological conditions and environmental changes were assessed from geochemistry and cluster analyses of molluscan fauna. This method was applied to the coastal plain of the Argens River in southern France. Depositional environments of prodelta, delta front, river channel, floodplain, marsh and abandoned channel were identified from the study of facies associations. The late Holocene sediment flux in the Argens River bayhead delta ranged from 15,800 ± 2300 to 52,000 ± 8500 m3·yr−1. The highest rate of sediment deposition between 2500 and 2000 cal yr BP was associated with increased river flooding in southeastern France. A general decrease in subaqueous sediment flux over the past 2500 years was primarily controlled by a decrease in accommodation space and delta slope. From 500 to 0 cal yr BP, a sharp increase in subaerial sediment flux probably due to hydroclimatic change was contemporaneous with a period of high flood frequency during the Little Ice Age. A southward shift of the North Atlantic westerlies combined with either a negative phase of the East Atlantic/West Russian pattern or a negative phase of the East Atlantic pattern coupled to a northward migration of the intertropical convergence zone could have led to increased fluvial activity in the lower Argens valley during the late Holocene.