The late Holocene is of particular interest to our understanding of the evolution of coastal sedimentary systems because this period encompasses warmer and cooler periods, and rising sea level in northern Europe. Based on an approach combining AMS 14C, sedimentological and rock magnetic analyses on sediment cores complemented with seismic data collected in the macrotidal Bay of Vilaine (south Brittany), we document the depositional history of the inner bay coeval to the mid- to late-Holocene transgression in south Brittany. Correlation between sedimentary archives revealed the main sedimentary infilling phases during the last 6000 years. Four units (U1–U4) are recognized in the coastal sediment wedge of the system, corresponding to the stepwise marine invasion of the bay. We show that (1) marine inundation, due to the steep morphology of the bedrock, is diachronous between distal and proximal records. A time lag of 1000 years is inferred over a distance of less than 5 km; (2) in the outer areas, the sedimentation has been condensed since 3000 years; (3) proximal estuarine archives offer the best record of sedimentary processes covering the last 2000 years, including the Medieval Warm Period (MWP). Correlations in proximal records in the Bay of Vilaine assess the connection between coastal sedimentary dynamics, climatic conditions and anthropogenic activities during the MWP. We match the preservation of clay deposits to increased river-borne suspended matter transported to the estuary probably as a result of accelerated land-use development (higher soil erosion) in the catchment area between ca. 880 and 1050 AD. Because the preservation of estuarine sedimentary successions is favoured when coastal wave sediment reworking is minimal, it is proposed that the prevailing climatic regime in south Brittany during the MWP likely resembled to that of the preferred negative phase of the North Atlantic Oscillation (NAO). Our data are fairly consistent with other late Holocene records from northern Europe including the Atlantic seaboard. However, they outline the difficulty in interpreting climatic and anthropogenic signatures in coastal sedimentary records where high-resolution chronologies required to unravel their respective influences are still missing.