Seasonal variations in the sedimentary regime in the mouth of the Seine river, a macrotidal estuary, are described for a 3-year period. The aim of this study is to characterize and to understand the main governing mechanisms, using data from more than a thousand of superficial sediment grab samples or box cores gathered throughout the study period. Analyses of lithofacies and rheological properties were carried out. The distribution of sediments is governed by seasonal meteorological variations. The surface covered by mud reaches a maximum (40% of the total mouth area) during winter. After the winter, the soft mud deposits are progressively redistributed throughout the whole estuary area and onto the shelf. During the lowest freshwater flow at the end of summer, the fine-grained sediments cover less than 20% of the river mouth area. These seasonal variations mainly depend on the river discharge intensity, but are also linked to wave activity. In the study area, the amount of fine-grained deposits after high river flow periods depends on (1) volume of mud erodable within the estuary, (2) the duration of the flood tidal influx, and (3) the duration preceding the particular annual high river flow. During the last decades, filling of the estuary upstream from Honfleur has led to a downstream shift of the fine-grained sediment deposition area; following this, the present-day mud deposition area is in the open part of the estuary, in the subtidal shallow area. Subsequently, fresh mud deposits undergo intense hydrodynamical and meteorological effects, and are partly reworked by waves and tidal currents effects. In this study, it is shown that the behaviour of suspended matter and of superficial sediments is strongly influenced by short but intense events including high river flows and gales.