This study details the sedimentary infilling of an original tidal-dominated estuary system during the final stage of the last marine transgression. The Bay of Brest is confined and connects the rivers Elorn and Aulne, to the sea of Iroise by a narrow strait encasing a well preserved paleo-channel. The compilation of high- and very-high-resolution bathymetric and seismic data, constrained by sediments datations, allows us to classify the paleo-morphology of the bay into three stepped domains: the paleo-valley floor surrounded by fluvial terraces, the central plateau, and the shallow embayments. Taking into account the main factors controlling the infilling, including sea-level rise, substratum morphology, and hydrodynamics, the stratigraphic scheme of the bay has been reconstructed. The lowstand system track (LST) is assumed to correspond to relict Pleistocene continental deposits associated with the last low sea level around 21,000 cal yr B.P. The transgressive phase, represented by the transgressive system track (TST), is divided into two parts. The lower part (TST1) constitutes the first stage of transgressive deposition in the bay. Starting around 9000 cal yr B.P. and currently conserved in the shallowest parts, it is characterized by tidal flats associated with deposits in the inner estuary. This stage ends at about 7000 cal yr B.P. and is separated from the upper part (TST2) by a tidal ravinement surface that occurs around 7700 cal yr B.P. at the foot slope. TST2 formed sand bodies in the central part of the bay between 6800 and 3000 cal yr B.P. These deposits, interpreted as tidal banks, are associated with the outer estuarine environment. The maximum flooding surface (MFS), dated around 3000 and 2000 cal yr B.P., marked the installation of a highstand system track (HST) under the combined influence of tidal currents, storms events, and anthropogenic activity. The geometry deposition of each system track is controlled at the first order by the combination of the irregular Holocene sea level rise and the inherited rocky substratum morphology. The retreat of the shoreline, and estuarine environments, is function of the successive flooding of stepped domains. The direct evolution of the volume of the assumed accumulated sea water in the bay favoured the gradual installation of the present-day hydrodynamic circulation.