The Bay of Brest (BB) is a mixed, tide-dominated estuarine system. The shore terraces of this bay are occupied by modern free-living (calcareous) coralline algae locally termed “maerl”, organized in bed-like morphologies (rhodolith deposits). Cores retrieved from around the bay reveal fossilized primitive maerl beds of Holocene age, interbedded in sandy-silt sedimentation. The alternation between biogenic constructions and estuarine sedimentation may provide evidence of varying environmental conditions of the late-Holocene period. This paper mainly focuses on the results of chronostratigraphic and bio-sedimentological interpretations of coring data collected in less than 15 m of water depth in an attempt to decipher the main stages of maerl colonization in the bay. In particular, this study raises several significant points allowing to draw links between centennial to millennial-scale climatic changes in marine estuary sedimentation and episodes within the development of maerl biocenoses. The paleo-bathymetry of the coastal terraces has not changed significantly over the last 5000 years. Yet, the first maerl occurrence only appeared around 2000 cal yr B.P., likely showing that the environmental conditions were not favorable for their emergence prior to that time. Pioneer maerl beds developed on coarse shell deposits inherited from the paleostorms affecting the Atlantic coasts during the colder climatic period of the Iron Age (3100–1950 cal yr B.P.). The accumulations then aggraded at various and discontinuous rates, sometimes reaching up to 2.1 m/kyr. Maerl beds temporarily disappeared in the southern part of the Bay of Brest when sedimentation rates increased throughout the bay during the Dark-Age cold period (1375–1250 cal yr B.P.), suggesting that maerl formations could not keep up with sedimentation rate exceeded a certain threshold. Muddy sedimentation conditions also dramatically changed on two occasions, with the establishment of coarse storm levels, set at the intervals 825–600 cal yr B.P. (MWP) and 113–0 cal yr B.P. But maerl deposits reseed the environment as a result of each new cold period, demonstrating the persistence of such coralline algae against drastic palaeoenvironmental changes in coastal areas.