The genesis and distribution of marine notches around the microtidal Mediterranean basin has been widely debated in recent years. Here we provide new climate and geomorphological insights into the factors controlling notch formation based on the bathymetric distribution of marine notches found in Marseille Bay (NW Mediterranean). In this area, the notches exist (i) either near present Mean Sea Level (MSL); or (ii) at ∼35 cm below the MSL, but with no notch present at higher elevations on the same profile. We investigate the genesis of this unusual notch distribution using bio-geomorphological surveys, numerical modelling of nearshore hydrodynamics and palaeo-climate data. This analysis shows that the submerged notch only occurs in coastal sectors characterized by minimal or negligible hydrodynamics. Comparison with the millennial sea-level evolution shows that the present elevation of the submerged notch closely matches the sea-level stabilization that occurred during the Late Antique Little Ice Age (LALIA, ∼1400 to ∼1290 BP). During this period, the notch formed in sheltered areas of the coast, despite minor wave mechanical action and bioerosion, because relative sea-level stability concentrated erosion in the same portion of the cliff for ∼400 years. The increased rates of sea-level rise over the last 1500 years hampered the formation of a younger notch in sheltered sectors of the coast. By contrast, changes in sea-level rise rates did not affect notch formation at exposed sites where the mechanical action of waves coupled with intense bioerosion were the major control on notch formation. These data further confirm that the preservation of a fossil submerged notch is not only ascribable to co-seismic subsidence but also to climatic factors. This has implications for palaeo-seismic assessments of the Mediterranean region.