Mangroves can deliver important socio-economic benefits and store significant volumes of carbon along tropical to temperate coastlines, but the distribution is controlled by complex geomorphologic, hydrodynamic and salinity conditions, as well as human-related pressures. In the Mekong delta, the interaction of tide, wave and riverine hydrodynamic processes clearly impacts sedimentation and mangrove distribution. Extensive mangroves presently occur along the northeastern delta margin (Can Gio, located 40 km southeast of Ho Chi Minh City), in an embayed, back-barrier environment subject to the highest tidal range (c. 4 m) and away from major fluvial distributary channels. However, the development of the Can Gio mangrove system during the Holocene evolution of the Mekong delta is not fully understood. This study aims to constrain the sedimentary evolution of the back-barrier mangrove in Can Gio based on stratigraphic, palynological and geochronological analyses of sediment cores. Two deep borehole cores (15 and 30 m deep) and four short auger cores (up to 4 m deep) were taken at the modern mangrove to characterize a 20-km-long shore-normal cross section dated with radiocarbon and optically-stimulated luminescence (OSL) ages. The cores consist of a thick (> 20 m) subtidal mud from the base of the Holocene unit to the level of 3–4 m deep below the ground level, overlain by carbonaceous, intertidal mud. Chronological data reveal major episode of subtidal mud aggradation from 6 to 3.5 ka, forming the topography for mangrove development. Radiocarbon ages in the overlying intertidal mud range from 4 ka to modern and show some inconsistencies with the stratigraphy, suggesting mangrove root penetration and sediment mixing. The beach-ridge structure and OSL ages of the Can Gio barrier indicate that barrier formation initiated just before 3.2 ka. The transition from subtidal to intertidal mud aggradation and initiation of barrier formation, are broadly correlated with the onset of the subaqueous delta progradation and shift to a wave-dominated regime in the central delta. However, after 3.5 ka, the Can Gio shoreline had negligible sediment accretion while the central delta prograded up to 50 km seawards. Reduced sediment supply to Can Gio is consistent with more asymmetric, southwestward-dominated longshore drift after 3.5 ka. The negligible progradation at Can Gio also indicates minor sediment supply from the nearby Dong Nai River, which prevented upper intertidal accretion and translation of mangroves into a flood plain.