How past environments and communities responded to episodes of coastal inundation can inform preparations for future resilience to predicted rises in sea level. Southeast Asia's extensive coastlines and expanding coastal populations mean vast natural and human capital is at risk from future sea level rise. Regional mangroves provide many ecosystem services that can help mitigate such risks, but deforestation has left them threatened and compromised. The present study examines the Holocene development and human use of mangrove forest in northern Vietnam, where existing palaeo-records derive from sedimentary archives in tidal flat, estuarine and deltaic settings. Here, we expand that coverage by describing conditions at an enclosed doline within the Tràng An limestone karst in Ninh Binh province that would have been sheltered from deltaic and marine processes. We present a multi-proxy assessment incorporating pollen analysis of the 8125-year-old discontinuous sediment core obtained from the doline floor, combined with inferences from erosional tidal notches in the enclosing limestone, and analyses of phytolith, vertebrate and mollusc assemblages from an adjacent archaeological cave site with deposits of comparable age. The results provide a detailed example of how enclosed coastal environments and communities responded to Middle Holocene marine inundation. High percentages of pollen from mangroves (17–57%) suggest their colonisation of the doline from ∼8100 cal. BP and persistence until ∼250 cal. BP, well after the intertidal zone regressed seaward beyond the massif. Archaeological assemblages dating to ∼5500 cal. BP and containing palm and woody eudicot phytoliths and sponge spicules, neurocrania of the fish genus Pomadasys (‘grunts’, ‘grunters’ or ‘javelins’) and brackish-water molluscs Sermyla riqueti and Neripteron violaceum support the persistence of mangrove environments through the Middle Holocene high-stand, a period of hiatus within the core, and indicate human foraging and fishing activities took place in mangrove and lagoonal habitats alongside hunting in the surrounding limestone forest. Subsequent structural opening of this latter forest formation from ∼1075 cal. BP (875 CE), evident in the pollen record, coincides with the Medieval Climate Anomaly and with the adjacent development of the ancient capital at Hoa Lu. We propose that given the long-term persistence of mangrove habitats and associated resources documented in this study, regional initiatives aimed at rehabilitating mangroves (with the positive consequences that this holds for biodiversity and socio-economic conditions) may wish to consider selective restorative measures within Tràng An and similar sheltered sub-coastal karst settings.