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Mangrove forests are valuable ecosystems, but their extent and diversity are increasingly threatened by sea-level rise and anthropogenic pressures. Here we develop a bio-morphodynamic model that captures the interaction between multiple mangrove species and hydro-sedimentary processes across a dynamic coastal profile. Numerical experiments are conducted to elucidate the response of mangrove assemblages under a range of sea-level rise and sediment supply conditions, both in the absence and presence of anthropogenic barriers impeding inland migration. We find that mangrove coverage can increase despite sea-level rise if sediment supply is sufficient and landward accommodation space is available. Tidal barriers are mainly detrimental to mangrove coverage and result in species loss. Importantly, we show that bio-morphodynamic feedbacks can cause spatio-temporal variations in sediment delivery across the forest, leading to upper-forest sediment starvation and reduced deposition despite extended inundation. As such, bio-morphodynamic feedbacks can decouple accretion rates from inundation time, altering mangrove habitat conditions and causing mangrove diversity loss even when total forest coverage remains constant or is increasing. A further examination of bio-morphodynamic feedback strength reveals that vegetation-induced flow resistance linked to mangrove root density is a major factor steering the inundation-accretion decoupling and as such species distribution. Our findings have important implications for ecosystem vulnerability assessments, which should account for the interactions between bio-morphodynamics and mangrove diversity when evaluating the impacts of sea-level rise on species assemblages.