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Predictions of the effects of modern Relative Sea-Level (RSL) rise on mangroves should be based on decadal-millennial mangrove dynamics and the particularities of each depositional environment under past RSL changes. This work identified inland and seaward mangrove migrations along the Ceará-Mirim estuary (Rio Grande do Norte, northeastern Brazil) during the mid–late Holocene and Anthropocene based on sedimentary features, palynological, and geochemical (δ¹³C, δ¹⁵N, C/N) data integrated with spatial-temporal analysis based on satellite images. The data indicated three phases for the mangrove development: (1°) mangrove expansion on tidal flats with estuarine organic matter between >4420 and ~2870 cal yrs BP, under the influence of the mid-Holocene sea-level highstand; (2°) mangrove contraction with an increased contribution of C₃ terrestrial plants between ~2870 and ~84 cal yrs BP due to an RSL fall, and (3°) mangrove expansion onto the highest tidal flats since ~84 cal yr BP due to a relative sea-level rise. However, significant mangrove areas were converted to fish farming before 1984 CE. Spatial-temporal analysis also indicated a mangrove expansion since 1984 CE due to mangrove recolonization of shrimp farming areas previously deforested for pisciculture. This work mainly evidenced a trend of mangrove expansion due to RSL rise preceding the effects of anthropogenic emissions of CO₂ in the atmosphere and the resilience of these forests in the face of anthropogenic interventions.