Epikarst estuary response to hydroclimate change remains poorly understood, despite the well-studied link between climate and karst groundwater aquifers. The influence of sea-level rise and coastal geomorphic change on these estuaries obscures climate signals, thus requiring careful development of paleoenvironmental histories to interpret the paleoclimate archives. We used foraminifera assemblages, carbon stable isotope ratios (δ¹³C) and carbon:nitrogen (C:N) mass ratios of organic matter in sediment cores to infer environmental changes over the past 5300 years in Celestun Lagoon, Yucatan, Mexico. Specimens (> 125 µm) from modern core top sediments revealed three assemblages: (1) a brackish mangrove assemblage of agglutinated Miliammina and Ammotium taxa and hyaline Haynesina (2) an inner-shelf marine assemblage of Bolivina, Hanzawaia, and Rosalina, and (3) a brackish assemblage dominated by Ammonia and Elphidium. Assemblages changed along the lagoon channel in response to changes in salinity and vegetation, i.e. seagrass and mangrove. In addition to these three foraminifera assemblages, lagoon sediments deposited since 5300 cal yr BP are comprised of two more assemblages, defined by Archaias and Laevipeneroplis, which indicate marine Thalassia seagrasses, and Trichohyalus, which indicates restricted inland mangrove ponds. Our data suggest that Celestun Lagoon displayed four phases of development: (1) an inland mangrove pond (5300 BP) (2) a shallow unprotected coastline with marine seagrass and barrier island initiation (4900 BP) (3) a protected brackish lagoon (3000 BP), and (4) a protected lagoon surrounded by mangroves (1700 BP). Stratigraphic (temporal) changes in core assemblages resemble spatial differences in communities across the modern lagoon, from the southern marine sector to the northern brackish region. Similar temporal patterns have been reported from other Yucatan Peninsula lagoons and from cenotes (Nichupte, Aktun Ha), suggesting a regional coastal response to sea level rise and climate change, including geomorphic controls (longshore drift) on lagoon salinity, as observed today. Holocene barrier island development progressively protected the northwest Yucatan Peninsula coastline, reducing mixing between seawater and rain-fed submarine groundwater discharge. Superimposed on this geomorphic signal, assemblage changes that are observed reflect the most severe regional wet and dry climate episodes, which coincide with paleoclimate records from lowland lake archives (Chichancanab, Salpeten). Our results emphasize the need to consider coastal geomorphic evolution when using epikarst estuary and lagoon sediment archives for paleoclimate reconstruction and provide evidence of hydroclimate changes on the Yucatan Peninsula.