We studied a 13-meter sediment core collected from La Mancha coastal lagoon, Veracruz, Mexico, to determine paleoenvironmental variations linked to the mid- to late Holocene sea-level rise. We examined modern and fossil benthic foraminiferal assemblages, isotopic values in tests of Ammonia tepida (δ18O-foram and δ13C-foram), δ13C in organic matter (δ13C-org), and sediment elemental ratios (Fe/Ca, Ca/Ti, and K/Rb) to reconstruct salinity variations, coastal processes, and the morphologic evolution of a partially closed coastal lagoon. We identified four main periods of environmental change: (1) From ~7800 to 6500 cal. yr. BP, the core site was an open lagoon with higher oceanic influence than today, through the presence of a southern mouth, as evidenced by the euryhaline assemblage Ammonia-Quinqueloculina-Bolivina-Nonionella. Low δ18O-foram and high δ13C values on foraminifera shells indicate greater inputs of seawater, and δ13C-org values reflect a lagoon environment. Elemental ratios of lower Fe/Ca, moderate Ca/Ti, and higher K/Rb suggest increased coastal weathering and reduced detrital deposits than today. (2) From ~6500 to 4600 cal. yr. BP., the lagoon experienced the progressive closure of the southern mouth, to the point that sedimentation restricted seawater entrance, as evidenced by variable δ13C-org values, a lowering trend in δ18O-foram and δ13C-foram values, low Fe/Ca, higher Ca/Ti but moderate K/Rb values. At this time, benthic foraminifera were dominated by the opportunistic Ammonia-Elphidium polyhaline assemblage. (3) From ~4600 to 1400 cal. yr. BP, the northern mouth was the only source of seawater to the lagoon, establishing the optimal environment for calcareous foraminifera of the polyhaline assemblage Ammonia-Elphidium. Lowest δ13C-org values indicate greater organic input by terrestrial plants. (4) At 1400 cal. yr. BP, modern conditions of a partially closed lagoon were established, while increased terrigenous inputs and freshwater runoff favored the growth of agglutinated foraminifera species. At millennial time scales, in addition to the sea level rise effects, the lagoon evolution fits in the paleoclimatic context that links insolation, the latitudinal change of ITCZ, ocean currents, longshore drift and moisture transport, as driving factors of morphological change in the western coast of the Gulf of Mexico.