A sediment core was studied to characterize the influences of Holocene sea-level variations in the Barra Seca River valley, in the Atlantic rainforest, Linhares, Espírito Santo, southeastern Brazil. Biological proxies (pollen, spores, and sponge spicules), 14C dating, granulometry, δ13C, δ15N, C/N and major chemical elements revealed the establishment and the evolution of a paleo-estuary during the interval from ∼7700–585 cal BP. During the interval ∼7700–7000 cal BP, the study site was occupied by a bay-head delta, the inner portion of the paleo-estuary, presenting the most dense mangrove coverage of the entire record. In the interval ∼7000–3200 cal BP, the site was occupied by the central basin, possibly a consequence of the landward migration of the paleo-estuary. This interval presents reduced mangrove coverage, probably due to the permanent flooding of the valley. From ∼3200 cal BP, the marine influence at the site decreased probably as result of the seaward migration of the coast line. From ∼600 cal BP, the modern floodplain and freshwater lake were established. This interpretation is in agreement with the sea-level curves for the southeastern Brazilian coast, except for the fact that evidence of sea levels lower than the present at ∼4000 and ∼2500 cal BP as suggested by some authors were not found.