Micropaleontological and geochemical data were applied to sediments from southeastern Brazil to study the hydrodynamics associated with the Holocene sea level rise. Sediment cores were taken around Vitória Bay, examined for dinoflagellate cysts and subjected to isotopic analysis. The cyst assemblage mainly dominated by autotrophic species most notably O. centrocarpum, L. machaerophorum and T. vancampoae. The influence of the marine transgression and subsequent regression observed during the Holocene along the coast of Brazil could have initially favored the establishment of an oligotrophic and higher energy environment. The inflow of continental water from tributaries combined with a higher inflow of saline water into the estuarine system could have favored the establishment and subsequent deposition of the dinocysts.