Small vertical variations in occurrences of mangrove foraminifera and arcellaceans (thecamoebians) provide a zonation scheme that is applicable to the study of short-term sea-level change. Sampling along transects was carried out at three sites in southern Brazil and four sites along the Rio de Janeiro lagoon system. The Saí-Guaçú fluvial-estuarine point bar that divides the states of Santa Catarina and Paraná, and the Capinzal and Veiga islands at the ancient flood tidal delta of the Guaratuba Bay, were sampled during two summers for a total of 42 samples. In the state of Rio de Janeiro, the seaward borders of the Urussanga, Boqueirão and Fora lagoons, which comprise the incipient brackish mangroves of the Saquarema Lagoon system, were sampled in both summer and winter for a total of 17 samples. Three samples were collected during the summer at the freshwater marsh of Jacarepiá Lake. These coastal sedimentary environments differ in latitude, climate, physio-chemical conditions, vegetation, and sediment type. Altitude, rate of sediment transport and salinity influence the distribution of three faunal zones: higher, middle, and lower. Statistics on the dead foraminiferal distribution and ecological indications given by live occurrences showed that Haplophragmoides sp. is the dominant species at the uppermost stations (higher high water—HHW, with a 6-cm vertical range) in both Guaratuba and Rio de Janeiro transects, whereas Trochammina inflata dominates the southernmost Saí-Guaçú site. The Haplophragmoides-Trochammina association was also the most consistent in both dead and live HHW assemblages. Trochammina inflata and two forms of T. macrescens were found to be salinity-sensitive HHW assemblages, as were Polysaccammina hyperhalina and Miliammina fusca in the Guaratuba intertidal zone. In Saquarema, the intertidal zone is marked by T. macrescens, and Centropyxis aculeata predominates in Jacarepiá. The subtidal zone in Paraná contains Arenoparrella mexicana, Tiphotrocha comprimata, Trochammina macrescens f. macrescens, and Difflugia oblonga, whereas in Rio de Janeiro, T. macrescens f. polystoma predominates. Similar HHW assemblages are also observed in Oregon, British Columbia, Maritime Canada, and New England. Thus, the assemblages found in Brazil are potentially applicable to the study of sea-level variation as recorded in Quaternary deposits, like their counterparts in temperate marshes. These transects are the first well-constrained vertical transects of mangrove faunas in South America.