Marine and fluvial processes control sedimentation in the Guaratuba Estuary, Brazil, which contains a threefold structure as defined by sedimentology, foraminifera, thecamoebians, and physico-chemical data. Foraminiferal and thecamoebian biosedimentary facies are shown to be potentially diagnostic of specific estuarine conditions in which no macrofauna are present or of use. The inner, high-energy, river-dominated zone, with some marine influence, contains poorly to moderately sorted sediment, with high organic matter and low CaCO 3 content. Agglutinated foraminifera in this setting are well adapted to low salinity, and show the largest abundance and widest redistribution of foraminiferal mangrove species, reflecting the net bedload mixture. Thecamoebians are also present in this zone. Sand percentages and microfaunal data delineate a bilobed birdfoot bay-head delta, which progrades into the central basin. The low-energy, central basin is characterized by poorly sorted to well-sorted medium sand and fine silt, with the highest percentages of mud, organic matter, and CaCO 3 . Coarse sand mixed with mud may be present in scour holes of fluvial estuarine outlets. Fine sediment is present around shoals protected by islands. Foraminifera define a transitional biofacies in this central basin, which separates an inner domain with agglutinated species and a seaward domain with the first occurrence of calcareous species. In the lower, high-energy, marine-dominated zone of the estuary, sand is well sorted to very well sorted, and mud is restricted to tidal channels. Values of organic matter and CaCO 3 are low. More diversified assemblages of calcareous foraminifera are dominant. These are adapted to the higher salinity and pH of this deeper estuarine zone. The net bedload transport is headward at the narrow inlet and contiguous areas, and seaward at the rest. Although Guaratuba has a typical tripartite structure of wave-dominated estuaries, its narrow inlet enhances the tide energy, as observed at the ebb tidal delta, broad tidal flats, and inner, river-dominated zone. Waves and longshore currents outside the inlet rework the ebb tidal delta. Cuspate foreland morphology, wind and wave data, sediment sorting, and the presence of planktonic foraminifera indicate the existence of a remnant flood tidal delta. The stability of this remnant feature demonstrates a decrease in inlet efficiency and consequently in marine sediment supply. The recent estuarine basin, in which tide and wave influence is minor relative to river influence, represents a transitional state between an estuary and a delta. This is shown by the limits of estuarine biofacies and by the net bedload transport.