Depth measurements and chemical, sedimentological and microfaunal analyses were conducted in two microtidal estuaries, devoid of anthropogenic pollution, in the ecological reserve of Juréia-Itatins (E.E.J.I.). The spatial and temporal (summer and winter) variations in the composition of foraminifera and thecamoebian assemblages relative to hydrographic and sedimentological parameters were studied and compared with microfaunal data from other estuarine areas. Canonical correspondence analysis (CCA) was used to assess the relationship between microfaunal and abiotic variables. The distribution patterns of foraminifera and thecamoebians corresponded most strongly to bottom salinity and bottom temperature. The species distribution in the microtidal estuaries of E.E.J.I. was similar to that reported from macrotidal estuaries (Argentine and temperate regions) but differed from that observed in other tropical and subtropical microtidal estuaries of Brazilian and African coasts. Distribution patterns of foraminiferal and the-camoebian assemblages facilitated the development of hydrodynamic models of water circulation in the two estuaries. Such modeling would have been very difficult using only hydrological and chemical data because of the complex and highly variable water circulation.