Abstract A multivariate analysis of the foraminifera collected in three estuaries of southwestern Spain (Guadiana, Piedras, Tinto-Odiel) permits recognition of three main assemblages, with spatial distribution depending on sedimentary environments, grain size classes and salinity variations. Assemblage 1 ( Trochammina inflata, Jadammina macrescens) is typical of salt marsh deposits with high salinity variations and percentages of important silt. Assemblage 2 ( Ammonia beccarii, Ammonia tepida, Astrononion stelligerum, Elphidium williamsoni) includes the most abundant estuarine species, with increasing densities from the channel margin to the subtidal channel. Assemblage 3 ( Quinqueloculina seminulum, Elphidium crispum) is mainly found in the sandy sediments of the subtidal channels located near the mouth, with normal marine conditions. These results and the sedimentological interpretation of seven drill cores collected in the Domingo Rubio Channel (Tinto River) allow reconstruction of the palaeogeographic changes of this small estuary in the last ca. 6500 14C years BP. Seven phases were distinguished, with an evolution from an open marine bay to a very restricted channel limited by broad salt marshes.