Abstract South American estuaries are frequently not included in the search for general ecological models and studies dealing with biological assemblages in estuaries frequently do not sample the entire salinity gradient. We sampled three tropical estuaries, two times each, on ten stations distributed along each system. Six replicates were collected in each station for the benthic macroinfauna and sediment samples for grain size and inorganic contaminant analyses. There were finer sediments at the lower than at the upper estuarine portions. There was a decrease in the diversity, at family level, from marine to freshwater and the differences on the structure of the benthic assemblages were mostly spatial. In spite of the many different characteristics of the three estuaries (e.g. catchment size, pollution levels, proximity with the inner continental shelf) several consistent patterns of benthic macrofauna distribution along these systems were still observed. It suggested a general empirical model regarding the distribution of different benthic invertebrates along tropical salinity gradients which can be tested in different estuaries around the world.