The Santos Estuary, an estuarine system bordering the cities of Santos, São Vicente, and Cubatão in southeastern Brazil, contains the country’s largest harbor and main industrial center that have been impacted by industrial and domestic effluents since the late 19th century. We report here on the distribution of benthic foraminifera and related environmental parameters in this estuary system during the summer and winter of 2007. The foraminiferal fauna is representative of mixohaline environments, and includes 107 live + dead taxa, of which 73 are calcareous benthic, 33 agglutinated, and one planktonic. Most of the calcareous specimens belong to the genera Ammonia, Elphidium, and Quinqueloculina and the species Nonionella atlantica. The living population was ~10% of the total foraminiferal fauna, and the dominant living species were similar to those in the total live + dead fauna. Ammonia beccarii was dominant in most of the stations during summer and winter. It could be considered opportunistic due to its high abundance in samples with low diversity and richness. It is not evident if the effects of human population density on the study area impacted the distribution of the foraminiferal fauna, because low proportions of deformed tests and low values of abundance, richness, and diversity were also found in pristine areas near Santos, São Vicente, and Cubatão.