This study is focused on the characterization of Bertioga channel (Sao Paulo, Brazil) through foraminiferal distribution correlated to environmental gradients. Data for this study encompass Bertioga, Acari, Crumaú estuarine channels, Trindade river and adjacent mangrove ecosystems. Despite of its vicinity to Sao Paulo and Santos cities, Bertioga channel is still partially preserved in its natural conditions showing just a few antropic alterations. In this region, the natural estuarine variability determine foraminiferal zonation. Analysis of the results indicates that in terms of assemblage formation related to freshwater influence the environmental field should be divided into 3 regions. Euhaline environments in the channel north inlet includes Pararotalia sp. Pseudononion atlanticum and Hanzawaia boueana, mixohaline environments in the channel south inlet, south middle region and Largo do Candinho are dominated by species of Ammonia tepida and Elphidium spp. and mixohaline and brackish water presented Arenoparella mexicana, Haplophragmoides wilberti Ammotium salsum, Gaudryina exillis and Trochammina inflata. Species pattern also presented alterations related to tidal oscillations, land drainage and channel geomorphology. Through ecological indicators was possible to evaluate the environmental quality and water flushing time of Bertioga channel and also provide data on species natural history to be comparable to unpolluted and polluted sites.