Numerical analyses of modern foraminiferal abundance and environmental data from the Bertioga Channel (São Paulo, Brazil) reveal multiple biofacies within an overall paralic setting. Despite its fisheries, mariculture and attraction to tourists, the environmental state of Bertioga Channel remains poorly studied. The present investigation is an attempt to partly fill this gap; the parameters examined include depth, salinity, temperature, organic carbon, sulfur content and bottom sediment type. Muddy sediments with high organic carbon content derived from land drainage are found in the inner parts of the channel, whereas sandy sediment dominates the areas adjacent to the Atlantic Ocean. In the eastern entrance to the channel, sandy sediment contain species of Rotaliida from Facies 1 (including Elphidium discoidale, Elphidium poeyanum, Hanzawaia boueana, Pararotalia cananeiaensis and Nonionella atlantica), reflecting normal marine salinity. Sediments with high percentages of silt and clay in polyhaline and euryhaline environments of the eastern part and Itapanhaú River contain Facies 2, which includes Ammonia beccarii and Pararotalia cananeiaensis. In the western entrance and central, western and eastern parts, where salinities vary from 18 to 30 psu and the sediments contain both low and high organic carbon, the foraminifera from Facies 3 are dominated by Quinqueloculina milletti, Arenoparrella mexicana, Pararotalia cananeiaensis, Ammonia beccarii, Buliminella elegantissima, Elphidium sp., Elphidium excavatum, Elphidium gunteri and Elphidium poeyanum. In mesohaline and polyhaline waters of the central part, the organic-carbon-rich silt and clay contain Facies 4, which includes Ammonia beccarii, Pararotalia cananeiaensis, Elphidium excavatum and Elphidium sp. Most of organic-carbon-enriched, silty-clay substrates that are subject to the highest fresh-water discharge and high bottom temperatures support two different assemblages: one of mostly Rotaliina and the other mostly of Textulariida (Facies 5 and 6). Facies 5 includes Ammonia beccarii, Elphidium excavatum, Arenoparrella mexicana, Haplophragmoides wilberti, Siphotrochammina lobata, Trochammina inflata and Trochammina sp., all of which are typical of mesohaline sites (mainly Crumaú and Trindade rivers), and Facies 6 includes Bolivina sp., Ammoastuta salsa, Arenoparrella mexicana, Haplophragmoides wilberti and Trochammina sp., all of which are typical of oligohaline and mesohaline mangrove fringes. The foraminiferal species from the present study are frequently found in paralic environments in Brazil, western Africa and other estuaries around the world.