The present work focuses on fresh water signatures at the sediment-water interface (1 cm) using foraminiferal species in both austral winter and summer in eleven longitudinal transects on the Western South Atlantic continental margin between 27° and 37° S, at water depths of 11.7 to 250 m. Here we show that depth, salinity, temperature, oxygen, grain size (mud and sand percentage), suspended matter, organic matter, SiO₄, NO₂, and NO₃ in this order of importance are responsible for the distribution of foraminiferal species and thecamoebians. The presence of these microfossils indicate freshwater influx in four sectors over the continental shelf: Itajaí-Açu River, Laguna estuarine system, Patos Lagoon and RdlP (Rio de la Plata) will be explored further in detail. Our findings on freshwater signature on the continental shelf sediments through benthic species indicator are comparable to other continental systems worldwide, and a paleo record study would be useful for three South American countries (Brazil, Argentina and Uruguay). A freshwater signature in the continental shelf indicates deposition sites probably linked to anthropogenic impact since most of the pollutants and contaminants are dumped into water bodies that eventually reach and accumulate in the ocean. Therefore, the freshwater-related species on the continental shelf reflects exactly where the depositional sediment sites are, and where anthropogenic impacts accumulate. Foraminiferal microhabitat occupation within these zones is discussed in detail. And we conclude that together with the fauna, the abiotic parameters play an important role in determining the occurrence and degree of marine eutrophication induced by the input of polluted river waters, also showing possible anoxic environments on the shelf.