The Sepetiba Bay (SB, SE Brazil) is a highly anthropized and industrialized area that has experienced severe environmental degradation in recent decades. This study applies a multiproxy approach to document the response of living benthic foraminifera to environmental stress and to infer the Ecological Quality Status (EcoQS) in SB. Our methodology involved a comprehensive comparison of the density and percentage of benthic fora- miniferal species with physicochemical, textural, and geochemical data, specifically the concentrations of potentially toxic elements (PTEs). We also statistically compared two geochemical indices, the pollution load index (PLI) and the potential ecological risk index (PERI), with two ecological indices, the Tolerant Species Index (TSI) and the Exp(H’bc). The TSI and the Exp(H’bc) indices are significantly correlated with the environmental stressors in Sepetiba Bay, namely the PTEs concentrations (As, Cd, Pb, and Zn). The most tolerant species to the enrichment of PTEs and organic matter are Ammonia tepida (Cushman, 1926), Elphidium excavatum (Terquem, 1875), Ammonia buzasi Hayward and Holzmann, 2021 and Ammonia rolshauseni (Cushman and Bermúdez, 1946). The Exp(H’bc) and TSI reveal that most stations located in the inner zone and near the margins of the bay have poor and bad EcoQS, which agrees with the distribution of the environmental stressors. Thus, the current environmental conditions of the inner area of Sepetiba Bay are of great concern. This work also shows that using the TSI and the Exp(H’bc) indices, it is possible to classify EcoQS in transitional coastal environments in the North and South Atlantic transitional waters. This work has relevant scientific and social implications due to its importance in biomonitoring and the management of the coastal regions.