Abstract Purpose Some marine organisms can be used as Biological Quality Elements to estimate the degree of environmental impact and to monitor the health of benthic habitats. Organisms with mineralized protections, such as benthic foraminifera, can provide helpful information on the evolution of the coastal system over a long period and determine the Paleo-Ecological Quality Status (Paleo-EcoQS). This work aims at reconstructing the Paleo-EcoQS in the heavily anthropized Sepetiba Bay (SB; Rio de Janeiro State, SE Brazil). Materials and methods This work is based on a multiproxy approach, including textural, geochemical, and foraminiferal data along the core SP11 retrieved near the Pico da Marambaia (a mountain on the tip of the Marambaia Barrier Island). Geochemical analyses encompassing total organic carbon (TOC), total sulfur (S), total nitrogen (N), calcium carbonate (CaCO 3 ), stable isotopes in organic matter ( OM δ 13 C, and OM δ 15 N) and elemental concentrations as well as 201 Pb, 137 Cs, and radiocarbon dating were performed to characterize the Paleo-EcoQS in the bay. Results The values of the Paleo-EcoQS.st (standardized Paleo-EcoQS) index in core SP11 indicate that the paleoenvironmental quality varied from moderate to good between ≈50 AD and ≈1500 AD and from good to high between the ~ 1920s and ~ 1990s. Since the 1990s, the Paleo-EcoQS.st has deteriorated considerably, probably due to the deposition of contaminated dredging material in nearby areas. Ballast water discharge may have introduced alien species, such as Ammonia buzasi , into the SB. Conclusions The results obtained in core SP11, compared to those of another core (i.e., SP8) from a nearby area, suggest that the reference level of maximum environmental quality is not always reached in a period before industrialization in coastal ecosystems with significant interaction with the ocean; natural factors, related, for example, to sedimentary dynamic processes or geomorphological changes, can lead to unexpected results.