Due to economic importance of Guanabara Bay, a multidisciplinary approach was adopted to investigate 88 surficial sediment samples in order to use the benthic foraminifera as indicators for the characterization of environmental variations. Grain-size analyses indicate that bottom sediments of the inner part of the bay are mainly muddy while those close to the entrance of the bay are sandy. Geochemical data show high concentration of heavy metals mainly in the northern region of the bay. Micropalaeontological analyses indicate the boundaries of the areas with the highest concentration of heavy metals. The dominant benthic foraminifera in the bay are Ammonia beccarii and Buliminella elegantissima, taxa capable of differentiating the presence of pollutants of different sources. B. elegantissima, in particular, has shown to be an indicator of anthropogenic pollution. The study highlights the worsening of environmental conditions since 2000 and those areas of the bay in need of a priority recovery.