The Saronikos Gulf, including the industrial zone of Elefsis Bay, is subjected to a variety of urban and industrial impacts that significantly contribute to environmental degradation. Benthic foraminifera comprise a significant component of meiobenthic communities and they are widely used as reliable indicators for the determination of the natural environmental and anthropogenic impact in shallow coastal systems. The present study analyses the living benthic foraminifera composition and its relation to environmental parameters such as grain size, organic carbon content, and heavy metal concentrations, from the surficial sediment layer collected in the Elefsis Bay and the Inner Saronikos Gulf in February 2016. Canonical correspondence analysis and Spearman’s rho correlation show that the foraminiferal species composition is significantly influenced by the increase of organic carbon and Cu, Pb, Zn content. In particular, a relatively low diversity fauna dominated by the stress-tolerant species Ammonia tepida, Bulimina elongata, Bulimina marginata, and Nonionella turgida occurs in the restricted environment of the Elefsis Bay, demonstrating the negative environmental impact caused by the relatively elevated organic carbon and heavy metal contents.