The present study aims to evaluate the utilization of several benthic macroinvertebrate and fish species as bioindicators of heavy metal contamination in a relatively enclosed estuarine area, the Seixal Bay (Tagus estuary, Portugal). 266 specimens of 16 taxa were captured during four sampling campaigns and the concentration of lead, chromium, nickel, copper, zinc, cobalt and cadmium were quantified in fish muscle and whole soft body of the invertebrates, as well as in suspended particulate matter in the water column and sediments. Larger predator fishes with higher mobility presented low levels of contamination, probably due to their feedings sites being located outside the bay in less contaminated areas. The species of the Gobiidae family, Pomatoschistus microps, Pomatoschistus minutus and Gobius niger presented higher values of non-metabolic elements (Pb, Ni and Cd) while Scrobicularia plana, Nereis diversicolor, Carcinus maenas and Palaemon serratus were more associated to the accumulation of Cu, Cr and Zn. Nephtys hombergii and Crangon crangon, showed intermediate concentrations of all metals. These results points out to a future possible utilization of S. plana, N. diversicolor, P. serratus and C. maenas and of Pomatoschistus species as bioindicators of heavy metal contamination in ecological quality monitoring programs.