Heavy-metal pollution is an issue of concern in estuaries influenced by agriculture, urban, and harbor activities. Foraminiferal assemblages have been shown to be effective indicators of pollution. Sediment samples (n = 110) from Biscayne Bay were analyzed for heavy metals, foraminiferal assemblages, and grain-size distribution. Highest Cu, Zn, Cr, Hg, Pb, and Ni concentrations were found closest to Miami and near the mouths of several canals along the western margin of the bay. Few samples exceeded limits of possible biological effects as defined by previous studies. Ammonia and Cribroelphidium, two known stress-tolerant genera, correlated positively with Cu, Zn, Hg, and Ni (r ≥ 0.43). Symbiont-bearing foraminifers, Archaias, Laevipeneroplis, and Androsina, correlated negatively with Cu, Zn, Hg, and Ni (r ≤ −0.26).