The objectives of this study were to determine the effects of sediment contamination on the benthic macrofauna and to predict macrofaunal changes following remediation at a Superfund (uncontrolled hazardous waste) site in San Francisco Bay, California, USA. DDT and its metabolites (ΣDDT) were the contaminants of concern. With few small-scale exceptions, all (>100) other sediment contaminants ever measured at the site were present at background or non-toxic levels. In hierarchical regressions [Y=f(X1, X2, X3), where X1=sediment %silt + clay, X2=sediment total organic carbon (OC), and X3=log10 (ΣDDT μg g−1 OC)] with data from samples collected at the study site, log10(ΣDDT μg g−1 OC) explained a highly significant amount of the variance in the infaunal index (II ) and log10(number of Amphipoda excluding Grandidierella japonica + 1) after statistically controlling for the potential effects of sediment %silt + clay and OC. The ratios of change of II and log10(number of Amphipoda excluding G. japonica + 1) with respect to log10(ΣDDT μg g−1 OC) were about −9:1 and −0.4:1, respectively. Most of the 92 species collected were present at low to moderate densities over the entire range of ΣDDT sediment concentrations. The bivalve Theora lubrica, tubificids, most polychaetes, a tanaid (Zeuxo normani), and an amphipod (G. japonica), were common, while four other amphipods (Ampelisca abdita, Corophium heteroceratum, Photis brevipes, Dulichia rhabdoplastis), a phoronid (Phoronis cf. pallida), a bivalve (Cryptomya californica), and a cumacean (Eudorella pacifica), were rare or absent from sites with high ΣDDT sediment-concentrations.