An approach is presented for determining the influence of two key variables, pH and salinity (S), on the toxicity of four common heavy metals bound to sediments in estuaries. Two samples of environmental sediment taken from two estuaries in southern Spain (the Huelva estuary and the Guadalquivir River estuary), together with a dilution of toxic mud from the Aznalcóllar (Spain) mining spill (April 1998) were used to determine their toxicity at different values of pH (6.5, 7.5, and 8.5) and salinity (10, 20, and 30) on the estuarine clam Ruditapes philippinarum. Two different endpoints, sublethal, indicated by clam reburial (median effective burial time [ET50]), and relative mortality (median lethal concentration [LC50]), were used to quantify the toxicity associated with the heavy metals. Neither salinity nor pH was found to influence the toxic responses measured by the behavioral endpoint (ET50). However, a strong effect on the LC50 related to pH and salinity was detected, with the toxicity of the heavy metals being increased at low values of both variables (pH = 6.5 and S = 10). The mechanism of heavy metals uptake through water may explain this influence of pH and salinity on the lethal toxicity detected. The results show differences in the toxicity of these heavy metals bound to sediments depending on whether the origin of metal contamination is chronic or acute.