The role of two key-variables such as pH and salinity in chemical speciation and bioavailability of heavy metals originated by mining activities bound to sediments was evaluated under estuarine conditions. Two sediment samples collected in two estuaries in southern Spain (Ria of Huelva and Guadalquivir estuary) together with dilution of toxic mud from the Aznalcollar mining spill (April, 1998) were used to determine their chemical speciation and bioavailability at different pH (6.5, 7.5, 8.5) and salinity (10, 20, 35) values using the estuarine clam Ruditapes philippinarum. The chemical speciation was established by means of measurements of the mobilization of heavy metals from sediments to waters and determining in it pH, salinity, alkalinity and heavy metal concentration. The geochemical model MINTEQA2 was used to establish the thermodynamic species in the assays. To assess the bioavailability of the heavy metals the concentration of metallothioneins in the clam tissues and the mortality of this organism was measured at different pH and salinity values. The influence of both salinity and pH was detected in the chemical behavior of metals and in their associated biological responses established by metallothioneins and the percentage of mortality. At low values of both variables (pH=6.5 and S=10), the biological effects were highest, and it was related to the free ion Zn2+.