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The present study was conducted to determine the abilities of the living and nonliving Pseudomonas putida CZ1 cells, clays (goethite, kaolinite, smectite and manganite) and their composites to accumulate copper and zinc from a liquid medium, and elucidate the role of microbes on the mobility of heavy metals. Various mixtures of bacteria and clays were exposed to solutions of 0.025mM or 0.5mM Cu(II) and Zn(II) in 0.01M KNO3 to differentiate between so-called “high-affinity” sites and “low-affinity” sites. Clays associated in an edge-on orientation to the cells was observed by electron microscope (EM) examination of these metal-treated bacteria–clay aggregates. Adsorption experiments and desorption with 1.0M CH3COOK solution indicated that clays contain more high-affinity copper binding sites and less high-affinity zinc binding sites than that of bacteria, however, bacteria are involved in more low-affinity heavy-metal-binding sites. Carboxyl group activity is more important at weak-binding sites than at strong-binding sites. TEM-EDS analysis confirmed that most of Zn removed from solution was associated with P. putida CZ1 in the composites. These results suggest that bacteria play an important role in regulating the mobility of heavy metals in the soil environment. [Copyright &y& Elsevier]