Based on surface thermodynamics and XDLVO theory, free energy changes induced by hydrophobic interactions (GH), free energy changes originated from electrostatic force (GEL) and the total free energy changes in the adsorption of P. putida and B. subtilis on kaolinite and montmorillonite were obtained. The negative values of GH and the positive values of GEL suggested that the hydrophobic force favors, and the electrostatic force unfavors the bacterial adsorption on kaolinite and montmorillonite. The absolute values of GH were much larger than those of GEL, indicating that hydrophobic interactions play a role more important than electrostatic force does in bacterial adsorption. The negative total free energy changes (G) suggested that the sorption of bacteria on clay minerals is a thermodynamically spontaneous process. Greater G values for bacterial adsorption on kaolinite than on montmorillonite indicated higher affinity of the bacteria for kaolinite than for montmorillonite.