Exopolysaccharides (EPS), extracellular macromolecular biopolymers produced by soil microorganisms, are important in formation of soil microaggregate structures and in maintenance of proper soil moisture and bioavailability of nutrients. The objectives of this study are to investigate the effects of exopolysaccharides from Rhizobium Tropici on surface properties of two common clays, kaolinite and montmorillonite (STX-1). The effects of EPS alone and cation-substituted EPS (Na, Ca, and Al) on the particle size distribution, ζ-potential, and surface areas of clays were examined. Results show that EPS alone significantly increased the aggregate particle sizes of montmorillonite by 50−110-fold and kaolinite by 90-fold via formation of EPS-clay composites through interparticle associations of EPS. Cation-substituted EPS (EPS-Na/Ca/ Al) remarkably weakened such interparticle association in formation of the large particle sizes (increasing the particle size by 5−40-fold). Strong correlations between the mean aggregate sizes and ζ-potentials of these EPS-clay composites were observed. The more negative charge of the EPS/Na/Ca/Al-clay composites led to stronger repelling Coulomb forces between particles, thus decreasing the overall aggregate sizes. On the other hand, EPS adsorption on two clay minerals significantly reduced their surface area, especially on montmorillonite, by 61%. Montmorillonite's surface area was initially slowly reduced, followed by rapid decreases, while kaolinite initially slightly increased, followed by a slow decrease with further increases in EPS adsorption. Thus, the current study provides a deep understanding of mechanisms of EPS interaction with clay minerals and its effects on the sizes, ζ-potentials, and surface areas of clay minerals.