Soil hydraulic properties are crucial to agriculture and water management and depend on soil structure. The impact of Cu and Zn cations on the hydraulic properties of sandy and loamy clay soil samples of Central Greece, was investigated in the present study. Metal solutions with increased concentrations were used to contaminate the soil samples and the effect on hydraulic properties was evaluated, demonstrating the innovation of the current study. The soil samples were packed separately into transparent columns and the initial values of hydraulic conductivity, cumulative infiltration, infiltration rate and sorptivity were estimated. In order to evaluate soil adsorption, metal concentrations were measured at the water leachate. After the contamination of the soil samples, the hydraulic properties under investigation were determined again, using distilled water as the incoming fluid; the differences at the hydraulic parameters were observed. After doubling metal concentrations into the incoming solution of loamy clay soil, metal adsorption and the values of the hydraulic parameters increased significantly. Loamy clay soil showed interaction between the clay particles and the positive charge in the incoming fluid, which led to a possible increase in aggregation. Furthermore, aggregation may led to pore generation. Contamination of sandy soil exhibited no impact on aggregation and soil structure. In order to evaluate the differences on the hydraulic properties and soil structure, the experimental points were approximated with two infiltration models.