To evaluate the effect of olive mill wastewater (OMW) application on soil hydraulic and transport properties, two treatment sites, which had been irrigated with OMW for 5 and 15 years, and one control site being irrigated with freshwater were compared. The transport and leaching experiment results showed that a portion of the total soil water was available for transport processes while the remaining of the soil water was considered immobile and not readily accessible for solutes. The separation in water fractions of different mobilities was surprisingly consistent among OMW treatments. The bromide recovery rate decreased with the application of OMW showing that tracer molecules became trapped within immobile water phases. The application of OMW increased significantly the soil water-holding capacity, whereas the soil hydraulic conductivity in the near saturation range decreased significantly with long-term OMW application. The soil irrigated with OMW had significantly higher organic matter content, lower bulk density and relatively higher total porosity, but lower macroporosity than that of control sites. We concluded that the soil was increasingly coated with complex organic molecules originating from OMW, as a result, solute exchange between inter- and intrasoil aggregate water was hindered. Although OMW could cause soil and water pollution, its use in agriculture is promoted because of high nutrients and organic matter contents.