The effect of irrigation with treated wastewater (TWW) on soil physico-chemical and hydraulic properties was evaluated in this study. Field treatments were: non-irrigated (rain-fed) plot (control), rain-fed plot for the first three years and irrigated with TWW for the last two years (2 yr) and plot irrigated with TWW for five years (5 yr). Soil samples were collected from two depth intervals (0–15 and 15–30 cm) in five replicates. Irrigation with TWW significantly increased aggregate stability (AS), exchangeable sodium percentage (ESP), organic matter (OM), and electrical conductivity (EC). Both hydraulic conductivity (HC) and cumulative infiltration (F(t)) were decreased significantly with TWW use and period of application. Moreover, reduction of HC at different tension revealed that pore clogging occurred at both, macro and micro scale. Scanning electron microscopy (SEM) images showed that soil pores were clogged partially and/or fully as a result of suspended particulates and organic matter. Enhanced AS of treated areas indicated that infiltration was more affected by pore clogging than soil dispersion and swelling.