Thirty-nine paired soil samples belonging to Inceptisols, irrigated with wastewater and well water, were examined to monitor the combination of clay mineralogy, physicochemical properties, and trace metals (Zn, Cu, Cd, and Pb) following long-term wastewater irrigation. Results of XRD analysis indicated that the quantity of clay minerals did not change by long-term wastewater irrigation although some modifications in smectite were occurred in Fluvaquentic Endoaquepts compared to control (well water-irrigated soil). Irrigation with wastewater was resulted in an increase in clay content from 3 to 17%, EC from 90 to 160%, organic carbon from 13 to 44%, and CEC from 10 to 13%. In this context, improvement in total N was as 80-110%, available P as 270-330%, and available K as 5-50% as compared to the control soil. Irrigation with wastewater was led to a significant enrichment in both EDTA-extractable and total metals of Zn, Cu, Cd, Pb, mainly as result of the combination of their addition through wastewater along with interaction between the used wastewater and its receiving soils. In the light of this, wastewater irrigation system showed the relative enrichment (RE) for total-Zn, Cu, Cd, and Pb as 3.6-6.8, 2.8-4.9, 4.4-5.7, and 1.8-2.3, respectively. Fine particle-size fraction (< 0.002 mm), organic matter, and calcium carbonates were appeared as the main agents in retaining the total trace metals as reflected in significant positive correlation among the physicochemical properties and the examined metals. Degree of contamination (C-d) for the four analyzed metals was in the range of 3-5. Based on C-d values, the wastewater-irrigated soils were classified as moderate degree of contamination (2 a parts per thousand currency sign C-d < 4) to high degree of contamination (4 a parts per thousand currency sign C-d < 8). Fluvaquentic Endoaquepts highlighted to be a major contributor of the load and contamination rate of trace metals regarding to geoaccumulation index, contamination factor, and Degree of contamination.