Wastewater (WW) agricultural irrigation is becoming a common practice as an alternative to water scarcity. However, WW irrigation may affect the soil structure at different hierarchical levels. This issue was tackled by evaluating the long-term (>90 years) WW irrigation effects on soil structure. Samples of Ap and Ah horizons from eight rainfed and eight WW-irrigated plots were collected for physicochemical characterization. Undisturbed samples were analyzed for aggregate stability, and the pore space of small macroaggregates (0.5-1 mm) from Ah horizons of three rainfed and three WW-irrigated plots was analyzed by x-ray microtomography. Long-term WWirrigated plots had higher contents of C (Ap = 2.54%; Ah = 1.64%) and N (Ap = 0.24%; Ah = 0.16%) compared to rainfed soils, as well as higher aggregates stability (mean weight diameter = 23.6 mm, p = 0.001). However, soil organic matter accumulation was not the main driver of the higher aggregate stability in WW-irrigated soils (Spearman correlation coefficients of 0.467 and 0.476 for organic C and total N, respectively). It was proposed that a combination of factors including SOM and easily degradable OM (C/N = 2.10) input from WW was the reason for this higher stability. The results did not allow one to conclude on the long-term effect of WW irrigation on the microstructural pore space because the scatter in the data of the rainfed samples was high. Considering a higher number of samples may address this problem. Nevertheless, the findings of this research improve our understanding of the effects of WW irrigation on soil structure and provide a better assessment of the benefits and risks associated with this practice.