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 WW-irrigated 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.