Irrigation with treated wastewater (TWW) may affect soil structure and stability and the characteristics of dissolved organic matter (DOM) of the soil solution. The objectives of our study were (i) to evaluate the impact of TWW irrigation, as compared with fresh water (FW) irrigation, on aggregate stability and saturated hydraulic conductivity (indices of soil structure stability) and (ii) to determine whether these indices can be associated with the chromophoric indicators of water-extractable DOM in TWW- and FW-irrigated soils. We studied aggregate stability and soil hydraulic conductivity (HC) of four different soil types irrigated with either TWW (for at least 5 years) or FW. The results were linked to earlier published data on the concentration scores of fluorescent chromophoric DOM components (obtained from excitation-emission matrices of flouorescence coupled with parallel factor analysis), dissolved organic carbon (DOC) concentration and absorbance at 254 nm (Abs254). These were all obtained from water extracts of the same soils as those used in the current study. Irrigation with TWW decreased aggregate stability, in comparison to irrigation with FW, in the sandy clay and clay soils, while in the loamy sand TWW increased aggregate stability. The apparent steady state HCs in the TWW-irrigated samples in the loamy sand, sandy clay and clay soils were similar to, or significantly less than, those obtained in the FW-irrigated samples. In the sandy loam the opposite trend was noted. Results of principal component and classification analyses showed that the aggregate stability indices were directly associated with soil organic matter and DOM attributes in the coarse-textured soils, while in the fine-textured soils inverse associations were noted. Only in the fine-textured soils were the HC attributes associated (directly) with some of the DOM characteristics. Our results suggest that structural indices of fine-textured soils are more sensitive than those of coarse-textured soils to the composition of water extractable DOM.