Secondary treated wastewater, a commonly used water resource in agriculture in (semi-)arid areas, often contains salts, sodium, and organic matter which may affect soil structure and hydraulic properties. The main objective of this study was to jointly analyse the effects of long-term irrigation with treated wastewater on physicochemical soil characteristics, soil structure, and soil water dynamics in undisturbed soils. X-ray microtomography was used to determine changes in macro-porosity (> 19 μm), pore size distribution, and pore connectivity of a sandy clay loam and a loamy sand. Differences in the pore network among soils irrigated with treated wastewater, fresh water that replaced treated wastewater, and non-irrigated control plots could be explained by changes in textural composition, soil physicochemical parameters, and hydraulic properties. In this study we showed that irrigation led to the development of a connected macro-pore network, independent of the studied water quality. The leaching of silt and clay particles in the sandy soil due to treated wastewater irrigation resulted in an increase of pores < 130 μm. While this change in texture reduced water retention, the unsaturated hydraulic conductivity was diminished by physicochemical alteration, i.e. induced water repellency and clay mineral swelling. Overall, the fine textured sandy clay loam was much more resistant to soil alteration by treated wastewater irrigation than the loamy sand.