In many arid and semi-arid regions, the demand for drinking water and other domestic uses is constantly growing due to demographic growth and increasing standard of living. Therefore, less freshwater is available for agricultural irrigation and new water sources are needed. Treated wastewater (TWW) already serves as an important water source in Israel since more than 40 years and its usage will further be extended. Related to its high loads with nutrients, salts and organic materials its use as irrigation water can have major effects on the soil physical, chemical and biological properties, in the worst case leading to soil degradation. Additional organic matter reaches the soil with the effluent water and soil microbial activity is stimulated. Soil organic carbon (SOC) seems to accumulate in the topsoil and tends to decrease after long-term irrigation with secondary TWW in the subsoil. The amount of dissolved organic carbon increased and the aromaticity of the organic compounds in the soil percolates decreased over the irrigation period. Priming effects, occurring after stimulation of microbial activity by the addition of easily degradable substances, could be found in the soils and were stronger for subsoil (1 m depth).