Pressure-irrigation systems and, in particular, micro-irrigation provide an effective methodology for increasing irrigation efficiency. However, emitter clogging is a major problem in micro-irrigation systems, especially under irrigation with treated wastewater (TWW). Currently, farmers treat their irrigation system by periodical application of solutions of chemicals or washing the lateral lines. The aim of this study was to characterize treatments for the prevention of clogging in drip irrigation systems utilizing different qualities of TWW (secondary and tertiary TWW). A model system was designed and assembled to compare the flow rate (FR), fouling accumulation and fouling composition in laterals and drippers subjected to different treatments. Under irrigation with secondary TWW, control treatment function decreased rapidly while chemical treatment prolonged proper function of the drippers by maintaining a normal FR and coefficient of variation (CV). Wash treatment improved to some extent the irrigation function. Under irrigation with tertiary TWW the function of all treatments was significantly better than that of the secondary treatments. The total suspended solids level was found to be a significant factor in the mechanism of clogging formation according to biofouling development. The deposit chemical characterization could shed light on the mode of growth mechanism and properties of the biofouling. In general, oxidation treatments using hydrogen peroxide or hypochlorite acid were found to eliminate biofouling and in accordance also prevented clogging. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.