The aim of this work was to study the use of advanced oxidation technologies for micropollutant (atrazine, ATZ) removal in secondary effluents (SE). Experiments were carried out, for comparison purposes, in deionized water and in municipal SE. ATZ concentration, chemical oxygen demand (COD) and total organic carbon (TOC) were recorded along the reaction time and used to evaluate the system efficiency. Results demonstrate that the presence of effluent organic matter (EfOM) can reduce the effectiveness of the methods to remove ATZ due to the competition of EfOM components to react with OH radicals and/or molecular ozone. ATZ was more easily removed by hydroxyl radicals, however the presence of EfOM promoted higher inhibition of its removal by hydroxyl radicals than by ozone. The addition of Fe as catalyst in the UV/H2O2 system also increased the ATZ removal rate in SE. In addition, direct ATZ photolysis promoted by UV alone must be considered in the assessment of its degradation by UV-based methods.