This study involves batch reactor and fixed-bed continuous flow experiments to determine the effects of complexing agents (e.g., tartrate and citrate) on the treatment of chlorophenolic (CP) compounds using heterogeneous Fenton system with pyrite mineral as the iron source. While the addition of organic ligands to the batch systems adversely affected CP removal, organic ligands had a beneficial effect on CP removal in column systems. Although the ligands extended the life span of pyrite-packed columns by removing surface oxidation products through the formation of soluble Fe-ligand complexes, the ligands competed against CPs for hydroxyl radicals (HO*). The competitive effect was much higher in batch systems since pyrite loading was very low in order to generate sufficient hydroxyl radicals. On the other hand, at much higher pyrite loading of column experiments, the H* radicals generated during Fenton process were sufficient to overcome the competitive effect exerted by organic ligands. In spite of much higher Fe solubility in the presence of citrate, citrate was less effective in enhancing CP removal in column systems compared to tartrate since the competitive effect caused by citrate for HO* radicals was more than that exerted by tartrate.