The widely usage of ethylenediaminetetraacetic acid (EDTA) arises environmental concerns on toxic metal mobilization, and challenges the conventional processes in water treatment. In the study Cu(II)-EDTA in near natural water was efficiently removed during a two-step electrocoagulation using Fe(0) anode (Fe-EC), including a transformation to Fe(III)-EDTA induced mainly by structural Fe(II) in anoxic Fe-EC and further degradation in oxic Fe-EC. The degradation of Fe(III)-EDTA was mostly attributed to an oxygen activation mechanism that involving O2− and hydroxyl radical (OH) generation, as validated by the quenching experiments and electron spin resonance. Furthermore, O2− generated during Fe(II) oxidation took a dominant role on Fe(III)/Fe(II)-EDTA transformation instead of electrochemical reduction. Six intermediates during the Fe(III)-EDTA degradation were identified by LC-Q-TOF, indicating a pathway of stepwise breakage of NC bonds. The results revealed in this work is helpful to understand the contribution and fate of EDTA during Fe-EC treatment of metal-EDTA polluted water.