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We investigated the individual and combined contributions of two distinct heme proteins namely, ascorbate peroxidase (APX) and catalase (CAT) on the tolerance of Lemna minor plants to antibiotics. For our investigation, we used specific inhibitors of these two H2O2-scavenging enzymes (p-aminophenol, 3-amino,1,2,4-triazole, and salicylic acid). APX activity was central for the tolerance of this aquatic plant to amoxicillin (AMX), whereas CAT activity was important for avoiding oxidative damage when exposed to ciprofloxacin (CIP). Both monitored enzymes had important roles in the tolerance of Lemna minor to erythromycin (ERY). The use of molecular kinetic approaches to detect and increase APX and/or CAT scavenging activities could enhance tolerance, and, therefore, improve the use of L. minor plants to reclaim antibiotics from water bodies.