With the advent of technological advancements post the industrial revolution, thousands of chemicals are introduced into the market annually to enhance different facets of human life. Among these, pharmaceutical and personal care products (PPCPs), including antibiotics and disinfectants, such as benzalkonium chlorides (BACs), are prominent. BACs, often used for surface and hand disinfection in high concentrations or as preservatives in health products such as nasal sprays and eye drops, may present environmental risks if they seep into irrigation water through prolonged exposure or improper application. The primary objective of this study is to elucidate the tolerance mechanisms that may arise in Lemna minor plants, known for their remarkable capability to accumulate substances efficiently, in response to exogenously applied BACs at varying concentrations. The study applied six different concentrations of BACs, ranging from 0.25 to 10 mg L−1. The experimental period spanned seven days, during which the treatments were conducted in triplicate to ensure reliability and reproducibility of the results. It was observed that low concentrations of BACs (0.25, 0.5 and 1 mg L−1) did not elicit any statistically significant changes in growth parameters. However, higher concentrations of BACs (2.5, 5, and 10 mg L−1) resulted in a reduction in RGR by 20%, 28%, and 36%, respectively. Chlorophyll fluorescence declined significantly at BAC doses of 5 and 10 mg L−1, with Fv/Fm ratios decreasing by 9% and 15%, and Fv/Fo ratios by 40% and 39%, respectively. Proline content decreased in all treatment groups, with a 46% reduction at 10 mg L−1 BAC. TBARS and H2O2 contents increased proportionally with BAC dosage, showing the highest increases of 30% and 40% at 10 mg L−1, respectively. The noticeable increase in SOD enzyme activity at BAC concentrations of 0.5, 1, and 2.5 mg L−1, with increases of 2.7-fold, 2.2-fold, and 1.7-fold respectively, along with minimal accumulation of H2O2, suggests that L. minor plants have a strong tolerance to BAC. This is supported by the efficient functioning of the CAT and GST enzymes, especially evident at the same concentrations, where increased activities effectively reduce the buildup of H2O2. In the AsA-GSH cycle, although variations were observed between groups, the contribution of the GR enzyme to the preservation of GSH content by recycling GSSG likely maintained redox homeostasis in the plant, especially at low concentrations of BACs. The study revealed that L. minor effectively accumulates BAC alongside its tolerance mechanisms and high antioxidant activity. These results underscore the potential for environmental cleanup efforts through phytoremediation.