Purpose Besides classical organic pollutants and pesticides, pharmaceuticals and their residues have nowadays become recognized as relevant environmental contaminants. The risks of these chemicals for aquatic ecosystems are well known, but information about the pharmaca-plant interactions and metabolic pathways is scarce. Therefore, we investigate the process of uptake of acetaminophen (N-Acetyl-4-aminophenol) by Brassica juncea, drug-induced defense responses and detoxification mechanisms in different plant parts. Material and methods Hydroponically grown Indian mustard (Brassica juncea L. Czern.) plants were treated with acetaminophen and root and leaf samples were collected after 24, 72, and 168 h of treatment. The uptake of acetaminophen and the formation of its metabolites were analyzed using LC-MS/MS technique and enzyme activities including glutathione S-transferases (GSTs) as well as several plant defense enzymes like catalase, ascorbat peroxidase, peroxidase, and glutathione reductase were assayed spectrophotometrically. Results We determined the uptake and the translocation of acetaminophen, and we tried to identify the steps of the detoxification process by assaying typical enzymes, supposing the involvement of the same- or similar enzymes and reactions as in the mammalian detoxification process. After 24-h exposure, effective uptake and translocation were observed to the upper part of plants followed by two independent conjugative detoxification pathways. Changes in antioxidant defense enzyme activities connected to the defense pathway towards reactive oxygen species indicate an additional oxidative stress response in the plants. Conclusions The major metabolic pathways in mammals are conjugation with activated sulfate and glucuronic acid, while a small amount of acetaminophen forms a chemically reactive and highly toxic, hydroxylated metabolite. We identified a glutathionyl and a glycoside conjugate, which refer to the similarities to mammalian detoxification. Increased GST activities in leaf tissues were observed correlated with the appearance of the acetaminophen-glutathione conjugate which shows the involvement of this enzyme group in the metabolism of acetaminophen in plants to organic pollutants and xenobiotics. High acetaminophen concentrations lead to oxidative stress and irreversible damages in the plants, which necessitates further investigations using lower drug concentrations for the deeper understanding of the induced detoxification—and defense processes.