The contamination of the environment with pharmaceuticals and their residues has become a global issue. The main objective of study was to assess the genotoxicity, mutagenicity, and cytotoxicity of two drugs, diclofenac, sulfamethoxazole, and their binary mixture. The research focused on conducting a micronucleus assay using Vicia faba in water and soil environments. In the experiment, several parameters were monitored: mitotic index, presence of micronuclei, and chromosomal aberrations. The antioxidant enzymes activity in the plants leaves was measured. The concentrations of the drugs used in the analysis were representative of those currently detectable in the environment. The results indicated that diclofenac and sulfamethoxazole caused a reduction in the mitotic index by 45% and 47% in hydroponic, and 46% and 22% in soil cultures, respectively. Micronuclei and chromosomal aberrations were observed at the tested environmental concentrations (0.008–0.5 mg L−1). In the case of the drug mixture, the observed toxic effects in both cultivation were less significant than the predicted effects based on the Concentration Addition and Independent Action models. The tested compounds had an impact on the activity of enzymes. Even at environmental concentrations, the pharmaceuticals caused changes in catalase activity, with an average decrease of 39% in water and 10% in soil cultures, and in superoxide dismutase activity, showing an increase of 286% and 1835%, respectively. Overall, this study highlights the potential adverse effects of pharmaceutical contamination, even at low environmental concentrations. The findings underscore the importance of monitoring the presence of pharmaceutical residues to minimize their impact on ecosystems.