A comprehensive study of the removal of selected biologically active compounds (pharmaceuticals and pesticides) from different water types was conducted using bare TiO₂ nanoparticles and TiO₂/polyaniline (TP-50, TP-100, and TP-150) nanocomposite powders. In order to investigate how molecular structure of the substrate influences the rate of its removal, we compared degradation efficiency of the initial substrates and degree of mineralization for the active components of pharmaceuticals (propranolol, and amitriptyline) and pesticides (sulcotrione, and clomazone) in double distilled (DDW) and environmental waters. The results indicate that the efficiency of photocatalytic degradation of propranolol and amitriptyline was higher in environmental waters: rivers (Danube, Tisa, and Begej) and lakes (Moharač, and Sot) in comparison with DDW. On the contrary, degradation efficacy of sulcotrione and clomazone was lower in environmental waters. Further, of the all catalysts applied, bare TiO₂ and TP-100 were found to be most effective in the mineralization of propranolol and amitriptyline, respectively, while TP-150 appeared to be the most efficient in terms of sulcotrione and clomazone mineralization. Also, there was no significant toxicity observed after the irradiation of pharmaceuticals or pesticides solutions using appropriate catalysts on rat hepatoma (H-4-II-E), mouse neuroblastoma (Neuro-2a), human colon adenocarcinoma (HT-29), and human fetal lung (MRC-5) cell lines. Subsequently, detection and identification of the formed intermediates in the case of sulcotrione photocatalytic degradation using bare TiO₂ and TP-150 showed slightly different pathways of degradation. Furthermore, tentative pathways of sulcotrione photocatalytic degradation were proposed and discussed.