The elucidation of photocatalysis and adsorption mechanisms in the pollutant removal, as well as the efficiency for each process, provide key information for polluted water remediation. In this respect, the present study analyzed the application of nanomaterials based on niobium pentoxide (Nb2O5) and hydroxyapatite (HAP) during Prozac® and 4-(trifluoromethyl)phenol (TFMP) photodegradation. Removals for Prozac® and TFMP were respectively 93% after 2 min and 64% after 5 min. The photodegradation kinetic constants by Nb2O5 nanoparticles were 2.1 min‐1 (R2 = 0.943) and 0.185 min‐1 (R2 = 0.994), respectively, for Prozac® and TFMP, using a Hg-MDEL reactor operating at 70 W microwave power. A detailed study of the mechanisms for Prozac® and TFMP photodegradation was carried out, confirming that the adsorptive, oxidative, and photolytic processes work together to remove and/or convert the compounds into by-products. Therefore, Prozac® and the main by-products were quantified, and the cytotoxicity response was evaluated using the Lepidium sativum and Allium cepa plants. The results showed that 3-phenyl-propyl-methylamine (PPMA) by-product was more toxic than Prozac® to plant growth, exhibiting seed seability of 4% (PPMA), 33% (Prozac®), 77% (α-[2-(Methylamino) ethyl] benzyl-alcohol, MAEB), and 81% (TFMP). Furthermore, the presence of these contaminants may increase phytotoxicity at the cellular level, fostering mutation, and cell death.