The oxidation of eight pharmaceutical micropollutants by chloroperoxidase derived from Caldaromyces fumago using hydrogen peroxide as an electron acceptor is reported. All the tested compounds, namely trazadone, sulfamethoxazole, naproxen, tetracycline, estradiol, ketoconazole, ketorolac, and diclofenac, were found to be substrates for oxidation by chloroperoxidase. The respective oxidation products were identified by electrospray ionization–mass spectrometry. All the products contain at least one chloride atom in their structure after the enzymatic oxidation. Degradability experiments indicated that most of the reaction products are more biodegradable than the corresponding unmodified compounds. The enzyme was found to be catalytically active in effluent from a water treatment facility, transforming the micropollutants with high reaction rates and conversions. The enzyme was immobilized in chitosan macrospheres, which allowed the catalyst to be recycled for up to three treatment cycles in simulated samples of treated residual water. The conversion was high in the first two cycles; however, in the third, a 50% reduction in the capacity of the enzyme to oxidize ketorolac was observed. Additionally, immobilization improved the performance of the enzyme over a wider pH range, achieving the conversion of ketorolac at pH 5, while the free enzyme was not active at this pH. Overall, the results of this study suggest that chloroperoxidase represents a powerful potential catalyst in terms of its catalytic activity for the transformation of pharmaceutical micropollutants.