The study was focused on the application of catalytic wet peroxide oxidation (CWPO) with a synthesized magnetic catalyst (Fe3O4/MWCNTs) for the treatment of real water matrices spiked with pharmaceutical compounds. CWPO was carried out by modifying the initial pH of surface water (SW), wastewater treatment plant (WWTP) effluent, brewery wastewater (BW) and hospital wastewater (HW), and the effect of the addition of the emerging pollutants naproxen (NAP) and diclofenac (DCF). From the experimental results, pH and concentration of NAP and DCF in CWPO were crucial factors in the successful pollutants removal from water matrices. The lab-prepared catalyst showed high removal rates of NAP and DCF from different water matrices spiked with the NAP-DCF mixture at pH 5.0. The highest average removal rate of TOC (75%), NAP (66%), DCF (76%), TN (39%) and aromaticity (68.39%) was obtained for SW matrix using 1.0 g L−1 of catalyst, pH ≈ 5.0, 5 mM of H2O2 and 60 °C. The mineralization decreased with the increase of the initial TOC concentration of the tested matrix. By CWPO tests of the real water matrices it was demonstrated that DCF removal was higher than NAP. From the recyclability tests, the catalyst demonstrated high activity and stability along three consecutive CWPO cycles of 8 h each one. The pseudo-second order model well-described the degradation of NAP and DCF. Finally, aromaticity and toxicity of the effluents were greatly reduced after CWPO treatment. This work demonstrated that CWPO with the magnetic catalyst is an efficient method to remove DCF-NAP mixtures from real aqueous matrices.