Magnetite supported on multiwalled carbon nanotubes catalysts were synthesized by co-precipitation and hydrothermal treatment. The magnetic catalysts were characterized by X-ray diffraction, Fourier-transform infrared spectrometry, thermogravimetric analysis and N2 physisorption. The catalysts were then tested for their ability to remove diclofenac (DCF) and naproxen (NAP) from an aqueous solution at different conditions (pH, temperature, and hydrogen peroxide) to determine the optimum conditions for chemical oxidation. The optimization of the process parameters was conducted using response surface methodology (RSM) coupled with Box–Behnken design (BBD). By RSM–BBD methodology, the optimal parameters (1.75 mM H2O2 dosage, 70 °C and pH 6.5) were determined, and the removal percentages of NAP and DCF were 19 and 54%, respectively. The NAP–DCF degradation by catalytic wet peroxide oxidation (CWPO) was caused by •OH radicals. In CWPO of mixed drug solutions, DCF and NAP showed competitive oxidation. Hydrophobic interactions played an important role during the CWPO process. On the other hand, the magnetic catalyst reduced its activity after the second cycle of reuse. In addition, proof of concept and disinfection tests performed at the operating conditions showed results following the complexity of the water matrices. In this sense, the magnetic catalyst in CWPO has adequate potential to treat water contaminated with NAP–DCF mixtures.