The FeBTC metal–organic framework (MOF) incorporated with magnetite is proposed as a novel material to solve water contamination with last generation pollutants. The material was synthesized by in situ solvothermal methods, and Fe₃O₄ nanoparticles were added during FeBTC MOF synthesis and used in drug adsorption. X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and Raman spectroscopy characterized the materials, with N₂-physisorption at 77 K. Pseudo-second-order kinetic and Freundlich models were used to describe the adsorption process. The thermodynamic study revealed that the adsorption of three drugs was a feasible, spontaneous exothermic process. The incorporation of magnetite nanoparticles in the FeBTC increased the adsorption capacity of pristine FeBTC. The Fe₃O₄–FeBTC material showed a maximum adsorption capacity for diclofenac sodium (DCF), then by ibuprofen (IB), and to a lesser extent by naproxen sodium (NS). Additionally, hybridization of the FeBTC with magnetite nanoparticles reinforced the most vulnerable part of the MOF, increasing the stability of its thermal and aqueous media. The electrostatic interaction, H-bonding, and interactions in the open-metal sites played vital roles in the drug adsorption. The sites’ competition in the multicomponent mixture’s adsorption showed selective adsorption (DCF) and (NS). This work shows how superficial modification with a low-surface-area MOF can achieve significant adsorption results in water pollutants.