This paper presents a novel procedure for the treatment of contaminated water with high concentrations of nitrates, which are considered as one of the main causes of the eutrophication phenomena. For this purpose, magnetic nanoparticles functionalized with silver (Fe3O4@AgNPs) were synthesized and used as an adsorbent of nitrates. Experimental conditions, including the pH, adsorbent and adsorbate dose, temperature and contact time, were analyzed to obtain the highest adsorption efficiency for different concentration of nitrates in water. A maximum removal efficiency of 100% was reached for 2, 5, 10 and 50 mg/L of nitrate at pH = 5, room temperature, and 50, 100, 250 and 500 µL of Fe3O4@AgNPs, respectively. The characterization of the adsorbent, before and after adsorption, was performed by energy dispersive X-ray spectroscopy, scanning electron microscopy, Brunauer-Emmett-Teller analysis and Fourier-transform infrared spectroscopy. Nitrates can be desorbed, and the adsorbent can be reused using 500 µL of NaOH solution 0.01 M, remaining unchanged for the first three cycles, and exhibiting 90% adsorption efficiency after three regenerations. A deep study on equilibrium isotherms reveals a pH-dependent behavior, characterized by Langmuir and Freundlich models at pH = 5 and pH = 1, respectively. Thermodynamic studies were consistent with physicochemical adsorption for all experiments but showed a change from endothermic to exothermic behavior as the temperature increases. Interference studies of other ions commonly present in water were carried out, enabling this procedure as very selective for nitrate ions. In addition, the method was applied to real samples of seawater, showing its ability to eliminate the total nitrate content in eutrophized waters.