This paper investigates the adsorption of nitrate anions from aqueous solutions on ammonium-functionalized magnetic mesoporous silica. The adsorbent was prepared via two-step coating process of silica on magnetic core (Fe3O4). The resultant structure was modified by 3-aminopropyl triethoxysilane (APTES), and finally acidified in HCl solution to convert the grafted amino groups to ammonium ones. Field-emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), vibration sample magnetometer (VSM), Energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FT-IR), and N-2 adsorption/desorption were used to characterize the obtained samples. Experimental results showed that several factors affected the uptake behavior such as pH, contact time, and initial concentration of nitrate. The amount of sorbent loading were examined and the adsorbent shows great adsorption capacity for NO3- (ca.51.28 mg g(-1) at 25 degrees C). The nitrate loaded multifunctional microsphere can be easily regenerated with NaOH solution. The separation of multifunctional magnetic microspheres from solution by novel high gradient magnetic separation (HGMS), using the collection of rods, was also investigated in details. Contrast to other methods based on filter and batch conditions, large volumes of water can be easily handled by the new designed HGMS due to the decreasing pressure drop and retention times. The effect of a set of two different experimental variables, i.e. flowrate and magnetic field strength, were investigated to identify the best working conditions for the separation of adsorbent from treated water. The most efficient backwash system was offered to reuse the magnetic particles, too. The removal efficiency of NO3- from solution was around 86.24% by the constructed HGMS under the optimal experimental conditions of 7.5 mL s(-1) flowrate and: 3.49 mT magnitude of the magnetic field.