Conventional methods of desalination of water and wastewater are usually not economically viable for water required for agricultural production due to high energy consumption and equipment costs. This study was conducted with the aim of evaluating the efficiency of nano-biomagnetics produced from sugarcane bagasse in removing sodium and chloride ions from agricultural wastewater under the influence of a magnetic field. Non-nanoactive, nano-active and magnetic nano-active adsorbents were produced using a hot-decomposition process in electric furnaces at 600 °C, chemical activation with potassium hydroxide and magnetization with a combination of hexahydrate ferric chloride and heptahydrate ferric sulfate. The results showed that the highest removal of chloride (44.6%) and sodium (58.3%) ions was achieved in the magnetically activated nanosorbent under the influence of a 0.5 Tesla magnetic field, for an activator to biochar ratio of 3, a microwave power of 400 W, and an activation time of 10 minutes. Surface analyses including FT-IR spectroscopy and scanning electron microscopy (SEM) confirmed that the hydroxyl, carboxyl, and carbonyl functional groups on the surface of the adsorbent play a key role in the adsorption of sodium and chloride ions. It was also observed that applying a magnetic field improved the orientation of adsorbed molecules towards the adsorbent and weakened hydrogen bonds in water, which led to an increase in the efficiency of the adsorption process. This study shows that the use of magnetic nanobiochar under the influence of a magnetic field can be used as an economical and sustainable solution to reduce the salinity of agricultural wastewater.