Several studies have shown the presence of fluoride levels much higher than the 1.5 mg/L threshold concentration recommended by WHO in the spring waters and wells of the Ethiopian Rift Valley. Available defluoridation techniques can be costly, present complicated technical aspects, and show limited effectiveness. Therefore, it is necessary to devise innovative, sustainable, and effective solutions. This study proposes an alternative method of intervention to the known techniques for removing fluoride from water, particularly suitable for smaller rural communities. In particular, in this work, the possibility to use electromagnetic fields as a physical method for removing the excess fluoride was investigated. The study was carried out by developing a multiphysics model used for studying and envisaging the design of a device. In this framework, the combination of this approach with the use of highly reactive smectite clay was numerically studied. The results obtained, although preliminary, indicate that the proposed system could significantly impoverish the waters of the Rift Valley from fluoride, with the consequence of obtaining a resource suitable for human consumption, in particular for rural communities. However, further theoretical investigations and experimental phases will be necessary to achieve the desired results.