Currently, methods of water purification and aqueous solutions leading to effective reduction of introduced chemical compounds into water purification systems have become the subject of research. Physical methods have become an alternative, because by subjecting water and aqueous solutions to UV (ultraviolet) radiation or magnetic fields (MF), either ultrasonic or electric, it is possible to influence the change of structure, which results in changes in the properties of water and aqueous solutions. This paper attempts to verify the influence of a weak magnetic field on the removal of iron and manganese compounds in the filtration process on gravel of 1–2 mm granulation, sand of 0.4–0.8 mm granulation, activated alumina and activated carbon. The conducted research proved that MF has a significant influence on the effectiveness of iron and manganese removal from water in the case of alumina, while in the filtration process through other filter materials the effect of MF was small.