Carbon nanotubes (CNTs) have become the focus of attention of many scientists and companies worldwide. CNT-based filters have a prospective advantage in comparison to the commercial filters already in operation because they are light weight and do not require electricity to operate. This investigation handles the filtration efficiency of manganese and iron from aqueous solution using commercial multiwalled carbon nanotubes (MWCNTs) (Taunit). The effects of different parameters such as CNT filter mass, concentration of manganese and iron in aqueous solution and pH of aqueous solution on removal of these heavy metals are determined. From these investigations, the removal efficiency of manganese and iron could reach 71.5% and 52% respectively for concentration 50 ppm, suggesting that Taunit is an excellent adsorbent for manganese and iron removal from water. There was a significant increase in removal efficiency at pH = 3 for manganese and pH = 8 for iron. The effect of oxidation on the structural of MWCNTs was characterized by scanning electron microscope (SEM) and energy dispersive spectroscopy (EDS) techniques to investigate the functionalization with oxygen-containing and outer diameter distribution. It was found that functionalized CNT-based filters are more efficient at removing manganese and iron from aqueous solutions. Oxidized MWCNTs may be a promising candidate for heavy metal ion removal from industrial wastewater.