Carbon nanotubes (CNTs) are known to be a suitable adsorbent of organic contaminants due to their large surface area and hollow structures; but at the nanoscale, CNTs have poor solubility and can be difficult to remove from solution. Studies have shown that the use of peptides can control the size, shape, and structure of materials during synthesis. In this research, magnetic CNTs were synthesized in a co‐precipitation reaction in the presence of the M6A−B1 peptide to correct these deficiencies in CNTs. Characterization of nanoparticles was facilitated by analytical methods including scanning electron microscopy, infrared spectroscopy, x‐ray diffraction, elemental analysis, and more. Water remediation studies were conducted to study the effect of dye, pH, and adsorbent on the removal of Toluidine Blue O from an aqueous solution. Pseudo‐second order kinetics were used in describing the rate of adsorption while a Langmuir isotherm model was used to study the interaction between the peptide‐functionalized material and the adsorbate. The separation factor, RL, calculated for the studied dye concentrations showed that adsorption with the peptide‐functionalized material was favorable.