Heavy metal contamination in the world is increasing the impact on the environment and human life. Currently, carbon nanotubes and boron are some possible ideals for the nanofiltration of heavy metals due to the property of ion selectivity, optimized by the applications of the surface and the application of an external electric field. In this work, molecular dynamic was used to transport water with heavy metals under the force exerted by the electric field action inside nanotubes. This external electric field generates a propelling electrical force to expel only water molecules and retain ions. These metal ions were retained to pass through only water molecules, under constant temperature and pressure, for a time of 100 ps under the action of electric fields with values from 10^-8 to 10^-1 au. Each of the metallic contaminants evaluated (Pb²⁺, Cd²⁺, Fe²⁺, Zn²⁺, Hg²⁺) was subjected to molecular test simulations in the water. It was found that the measurement of the intensity of the electric field increased or the percentage of filtered water reduced (in both nanotubes), in which the intramolecular and intermolecular forces intensified by the action of the electric field contribute to retain the heavy metal ions due to the evanescent effect. The best results for nanofiltration in carbon and boron nanotubes occur under the field 10^-8 au. Since the filtration in the boron nitride nanotubes, a small difference in the percentage of filtered water for the boron nitride nanotube was the most effective (90 to 98%) in relation to the carbon nanotube (80 to 90%). The greater hydrophobicity and thermal stability of boron nanotubes are some of the factors that contributed to this result.