Water and air pollutants have huge impacts on the entire living system. In addition, the newly emerging nanopollutants, increasing global warming, and consequent climate changes are posing major threats to the freshwater or fresh air availability. This has made it urgent to invent an appropriate water/air treatment technology that removes nanopollutants and also desalinates water to a significant extent. Carbon-based nanomaterials have generated marvelous interest in a wide range of research activities due to their high adsorption capacities. Carbon nanotubes, carbon nanotube bundles, and related materials have potential applications in gas/ion separation and water purification. Recently, gas/ion separation and water purification through carbon-based nanomaterials have received increasing attention. This review summarizes the properties of carbon nanotubes and carbon nanotube bundles related to gas separation, ion separation, and water purification using molecular dynamics simulations. Membranes-based carbon nanomaterials show promise of water purification and gas separation. These attractive properties of carbon nanotubes-based and carbon nanotube bundles-based nanomaterials make them proper candidates for gas separation, gas molecular-sieving processes, and desalination purposes in nanoscale dimensions.