We have shown from both simulations and experiments that zwitterion functionalized carbon nanotubes (CNTs) can be used to construct highly efficient desalination membranes. Our simulations predicted that zwitterion functional groups at the ends of CNTs allow a high flux of water, while rejecting essentially all ions. We have synthesized zwitterion functionalized CNT/polyamide nanocomposite membranes with varying loadings of CNTs and assessed these membranes for water desalination. The CNTs within the polyamide layer were partially aligned through a high-vacuum filtration step during membrane synthesis. Addition of zwitterion functionalized CNTs into a polyamide membrane increased both the flux of water and the salt rejection ratio. The flux of water was found to increase by more than a factor of 4, from 6.8 to 28.7 GFD (gallons per square foot per day), as the fraction of CNTs was increased from 0 to 20 wt %. Importantly, the ion rejection ratio increased slightly from 97.6% to 98.6%. Thus, the nanotubes imparted an additional transport mechanism to the polyamide membrane, having higher flow rate and the same or slightly better selectivity. Simulations show that when two zwitterions are attached to each end of CNTs having diameters of about 15 Å, the ion rejection ratio is essentially 100%. In contrast, the rejection ratio for nonfunctionalized CNTs is about 0%, and roughly 20% for CNTs having five carboxylic acid groups per end. The increase in ion rejection for the zwitterion functionalized CNTs is due to a combination of steric hindrance from the functional groups partially blocking the tube ends and electrostatic repulsion between functional groups and ions, with steric effects dominating. Theoretical predictions indicate that an ideal CNT/polymer membrane having a loading of 20 wt % CNTs would have a maximum flux of about 20000 GFD at the conditions of our experiments.