The use of semipermeable membranes containing carbon nanotubes (CNTs) that form continuous pores has been suggested as a way to reduce the cost of desalination viareverse osmosis. Example membranes containing aligned CNTs have been fabricated, but obtaining only the very narrow pores that are able to block the passage of ions while allowing a rapid flow of water remains a challenge and previous computational studies have focused on idealised tubes. Here molecular dynamics simulations are used to examine water and ion transport through functionalised CNTs with the aim of investigating whether such chemical modification allows the performance of CNT based membranes to be improved, or for larger diameter pores to be used. A range of different charged and polar functional groups were added to a 1.1 nm diameter (8,8) CNT that was previously found to be only moderately effective at rejecting ions. These CNTs were incorporated into membranes and simulations were conducted with a hydrostatic pressure difference to determine the ion rejection and flux of water passing through each as well as the energy barriers presented to ions and water molecules. The results show that the addition of charges at the entrance of the pore can help to prevent the passage of ions, however, any functionalisation also reduces the flow of water through the membrane due to increased electrostatic interactions between the water molecules and the CNT. Assuming pore densities that have previously been achieved, the performance of these membranes in the simulations is still many times better than existing technology and thus the inclusion of functionalised CNTs in desalination membranes may prove to be useful in achieving salt rejection and rapid water flow.