Carbon nanotubes have attracted interest as possible membranes for desalination based on the observation of fast diffusion of water in simulations of long or infinitely periodic systems. When carbon nanotubes are finite they have often been simulated in force-field studies as having unsaturated dangling bonds for convenience, even though this is chemically unrealistic. In the present work, the influence of realistic terminations on the diffusion of water through the nanotubes is examined through computer simulation as well as the nature of the interface with saline solution at seawater concentrations. Termination of the cleaved nanotubes by hydrogen with a range of functional groups is explored including hydroxyl, carboxylic acid, and carboxylate anions with sodium counter cations. Realistic structures are found to lead to a reduced alignment of the nanotubes within the membrane layer and therefore a broader interfacial region. Diffusion of water within the finite nanotubes is slower than observed in the infinite limit and is, in general, further reduced as the polarity of the end functional groups increases. The largest impact occurs for carboxylate termination in contact with saline solution, where the ionic atmosphere of sodium ions retards water diffusion across the interface.