Membranes with sub-nano channels formed by self-organization of ionic liquid-crystalline (LC) compounds have great potential as water treatment membranes. In this study, the transport mechanisms of water molecules and ions in the sub-nano channels of the LC membranes are investigated by molecular dynamics simulations for NaCl and NaNO 3 solutions. The simulation results suggest that there are different transport mechanisms for water molecules and ions; the transport of water molecules occurs by Brownian diffusion, whereas that of ions occurs by jump diffusion between particular sites in the sub-nano channel. A free-energy landscape of an ion in the channel is analyzed using a metadynamics method, which indicates distinct local minima at particular sites and supports the jump diffusion mechanism. The effects of the LC compounds' structural flexibility and the electrostatic interaction with the wall of the sub-nano channels on the permeability of water molecules and ions are also investigated by molecular dynamics simulations. Simulation results suggest both the structural flexibility and the electrostatic interaction, which are characteristics of the LC membranes, are important factors in determining the water treatment performance. The structural flexibility affects the permeability of the membrane to water molecules and the electrostatic interaction reduces the permeability to ions. 604 | Environ. Sci.: Water Res. Technol., 2020, 6, 604-611This journal is † Electronic supplementary information (ESI) available: Details of the simulation method, MD simulations of the bulk solutions, an example of the jump diffusion mechanism for Na + observed during the simulation, and the mobility of water molecules in a nonequilibrium MD simulation. See Recently, we developed liquid crystalline (LC) membranes with sub-nano channels formed by self-organization of thermotropic ionic LC compounds. The LC membranes have great potential as excellent water treat membranes. In this work, we elucidated the transport mechanisms of water molecules and ions in the LC membranes by molecular dynamics simulations. We also elucidated the effects of the structural flexibility and the electrostatic interaction, which are characteristics of the LC membranes, on the water treatment performance. The knowledge obtained in this work has great potential to realize the development of future LC membranes of which the performances to water treatment are significantly improved.