Both nanostructured materials and nanotubes hold tremendous promises for separation and purification applications, such as water desalination. By using molecular dynamics, herein, we compare the transport of aqueous electrolyte solutions through a Y-zeolite, which features interconnected, tortuous sub-nanometer nanopores, and a model silica nanotube, which has the same composition but is straight and has much lower surface complexity. In the Y-zeolite, ion transport is faster than the transport of water molecules, thus leading to a phenomenon of phase separation in which a gradient of salt concentration is generated along the flow direction. However, similar transport characteristics and phase separation are not found in the model silica nanotube. Detailed analysis suggests that, in nanochannels with complicated geometries, such as those of the Y-zeolite, the structural and flow characteristics of confined nanofluids are highly coupled, thus influencing the transport of ions and solvents and causing the phenomenon of phase separation.