We report the transport behavior of water molecules along a system of coaxial single-walled carbon nanotubes (SWCNTs) of different diameters with junctions under the driving force of methane molecules. The junctions are potential barriers to the transport of water molecules through SWCNTs. However, methane molecules can overcome these potential barriers and pull the water molecules across the junction region from one compartment to the next. Although a junction is an obstacle to water transport through SWCNTs, the presence of more junctions gives methane molecules a longer lasting driving force that helps them to pull the water molecules out of the SWCNTs.