Molecular transport through nanopores has recently received considerable attention as a result of advances in nanofabrication and nanomaterial synthesis technologies. Surprisingly, water transport investigations through carbon nanochannels resulted in two contradicting observations: extremely fast transport or rejection of water molecules. In this paper, we elucidate the mechanism of impeded water vapor transport through the interstitial space of aligned multiwalled carbon nanotubes (aligned-MWCNTs)—capillary condensation, agglomeration, reverse capillary flow, and removal by superhydrophobicity at the tip of the nanotubes. The origin of separation comes from the water's phase change from gas to liquid, followed by reverse capillary flow. First, the saturation water vapor pressure is decreased in a confined space, which is favorable for the phase change of incoming water vapor into liquid drops. Once continuous water meniscus is formed between the nanotubes by the adsoprtion and agglomeration of water molecules, a high reverse Laplace pressure is induced in the mushroom-shaped liquid meniscus at the entry region of the aligned-MWCNTs. The reverse Laplace pressure can be significantly enhanced by decreasing the pore size. Finally, the droplets pushed backward by the reverse Laplace pressure can be removed by superhydrophobicity at the tip of the aligned-MWCNTs. The analytical analysis was also supported by experiments carried out using 4 mm-long aligned-MWCNTs with different intertube distances. The water rejection rate and the separation factor increased as the intertube distance decreased, resulting in 90% and 10, respectively, at an intertube distance of 4 nm. This mechanism and nanotube membrane may be useful for energy-efficient water vapor separation and dehumidification.