Water transport through membranes is an attractive topic among the research dedicated to dehydration processes, microenvironment regulation, or more simply, recovery of freshwater. Herein, an atomistic computer simulation is proposed to provide new insights about a water vapor transport mechanism through PEBAX membranes filled with ionic liquid (IL) [C12C1im]Cl. Starting from experimental evidence that indicates an effective increase in water permeation as the IL is added to the polymer matrix (e.g., up to 85·10−3 (g·m)/(m2·day) at 318.15 K for PEBAX@2533 membranes loaded with 70% of IL), molecular dynamics simulations are proposed to explore the key role of IL in water transport inside membranes. The polar region composed of anions and cationic head groups of the IL is demonstrated to serve as the pathway for water transport through the membrane. Water molecules always stay near the pathway, which becomes wider and thus has a larger water-accessible area with increasing IL concentration. Hence, the diffusion coefficients of water molecules and ions increase as the IL concentration increases. The simulation provides useful indications about a microscopic mechanism that regulates the transport of water vapor through a kind of PEBAX/IL membrane, resulting in full agreement with the experimental evidence.