The properties of an aqueous solution are interesting depending on its application. Their characteristics are mainly a result of a hydrophobic interaction. The permeation behavior, particularly for an aqueous solution with a hydrophilic solute, is affected by the hydration of water to the solute. In case of an aqueous solution of organic compounds, generally, the water molecule adjacent to the solute become less mobile than in the pure water due to hydration. The hydration may affect the diffusivity of solute molecules during permeation. In this study, we investigated the pervaporation through a poly(dimethylsiloxane (PDMS) membrane and the hydration effect on the solution-diffusion mechanism for various organic compounds. When the concentration of the solution was over the concentration calculated by the number of water molecules adjacent to a solute molecule, the hydration number, the water molecules hydrate to several solute molecules, and the motion of the water molecules was prevented. During pervaporation, the solute was concentrated in the PDMS membrane and the diffusion of water molecules was prevented.