Plasma-enhanced chemical vapor deposition (PECVD) of SiOx thin coatings on polymer surfaces yields tough hybrid materials with the gas barrier properties and transparency of glass. Combination of these properties makes these materials ideally suited for food packaging and biomedical device applications. In this study, we employ a Non-Parametric Response Surface Methods optimization to identify the Magnetron-PECVD conditions responsible for superlative SiOx, barrier coatings on poly(ethylene terephthalate) (PET). Oxygen and water vapor permeances of optimized PET/SiOx, composites produced by hexamethyldisiloxane and trimethylsilane have been measured as functions of temperature and are found to exhibit Arrhenius behavior. The thermal activation energy for water val,or permeation, unlike that for oxygen permeation, depends on barrier performance and increases by as much as 20 kJ/mol with an increase in barrier efficacy. Examination of these materials by phase-imaging atomic force microscopy and energy-filtered transmission electron microscopy reveals a correlation between SiOx, morphology (including defects) and barrier performance. Morphological and permeation results are compared to identify some of the physical factors governing water vapor permeation through SiOx-modified polymers.