The permeation of water vapour through a coated polymer gas barrier film is controlled by the defects in the coating. By modelling these defects as a combination of macro-defects (in which the activation energy of permeation is that of the underlying polymer substrate) and nano-defects (in which the activation energy of permeation is something greater than that of the polymer substrate), we are able to understand the mechanisms of permeation in high gas barrier layers. Permeation is controlled by the amounts of such defects, with the observed overall activation energy informing us of the relative permeation through macro-and nano-defects. Three examples of aluminium oxide (AlOx)-coated polymers are given to illustrate this: a comparison of pofyfethylene naphthalate) and polypropylene (OPP) substrates, the role of sputter power in AlOx/OPP films and the role of oxide thickness in AlOx/OPP films. When the amount of permeation through macro-defects is quite low, and hence nano-defect permeation is a significant proportion of the overall water vapour transport, control of each of the two defect types becomes important. Contrary to what has been previously assumed, the activation energy can be observed as greater in some cases in which the overall permeation is also greater, and this can be explained by an increase in the proportion of permeation taking place through nanodefects. This model is evidenced by reference to microstructural and other characterisation, and hence gives rise to understanding of the relationship between process properties, microstructure and permeation.