For the first time in atmospheric pressure-plasma enhanced chemical vapour deposition of amorphous silica onto flexible polymer substrates, pinholes have been visibly detected using interferometric microscopy and their average diameter of 1.7 μm calculated. Pinholes were found to control the water vapour transmission rate of all 30 nm films deposited with input energies greater than 9 keV per precursor molecule, thus presenting an opportunity for the synthesis of single layer thin films with precisely targeted permeation rates. The pinholes themselves were understood to originate from interactions between the polymer substrate and filaments in the plasma. The non-uniformity of the discharge was attributed to the reduced concentrations of pr...