This paper seeks to establish a correlation between surface topographical defects and water vapour transmission rate (WVTR) measured under laboratory conditions for aluminium–oxide (Al2O3) barrier film employed in flexible photovoltaic (PV) modules. Defects in the barrier layers of PV modules causing high WVTR are not well characterised and understood. A WVTR of ~10−1 g/m2/day is sufficient for the most packaging applications, but ≤10−6 g/m2/day is required for the encapsulation of long–life flexible PV modules (Carcia et al., 2010a, 2010b). In this study, surface metrology techniques along with scanning electron microscopy (SEM) were used for a quantitative characterisation of the barrier film defects. The investigation have provided clear evidence for the correlation of surface defect density and the transmission of water vapour through the barrier coating layer. The outcomes would appear to suggest that small numbers of large defects are the dominant factor in determining WVTR for these barrier layers.