The development of new reverse osmosis (RO) membranes with enhanced performance would benefit from a detailed knowledge of the membrane structures which participate in the filtration process. Here, we examined the hierarchical structures of the polyamide (PA) active layer of the SW30HR RO membrane. Scanning electron microscopy combined with focused ion beam milling (FIB-SEM) was used to obtain the 3-D reconstructions of membrane morphology with 5 nm cross-sectional resolution (comparable with the resolution of low magnification TEM imaging in 2D) and 30 nm slice thickness. The complex folding of the PA layer was examined in 3 dimensions, enabling the quantification of key structural properties of the PA layer, including the local thickness, volume, surface area and their derivatives. The PA layer was found to exhibit a much higher and convoluted surface area than that estimated via atomic force microscopy (AFM). Cross-sectional scanning transmission electron microscopy (STEM) was used to observe the distribution of a tracer stain under various conditions. The behaviour of stain in dry and wet PA indicated that the permeation pathways have a dynamic nature and are activated by water. High resolution STEM imaging of the stained PA nano-films revealed the presence of <1 nm pore-like structures with a size compatible with free volume estimations by positron annihilation lifetime spectroscopy (PALS). This study presents a comprehensive map of the active PA layer across different length scales (from micro- to sub-nanometre) and mechanistic insight into their role in the permeation process.