As water availability becomes a growing challenge in various regions throughout the world, desalination and wastewater reclamation through technologies such as reverse osmosis (RO) are becoming more important. Nevertheless, many open questions remain regarding the internal structure of thin-film composite RO membranes. In this work, fully aromatic polyamide films that serve as the active layer of state-of-the-art water filtration membranes were investigated using high-angle annular dark-field scanning transmission electron microscopy tomography. Reconstructions of the 3D morphology reveal intricate aspects of the complex microstructure not visible from 2D projections. We find that internal voids of the active layer of compressed commercial membranes account for less than 0.2% of the total polymer volume, contrary to previously reported values that are two orders of magnitude higher. Measurements of the local variation in polyamide density from electron tomography reveal that the polymer density is highest at the permeable surface for the two membranes tested and establish the significance of surface area on RO membrane transport properties. The same type of analyses could provide explanations for different flux variations with surface area for other types of membranes where the density is distributed differently. Thus, 3D reconstructions and quantitative analyses will be crucial to characterize the complex morphology of polymeric membranes used in next-generation water-purification membranes.