The nanoscale structure of composite polyamide reverse osmosis (RO) and nanofiltration (NF) membranes was investigated by transmission electron microscopy and atomic force microscopy. The study demonstrated that the polymer density and charge are distributed across the active polyamide layer in a highly nonuniform fashion. The polyamide films appear to be built of a negatively charged outer layer sitting on top of an inner layer possessing a small positive charge. This picture appears to be fairly general for all types of composite membranes and seems to reconcile previously reported contradictory experimental facts concerning measurements of charge for this type of membrane. The sharp boundary between the layers roughly corresponds to the region of the highest polymer density, that is, the actual selective barrier. The location of this barrier deep inside the RO films indicates that formation of the RO polyamide is not limited solely by monomer diffusion through the film, as was suggested previously, but by other factors as well. In the NF polyamide, the location of the boundary nearer toward the surface might suggest a larger role of the diffusion-limited regime in this type of membrane. Comparison of the morphology of standard and high flux RO membranes showed that the modified procedure used to manufacture the latter apparently results in a more open structure of the active layer, and hence increased surface roughness, and a smaller thickness of the densest barrier. This finding contradicts the currently held view that the high permeability of this type of membrane is a function of increased surface roughness. The results largely support a recently presented theoretical model of polyamide membrane formation via interfacial polymerization.