Biological membranes can achieve remarkably high permeabilities, while maintaining ideal selectivities, by relying on well-defined internal nanoscale structures in the form of membrane proteins. Here, we apply such design strategies to desalination membranes. A series of polyamide desalination membranes - which were synthesized in an industrial-scale manufacturing line and varied in processing conditions but retained similar chemical compositions - show increasing water permeability and active layer thickness with constant sodium chloride selectivity. Transmission electron microscopy measurements enabled us to determine nanoscale three-dimensional polyamide density maps and predict water permeability with zero adjustable parameters. Density fluctuations are detrimental to water transport, which makes systematic control over nanoscale polyamide inhomogeneity a key route to maximizing water permeability without sacrificing salt selectivity in desalination membranes.