This study aimed to test the hypothesis that organic volume is the main variable for explaining the optical properties and predictive degree of diffusion of enamel histological points at zones of natural enamel caries (NEC; surface layer, SL, n = 30, and body of the lesion, BL, n = 58) and normal enamel (NE, n = 131). Molars with either NEC or NE were quantitatively analyzed regarding the mineral, organic and water volumes (considered as effective pore volume), opacity (predicted in 94% of cases by water volume in NEC), and water volume more easily available for diffusion, αd (squared water volume divided by the nonmineral volume; related to permeability). NEC presented lower mineral volumes and higher organic volumes, effective pore volume and opacity than NE. External origin of organic volume in NEC was evidenced by an organic gradient decreasing from the surface inward (R2 = -0.7), which was not detected in teeth with NE only; αd values of the SL and NE were similar and both were lower (p < 0.0001) than that of the BL. Comparing the SL from both NEC and artificial enamel caries (AEC; published data; n = 71), with similar mineral volumes, against developing enamel (published data), AEC showed more effective pore volume (3 times higher), higher αd and opacity than NEC mainly due to differences in organic volumes. Our results reasonably matched widely known features of NEC histological zones, and confirmed the organic volume as the main variable for explaining optical properties and αd (related to permeability).