Nanoporous anodic alumina membranes (NPAMs) were produced by the two-step anodization method in sulphuric, oxalic and phosphoric acidic electrolytes displaying a hexagonally ordered spatial arrangement of pores with well controlled nanopore size distribution and low porosity. Some selected NPAMs were further modified by conformal coating their surface and inner pore walls with a thin layer of SiO2 by means of atomic layer deposition (ALD), which reduces both the pore radii and porosity but it also seems to affect to the electric fixed charge on the membranes surface. A comparative study about the influence of silica modification of NPAMs surfaces on the ionic transport through the nanoporous membranes has been performed by measuring membrane potentials and electrochemical impedance spectroscopy with NaCl solutions. According to these results, a direct correlation between the membrane effective fixed charge and the NaCl diffusion coefficient can be established. The coating with a SiO2 thin layer causes a reduction of 75% in the positive effective fixed charge of the NPAMs independently of their pore radii and the increase in counterion transport (cation transport number and diffusion coefficient) even through constrained nanopores, which can be of interest in several applications (microfluidics, drug delivery, nanofilter devices, etc.). Moreover, slight changes in the membrane/solution interface due to the SiO2 cover layer are also indicated.