The role of surface nanoscale roughness on the charging behavior of nanostructured γ-AlOOH (Boehmite) and β-FeOOH (Akaganeite)/γ-AlOOH (Boehmite) mesostructures deposited onto siliceous substrates has been investigated. Two-dimensional (2D) quantum-sized and one-dimensional (1D) nanometer size γ-AlOOH (Boehmite) structures and 2D atomically-thin β-FeOOH (Akaganeite) nanobelts with a mean width of approximately 10 nm were deposited onto siliceous substrates in aqueous processes at moderate temperatures. Low cost and large scale manufacturing of siliceous substrates coated with 2D and 1D γ-AlOOH (Boehmite) crystallites of 2.7 ± 0.5 nm in diameter, with an average length of 2.9 ± 0.9 nm and 250 ± 50 nm, respectively, that were further functionalized with atomically thin 2D β-FeOOH (Akaganeite) nanobelts was demonstrated. Zeta potentials of surfaces have been characterized by direct measurement of streaming potentials in NaCl aqueous electrolyte. A model explaining the pH dependent behavior of the zeta potential was proposed. The isoelectric point values of rough nanostructured surfaces are three pH units higher as compare to the flat crystalline γ-AlOOH (Boehmite) and β-FeOOH (Akaganeite) surfaces, resulting in a high removal efficacy of submicron particles from aqueous suspension by the surfaces with combined microscale and nanoscale structures. This suggests the existence of a coupling electrokinetic effect of the local electrical double layer (EDL) fields with the local flow fields.