Graphene oxide flakes functionalized with 3-amino-1-propanesulfonic acid (denoted as GOSULF) as powder or incorporated into an ionomer membrane such as Nafion (DuPont) were studied for water purification applications. The adsorption and the photocatalytic activity of GOSULF powder itself or confined as nano-additive in the membrane (Nafion-GOSULF) were investigated by measuring the degradation of a cationic dye, methylene blue (MB), in dark and under UV/visible light illumination. The results were compared with the ability of these systems to degrade an anionic dye, methyl orange (MO), in order to evaluate the role of polymer-dye interaction. The degradation of the azo dyes depends on the mutual interaction between GOSULF flakes, the polymeric matrix and the dye: Nafion-GOSULF strongly reduces MB both in dark and illumination condition in the same way of the GOSULF powder, while, for MO degradation, the composite membrane is more efficient than GOSULF alone. Finally, the possibility to reuse the same photocatalytic material several times, that is the main advantage of embedding active nanomaterials in a polymer matrix, is demonstrated by effective regeneration of the nanocomposite membranes.