Covalent attachment of photoacid dye molecules to perfluorinated sulfonic acid membranes is a promising route to enable active light-driven ion pumps, but the complex relationship between chemical modification and morphology is not well understood in this class of functional materials. In this study we demonstrate the effect of bound photoacid dyes on phase-segregated membrane morphology. Resonant X-ray scattering near the sulfur K-edge reveals that introduction of photoacid dyes to the end of the ionomer side chains enhances phase segregation among ionomer domains, and the ionomer domain spacing increases with increasing amount of bound dye. Furthermore, relative crystallinity is marginally enhanced within semicrystalline domains composed of the perfluorinated backbone. X-ray absorption spectroscopy coupled with first-principles density functional theory calculations suggest that above a critical concentration, the multiple hydrophilic groups on the attached photoacid dye may help increase residual water content and promote hydration of adjacent sulfonic acid side chains under dry or ambient conditions.