We investigate the dynamics of water confined in soft ionic nano-assemblies, an issue critical for a general understanding of the multi-scale structure-function interplay in advanced materials. We focus in particular on hydrated perfluoro-sulfonic acid compounds employed as electrolytes in fuel cells. These materials form phase-separated morphologies that show outstanding proton-conducting properties, directly related to the state and dynamics of the absorbed water. We have quantified water motion and ion transport by combining Quasi Elastic Neutron Scattering, Pulsed Field Gradient Nuclear Magnetic Resonance, and Molecular Dynamics computer simulation. Effective water and ion diffusion coefficients have been determined together with their variation upon hydration at the relevant atomic, nanoscopic and macroscopic scales, providing a complete picture of transport. We demonstrate that confinement at the nanoscale and direct interaction with the charged interfaces produce anomalous sub-diffusion, due to a heterogeneous space-dependent dynamics within the ionic nanochannels. This is irrespective of the details of the chemistry of the hydrophobic confining matrix, confirming the statistical significance of our conclusions. Our findings turn out to indicate interesting connections and possibilities of cross-fertilization with other domains, including biophysics. They also establish fruitful correspondences with advanced topics in statistical mechanics, resulting in new possibilities for the analysis of Neutron scattering data.