Nafion(R) is a commercially available perfluorosulphonate cation exchange membrane commonly used as a perm-selective separator in chlor-alkali electrolysers and as the electrolyte in solid polymer fuel cells. This usage arises because of its high mechanical, thermal and chemical stability coupled with its high conductivity and ionic selectivity, which depend strongly on the water content. The membrane was therefore studied in different states of hydration with two complementary techniques: atomic force microscopy (AFM) and small angle X-ray scattering (SAXS) combined with a maximum entropy (MaxEnt) reconstruction. Tapping mode phase imaging was successfully used to identify the hydrophobic and hydrophilic regions of Nafion. The images support the MaxEnt interpretation of a cluster model of ionic aggregation, with spacings between individual clusters ranging from 3 to 5 nm, aggregating to form cluster agglomerates with sizes from 5 to 30 nm. Both techniques indicate that the number density of ionic clusters changes as a function of water content, and this explains why the bulk volumetric swelling in water is observed to be significantly less than the swelling inferred from scattering measurements.