This work reports the influence of the chemical structure of two sulfonated poly(aryl ether ketone)s (SPAEK) on the hydration and gas transport mechanism of thin membranes made thereupon. For this purpose, two sulfonated poly(aryl ether ketone)s having the same ionic exchange capacity (IEC) but bearing a different repartition of the sulfonic acid groups along the polymer backbone were prepared. These polymers were synthesized by direct copolymerization of two specific sulfonated precursors, bisphenol AF and 4,4'-difluorobenzophenone. The morphology of the membranes was studied by transmission electron microscopy, and the thermal properties of the ionomers were determined from differential scanning calorimetry and thermogravimetric analyses. A detailed analysis of the water sorption isotherms and kinetics was performed. The gas transport properties were also determined for He, H-2, and CO2 in the full range of water activity. From the detailed analysis sorption isotherm and of the relative contributions of the Fickian diffusion and relaxation phenomena, a water sorption mechanism was proposed in relation with the SPAEK architectures and polymers' chain mobility. This mechanism allowed explaining the different evolution of the gas transport properties observed as a function of the gas nature and hydration rate.