Poly(arylene ether sulfone)-based ionomers with sulfonate groups of varying acidity (perfluoroalkyl sulfonate, aryl sulfonate and alkyl sulfonate) were synthesized via borylation of aromatic C–H bonds and Suzuki coupling with sulfonated phenyl bromides. Properties of the ionomers, such as thermal stability, water uptake, ion exchange capacity, morphology and proton conductivity, were analyzed with respect to the effect of the sulfonate group. Superacidic fluoroalkyl sulfonated ionomers displayed much higher conductivity at low relative humidity than less acidic aryl and alkyl sulfonated ionomers in spite of their lower ion exchange capacities. The water uptake of the membranes correlated with their IEC, regardless of the acid group identity. The membranes with fluoroalkyl and alkyl sulfonate groups had similar hydration numbers as a function of RH, but the hydration number of the aromatic sulfonate sample was greater than the other polymers. Ionic domain structure analysis by atomic force microscopy, transmission electron microscopy and small-angle X-ray scattering revealed that all of the aromatic ionomers in this study had a small, disorganized phase structure. These results demonstrate that the primary influence on the proton conductivity of these randomly sulfonated copolymers is the acid strength while the nanoscale domain structure plays a secondary role in the low RH proton transport.