Ion-conducting polymers are ideal solid electrolytes for most energy storage and conversion devices where ion transport is a critical functionality. The system performance and stability are related to the transport and mechanical properties of the ionomers, which are correlated through physiochemical interactions and morphology. Thus, there exists a balance between the chemical and mechanical energies which controls the structure–function relationship of the ionomer. In this paper, it is reported how and why thermal treatments result in different water uptakes and nanostructures for a perfluorinated sulfonic acid (PFSA) membrane. The nanostructure of the PFSA membrane is characterized using small- and wide-angle X-ray scattering experiments. These changes are correlated with water content and mechanical properties and result in fundamental relationships to characterize the membrane with different thermal histories. Moreover, quasi-equilibrium water uptake and domain spacing both decrease with predrying or preconstraining the membrane, thereby suggesting that similar mechanical energies govern the structural changes via internal and external constraints, respectively. The findings suggest that heat treatments alter the balance between the chemical–mechanical energies where the interplay of the morphology and mechanical properties controls the structure–function relationship of the membrane. Finally, a model is developed using an energy-balance approach with inputs of the mechanical and structural properties; the dependence of water uptake on pretreatment is successfully predicted.