Increasing the operating temperature and pressure of proton exchange membrane water electrolysis (PEM WE) enhances energy efficiency at high hydrogen production rates, but membrane stability is a limiting factor in this approach. Excessive water uptake (excessive swelling) is an often-overlooked phenomenon in PEM water electrolysis field, despite its significant impact on membrane properties and system performance. In this study, four commercial PEMs were selected to investigate effects of side chain length and equivalent weight on their excessive swelling. Membrane samples were exposed to liquid water at 120 °C and 600 kPa for 800 hours, while in-plane resistivity was continuously monitored. All membranes showed a gradual increase in resistivity over time. Before and after the hydrothermal treatment, the membranes were characterized using small-angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), and atomic force microscopy (AFM). The results show that swelling is mainly governed by membrane hydrophilicity and that, unlike previous reports, exceeding the α-transition temperature is not required for excessive swelling to occur. Long side chains were associated with a lesser degree of resistivity increase, which was connected to larger hydrophilic domains that likely promote a more favourable mesoscale morphology at very high water contents. Our study showed that while excessive water uptake at elevated temperature and pressure represents serious stability issues. Careful design of the membrane's internal morphology might help mitigate these undesirable effects.