Perfluorinated sulfonic-acid ionomers are the most common proton exchange membrane material whose structure underpins their unique water and chemical/mechanical stability properties. Understanding this performance-stability trade-offs is therefore vital for realising optimal membranes. Terahertz time-domain spectroscopy has been demonstrated to resolve molecular water states and retention properties inside thick Nafion membranes. By developing a parametric-based algorithm for data analysis, we demonstrate the broad applicability of this technique to industrially relevant thin ionomers (13–70 μm) prepared under various processing conditions where results are supported by conventional gravimetric analysis and prior demonstrations. Using this technique therefore opens up opportunities for rapid future parameter space investigation for membrane optimisation.