Polymer electrolyte membrane water electrolyzers (PEMWEs) offer clean hydrogen production when coupled to renewables, requiring minimal overvoltages for efficient operation. This study adapts and improves upon a three-electrode configuration utilized in fuel cell and electrolyzer technologies for comprehensive in operando thermodynamic analyses of PEMWE operation by accounting for the impact of catalyst layer dimensions and alignment. Catalyst-coated membrane Nafion N117-based cells with precise dimensions were developed, with design tolerances determined using finite-element simulations and verified by microscopic imaging. An external membrane strip connected to a Ag/AgCl reference electrode in acid solution enabled threeelectrode electrochemical analyses of model platinum on Vulcan carbon and IrO 2 catalysts in PEMWEs with minimal artifacts. This design enabled thermodynamic analysis and indicated cathodic and anodic contributions to the cell voltage. Under 1 atm hydrogen, liquid-fed conditions, the cathode exhibited non-negligible voltage contributions attributed to hydrogen transport processes, while charge transport in the anode accounted for ca. 15% of the series resistance. Above 1 A cm −2 , the cathode became the main polarization resistance while the anode exhibited a low frequency inductive response. This work provides critical insights into PEMWE operation and methods for in operando analyses.