Proton exchange membrane (PEM) fuel cells have emerged as a potential alternative to internal combustion engines in order to curb dependency on fossil fuels and reduce harmful CO₂ emissions. Water management has been identified as a key research area for the advancement of PEM fuel cell technology, especially as it affects the purge protocol prior to cell shutdown. The presence of water in the cell is necessary to sustain membrane hydration, but the accumulation of excess liquid water, referred to as flooding, can lead to increased mass transport losses and reductions in performance and durability. In this work, a technique was developed to characterize the two-phase flow in the anode and cathode flow field channels simultaneously using a transparent fuel cell with dual-visualization capability. The transparent fuel cell used in this work was designed to represent actual full scale automotive fuel cell geometry. A video processing algorithm was developed to automatically detect dynamic and static liquid water present in the gas channels and generate relevant quantitative information. The water coverage ratio is introduced as a parameter to capture the time-averaged flow field water content information through recorded video sequences. The algorithm also yields information pertaining to the distribution of water among different two-phase flow structures. The water coverage ratio and distribution metrics were employed in comparing the performance of Freudenberg and Toray gas diffusion layers (GDLs) from a water management perspective, including direct anode to cathode comparisons for each GDL sample. This technique was able to provide a unique and comprehensive characterization of liquid water in an operating fuel cell which can be used towards the optimization of water management and purge strategies, as well as data generation for model validation purposes.