This paper presents a study of single‐channel proton exchange membrane fuel cells (PEMFCs) using computational modeling and simulation. For this analysis, the commercial software COMSOL Multiphysics was used to build a single‐phase isothermal and tridimensional fuel cell model. For the mathematical description of the catalyst layer, the flooded agglomerate model was implemented, and it proved to be more accurate than Butler‐Volmer model, which is the pre‐built model in the software. Such evidence was verified when comparing the polarization curves obtained using both models with an experimental curve. After definition of the model, the main objective of this study was to analyze the influence of the flow channel cross‐section in the water distribution inside the cell, studying rectangular, trapezoidal and hybrid stepped geometries. The fuel cell with stepped channel was equivalent to the trapezoidal cell in all aspects analyzed, and both provided superior water management than the rectangular cell. However, the current generation in the rectangular design was slightly higher. It was noted that the simulation of a tridimensional model provided a better understanding of the regions where higher concentrations of water can occur, and that different flow channel designs can be used to enhance water management.