Effective water management increases the performance of proton exchange membrane fuel cells (PEMFCs). The liquid droplet movement mechanism in the cathode channel, the gas-liquid two-phase flow pattern, and the resulting pressure drop are important to water management in PEMFCs. This work employed computational fluid dynamics (CFD) with a volume of fluid (VOF) to simulate the effects of two operating parameters on the liquid water flow in the cathode flow channel: Gas diffusion layer (GDL) pore shape for water emergence, and distance between GDL pores. From seven pore shapes considered in this work, the longer the windward side of the micropore is, the larger the droplet can grow, and the duration of droplet growth movement will be longer. In the cases of two micropores for water introduction, a critical pore distance is noted for whether two droplets coalesce. When the micropore distance was shorter than this critical value, different droplets coalesce after the droplets grew to a certain extent. These results indicate that the pore shape and the distance between pores should be accounted for in future simulations of PEMFC droplet dynamics and that these parameters need to be optimized when designing novel GDL structures.