The formation of discrete water clusters in polymer electrolyte fuel cell gas diffusion layers (GDL) can lead to increased resistance for oxygen transport in the catalyst layer. This study investigates the effect of MPL crack propagation on the water cluster development in a X-ray computed tomography (CT) microstructure using the volume-of-fluid method (VoF). The VoF calculation was compared to operando CT data by voxel matching, obtaining a maximum 88 % accuracy. Using 3D contact angle extraction, the local scale heterogeneous wettability in the GDL was investigated. In a simulation study, MPL cracks were created as the boundary sources for water and the effect of increasing the area fraction covered by cracks on the water distribution in the GDL was investigated. The increased cracking, created larger discrete water clusters in the GDL with greater connectivity, due to in-plane coalescence. The in-plane movement leads to coalescence of clusters, forming fewer, larger clusters at later times close to breakthrough to the channel. This phenomena is shown by the decrease in water cluster density (n mm−2) from 10 to 5. This immobile water impacts the distribution of oxygen at the catalyst layer (10 % local difference) and therefore the current density distribution.