Depending on the operating conditions, the overall performance and durability of polymer electrolyte membrane fuel cells (PEMFC) can be strongly influenced by liquid water saturation of pores within the gas diffusion layer (GDL). Water agglomerations in the GDL may occur due to material morphology, surface characteristics and local boundary conditions. In the catalyst layer (CL) and microporous layer (MPL) these parameters are considerably different than those of the fibre substrate. The MPL and CL feature by orders of magnitude smaller pores than the substrate and the boundary conditions, e.g. temperature and relative humidity, are different than those in the substrate near the bipolar plate. Thus, different physical behavior within each layer can be observed, e.g. local liquid sorption. Therefore, finding an optimal strategy regarding water management requires knowledge on virtually all the factors involved. To approach this target, we are using and further developing a 3D Monte Carlo (MC) model which simulates water distribution within the GDL, employing the real GDL structure and operating conditions, exploited respectively from tomography and computational fluid dynamics (CFD) studies1. The 3D images are obtained from an assembled fuel cell and therefore, the results include compression and inhomogeneity information of the GDL. Furthermore, recent progress of the model has enabled simulations on the length scales relevant for the MPL and CL in addition to the fibre substrate. GDL substrates usually have an average pore size in the micrometer scale, whereas this value for the MPLs and CLs may go down to the nanometer scale. Therefore, a complete simulation of the water distribution in GDL includes working on at least two scales. Although obtaining accurate results on all three sub-layers is equally important, MPL and CL are the more challenging ones from the point of view of both structure and surface properties acquisition. Furthermore, simulating relevant domains within the material requires expensive computational effort. In this study, we report first results on MC simulations of the water distribution within the MPL and CL pores for different operating conditions. The 3D reconstruction of the material is obtained from the focused ion beam - scanning electron microscope (FIB-SEM) tomography2. By using atomic layer deposition (ALD) of ZnO, a good material contrast between pores and solid particles is achieved and therefore a reliable binarization can be obtained3. The voxel size is set to 45 nm in order to achieve both, an accurate computation with respect to the applied equations and an appropriately sized simulation domain. Our MC model provides the water distribution within the actual MPL and CL structures based on the local boundary conditions. The results show how the water distribution depends on parameters such as contact angle, porosity, local temperature and relative humidity. An example of simulation results is illustrated in the Figure 1.