The local proton density in the cathode catalyst layer (CCL) is a crucial parameter in determining performance, durability and lifetime of polymer electrolyte fuel cells (PEFC). The presented work in molecular modeling focuses on the distribution of protons and structure of interfacial water layers in the region between proton conducting ionomer layer and the surface of the catalyst-decorated support. The proton density distribution depends on the molecular structure and properties of the ionomer film as well as the adsorption and charging state of the metal surface. Classical molecular dynamics simulations serve as a valuable tool to rationalize the impact of these properties on the equilibrium proton density distribution in a water filled, slab-like pore. The slab is confined by two distinct boundaries, the first consisting of a Pt/C surface, and the second being an ionomer skin layer. The proton density distribution and interfacial water structure are explored as a function of oxide coverage at the metal surface, excess surface charge density, water layer thickness, ionomer film structure, and Pt surface facet. Simulation results are analyzed to gain deeper understanding of interactions and reaction conditions that prevail at the agglomerate level in the catalyst layer.