Understanding the local reaction conditions at the catalyst-ionomer interfaces inside polymer electrolyte fuel cells is vital for improving cell performance and stability. Properties of the water film and distributions of protons and oxygen molecules at the catalyst-ionomer interface are affected by the state of the catalyst and support surfaces and the structure of the ionomer skin layer. In this work, the interfacial region between catalyst and support surface and ionomer skin is simulated using molecular dynamics. This water-filled nanopore model is constructed to study the impact of local charge density, density of sidechains at the ionomer layer, and water layer thickness on the water structure and electrostatic conditions in the pore as well as the transport properties of water, hydronium, and molecular oxygen at the interface. The analysis of the flooded pore model indicates that surface hydrophilicity, represented by water adsorption and the formation of an ordered water layer at the surface, is a major factor determining the interfacial proton density, ionomer sidechain mobility, and interfacial oxygen transport resistance. The results obtained can guide the design of new catalyst materials, where the hydrophilicity of the surface can be tailored to minimize the local proton transport resistance and improve electrode performance.