Nafion nanocomposites for energy-related applications are being used extensively because of the attractive properties such as enhanced water retention, low unwanted crossover of electrolytes, and high proton conductivity. We present the results of the molecular dynamics modeling of Nafion films confined between two walls (substrates) of different polymer–wall interaction strengths and of different separation distances to model Nafion nanocomposites. Our goal is to provide insights into the effects of varying hydrophilicity and volume fraction of fillers/nanoparticles on the internal structure and water transport inside the Nafion membrane. The sulfur–sulfur radial distribution function first peak distance and the sulfur–oxygen (water) coord...