Atomistic molecular dynamics simulations were performed to study hydrated Nafion systems large enough (similar to 2 million atoms, similar to 30 nm box length) to directly observe several hydrophilic domains at the molecular level. These systems consisted of six of the most significant and relevant morphological models of Nation to-date: (1) the cluster-channel model, (2) the parallel cylinder model, (3) the local order model, (4) the lamellar model, (5) the rod network model, and (6) a "random" model that does not directly assume any particular geometry, distribution, or morphology. Each system was initially built to closely approximate the proposed hydrophilic cluster structure in a given model. Molecular dynamics simulations were then used to observe resulting changes from and behavior of the assumed initial configurations. These simulations revealed fast intercluster "bridge" formation and network percolation in all models. Sulfonate groups were found inside these bridges and played a significant role in percolation. Sulfonates also strongly aggregated around and inside Clusters. Cluster surfaces were analyzed to study the hydrophilic-hydrophobic interface. Interfacial area and Cluster Volume significantly increased during the Simulations, and radial distribution functions and structure factors were also calculated. All nonrandom models clearly exhibited the characteristic experimental scattering peak, underscoring the insensitivity of this measurement to hydrophilic domain structure and highlighting the need for Future work to clearly distinguish morphological models of Nafion.