A reactive molecular dynamics simulation has been performed for the characterization of the relationship between proton transport and water clustering in polymer electrolyte membranes. We have demonstrated that the anharmonic two-state empirical valence bond model is capable of describing efficiently excess proton transport through the Grotthuss hopping mechanism within the simplicity of the theoretical framework. To explore the long-time diffusion behavior in perfluorosulfonic acid membranes with statistical certainty, simulations that are longer than 10 ns are needed. The contribution of the Grotthuss mechanism to the proton transport yields a larger fraction compared to the vehicular mechanism, when the estimated percolation threshold of λ = 5.6 is surpassed. The cluster analyses elicit a consistent outlook in regard to the relationship between the connectivity and the confinement of water clusters and proton transport. The cluster growth behavior findings reveal that, below the percolation threshold, the water domains grow along the channel length to form the connected, elongated clusters, thus contributing to an increase in connectivity and a decrease in confinement, whereas above the percolation threshold the channel widths of water domains increase, while the elongated structure of clusters is retained, thereby contributing to further confinement decreases.