Previous experiments of water vapor penetration into polyelectrolyte membrane (PEM) thin films have indicated the influence of the water concentration gradient and polymer chemistry on the interface evolution, which will eventually affect the efficiency of the fuel cell operation. Moreover, PEMs of different side chains have shown differences in water cluster structure and diffusion. The evolution of the interface between water and polyelectrolyte membranes (PEMs), which are used in fuel cells and flow batteries, of three different side-chain lengths has been studied using dissipative particle dynamics (DPD) simulations. Higher and faster water uptake is usually beneficial in the operation of fuel cells and flow batteries. The simulated water uptake increased with the increasing side chain length. In addition, the water uptake was rapid initially and slowed down afterwards, which is in agreement with the experimental observations. The water cluster formation rate was also found to increase with the increasing side-chain length, whereas the water cluster shapes were unaffected. Water diffusion in the membranes, which affects proton mobility in the PEMs, increased with the side-chain length at all distances from the interface. In conclusion, side-chain length was found to have a strong influence on the interface water structure and water penetration rates, which can be harnessed for the better design of PEMs. Since the PEM can undergo cycles of dehydration and rehydration, faster water uptake increases the efficiency of these devices. We show that the longer side chains with backbone structure similar to Nafion should be more suitable for fuel cell/flow battery usage.