Short side-chain ionomers such as Aquivion are increasingly used in the fabrication of polymer electrolyte membrane fuel cells. Aquivion exhibits reduced gas crossover, enhanced glass transition temperature, better mechanical stability, and higher conductivity in comparison to Nafion, their long side chain relative. We performed atomistic molecular dynamics simulations of Aquivion at varying water contents and proportion of isopropanol mixed into the solvent and examined the structure and dynamics of the system. Atomistic simulations are followed by coarse-grained simulations to develop a coarse-grained model applicable to both long and short side chain ionomers. The density of Aquivion and Nafion membranes from simulations is calculated and compared with that from the experiment. The Aquivion system shows higher diffusion coefficients for water molecules and hydronium ions than the Nafion system. The water network morphology is analyzed as a function of water content.