Dissipative particle dynamics simulations have been utilized to study the morphology of the short-side-chain (SSC) perfluorosulfonic acid (PFSA) ionomer as a function of equivalent weight (EW) and degree of hydration. Equilibrated morphologies were determined for SSC PFSA membranes with EWs of 678 and 1278 g/mol at hydration levels corresponding to 5, 7, 9, 11 and 16 H 2 O/SO 3 H. Water contour plots reveal that isolated water clusters at lower water contents increase in size with increasing hydration, and form continuous water domains at the highest hydration level. The ionomer with an EW=1278 induces stronger aggregation of the water and results in larger water domains that are less connected when compared to the lower EW ionomer at 16 H 2 O/SO 3 H. The size of the water clusters are estimated from radial distribution functions and indicate that the spacing between the water domains increases with increasing EW of the ionomer.