Molecular-dynamics simulations were used to study the structure of water clusters in different perfluorinated ionomers. The ionomers included in this work were Perfluorosulfonic Acid (PFSA) and Perfluoroimide Acid (PFIA). Different shapes and sizes of water domains in PFSA and PFIA were observed. In PFSA, ionomer water domains have spherical-like shape while water domains have complicated branch structure in PFIA ionomer. The mean water-cluster size for PFSA and PFIA ionomers as a function of water content lie on one universal curve, which indicates that the size of water clusters depends primarily on water content and weakly on ionomer chemistry. In PFSA, almost all hydronium ions are located predominantly close to the water cluster/backbone interface for both large and small values of water content; while in PFIA a relatively large fraction of hydronium ions are distributed within the bulk of the water clusters. A similar distribution of acidic groups was observed in both ionomers. In PFSA ionomer, all sulfonic groups are located in the surface water layer at the distance from 3 Å to 6 Å from the backbone. In PFIA ionomer, approximately 60% of sulfonic groups are located in the surface water layer and 40% of sulfonic groups are immersed into the bulk of water cluster. Perfluorinated ion-exchange membranes are widely used in both fuel cells and flow-battery cells. Flow batteries, such as vanadium redox batteries (VRBs), are promising devices for the large-scale Electrical Energy Storage (EES) applications 1 and are receiving increasing interest due to the demand for grid-scale EES solutions and recent improvements in VRB cell performance.2 The ion-exchange membrane is a critical component in these different types of electrochemical flow cells, which conducts the charge-carrier ions (e.g., protons) while preventing the flow of electrons through it. Additionally, in a flow-battery cell, the membrane separates the positive and negative liquid electrolytes containing the active redox-species ions. For example, in a VRB cell, it is desirable to prevent the crossover of vanadium ions through the membrane since the result is a decrease in both the energy efficiency and energy capacity of the VRB system. 2,3 In VRBs, this energy-capacity loss is recoverable, since the vanadium can be simply rebalanced by pumping some of the electrolyte with the excess V to the other electrolyte tank (albeit with an additional energy loss due to self-discharging that results from mixing the two reactants). In flow-battery chemistries with dissimilar active-species ions (e.g., Fe-Cr systems), crossover can also cause contamination of the electrolytes and/or electrodes, which can result in additional adverse effects on the flow-battery system. 1 In any case, the activespecies ions are transported through the membrane in the hydrophilic phase (i.e., the water clusters) of the membrane. Therefore, the study of the water-cluster structure is required to understand and model the transport of different ions in the membrane. One of the ultimate...