Nanostructured polyelectrolyte membranes (PEM) are widely used as perm-selective diffusion barriers in fuel cell technologies and electrochemical processing. For example, in Nafion polymer hydrophilic sulfonate sidechains are attached to a hydrophobic perfluorocarbon backbone. Upon hydration, PEM segregate into hydrophobic and hydrophilic subphases. The former is made by the hydrophobic backbone; the latter comprises water, counterions and polymer sidechains, forming a dynamic network of nanochannels in the hydrophobic organic matrix. Mesoscale simulations of nanoscale segregation in PEM provide a powerful tool for optimization of the polymer structure and membrane composition. We describe two different approaches to mesoscale modeling of PEM, using Nafion and sulfonated polystyrene-polyolefine-polystyrene triblocks as examples. First, we developed a dissipative particle dynamics scheme suitable for PEM, which includes smearing of the charges of ionic groups and conservative DPD parameters obtained from thermodynamic properties of reference solutions. The second approach to mesoscale modeling of PEM is based on self-consistent field (SCF) theory, which we extended to triblock ionomers. SCF is parameterized from available experiments and thermodynamic properties of reference solutions. With these techniques we explored nanosegregarion in Nafion and sSEBS. We predicted the morphology of hydrated Nafion with equivalent weight between 1200 and 1800D and 4-17 wt % water content, observing a transition between separated hydrophilic clusters and a continuous 3D network of hydrophilic channels. No regular morphology in Nafion was detected. In sSEBS, the morphology was more regular, transiting from reverse micelles at lower hydration to lamellae and even reverse micelles as water and DMMP content increased. We discuss the influence of polymer composition and hydration on the shape and connectivity of hydrophilic channels. Using this information on the membrane morphology, we perform lattice Monte Carlo simulations of water and chemical agent transport through PEMs and compare our results with the experiments.