A simple lattice model for simulating water-containing ionomer membranes is presented. It consists of water molecules, hydronium ions and coarse-grained representations of sulfonated polymer entities with and without side chains. Nafion® can be represented by a polymer entity, which is sulfonated at the end of the short pendant side chain. Similarly, polyphenylene-ether-keto compounds such as sulfonated sPEEK can be represented by the main chain sulfonated entity. Lattice Monte Carlo simulations on a diamond lattice of two model compounds show that the aqueous domains increase in size with increasing water content. They also show that the compound with side chain sulfonation forms larger and less rugged water domains than the main chain sulfonated compound. This behavior is in good agreement with literature data on small angle X-ray and neutron scattering experiments of Nafion® and sPEEK, suggesting that the observed differences are partly a consequence of molecular topology.