We have investigated the nanostructure of five ionenes based on three different benzimidazolium- and imidizolium-based backbones as a function of hydration using atomistic molecular dynamics simulations supplemented with X-ray scattering. All five samples reveal sponge-like nanostructures with near-complete percolation, even at low degrees of hydration, and no evidence of long-range phase separation. Analysis of the structure and ion dynamics shows that, while connectivity is highest among the samples functionalized with methyl alkylating units, the ionic pathways in the imidizolium-based backbones functionalized with butyl alkylating units are less tortuous, leading to faster ion diffusion at low water content.