Hydrated ion-containing polymer membranes are used as electrolytes in a variety of applications, including in fuel cells and in alkaline batteries. Achieving high conductivity typically requires the hydrophobic backbone of the polymers to be nano-phase separated from the hydrophilic domains so that the ions (protons or hydroxide ions) have well-defined water channels for efficient transport. The ion transport thus depends strongly on the hydration level and the detailed morphology of the hydrophilic domains. It is often difficult to determine the morphology of these domains experimentally. Here I will present results from atomistic molecular dynamics (MD) simulations that reveal the domain morphology in three different ion-containing polymers. In all cases, increasing water content leads to the swelling of and an increase in the characteristic spacing between hydrophilic domains. However, this swelling can be obscured in X-ray scattering due to a loss of scattering contrast between the hydrophobic and hydrophilic domains. The MD simulations reveal that the systems are still nano-phase separated, even when X-ray scattering appears to indicate otherwise. Calculated and measured scattering profiles are in good qualitative agreement. Ion diffusivities calculated from the MD simulations follow the experimentally-measured trends in conductivity and are consistent with changes in the nanoscale morphology with changing water content. I will discuss implications of the results for the future design of ion-conducting polymers.