Small-angle neutron scattering (SANS) and ultra-small-angle X-ray scattering (USAXS) have been used to study the structural changes in fluorinated polyisoprene/sulfonated polystyrene (FISS) diblock copolymers as they evolved from the dry state to the water swollen state. A dilation of the nanometer-scale hydrophilic domains has been observed as hydration increased, with greater dilation occurring in the more highly sulfonated samples or upon hydration at higher temperatures. Furthermore, a decrease in the order in these phase separated structures is observed upon swelling. The glass transition temperatures of the fluorinated blocks have been observed to decrease upon hydration of these materials, and at the highest hydration levels, differential scanning calorimetry (DSC) has shown the presence of tightly bound water. A precipitous drop in the mechanical integrity of the 50% sulfonated materials is also observed upon exceeding the glass transition temperature (Tg), as measured by dynamic mechanical analysis (DMA).