Ionomers are thermoplastics that contain a relatively low content of ionic functional groups in the polymer backbone. Due to the energy difference between the nonpolar carbon chains and the polar functional groups, clustering of the ion-rich zones appears, leading to a nanoseparation of the two regions, the ion-rich domains acting as physical crosslinks. These regions go to a morphological transformation, which is responsible for an endothermic peak at low temperature, visualized in a DSC. Using a sodium neutralized poly(ethylene-random-methacrylic acid) (E/MAA) ionomers here we show it to be the result of two different and dependent morphological transformations, i.e. relaxation of the ionic aggregates and molecular reordering of ethylene chain segments. These two events were separated applying a hydrothermal treatment that swells the ionic clusters and thickens the secondary PE crystals. Water plasticizes the ionic aggregates, downshifting their glass transition temperature. On the other hand the endothermic peak due to the molecular reordering of the thicker secondary crystals independently shifts upwards. The relaxation of the ionic aggregates was detected either by static (DSC) or dynamic (DMTA) thermal analysis. The reordering of ethylene segments were observed optically by cross-polarized transmitted light intensity and X-Ray diffraction pattern. Both, primary and secondary PE crystals, after either dry or wet thermal annealing improve the PE chains packing by expelling out the non-crystallizable methacrylic comonomer mers.