The temperature-induced structural changes and thermodynamics of ionic microgels based on poly(acrylic acid) (PAA) networks bonded with poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO-PPO-PEO) (Pluronic) copolymers have been studied by small-angle neutron scattering (SANS), ultra-small-angle neutron scattering (USANS), differential scanning calorimetry (DSC), and equilibrium swelling techniques. Aggregation within microgels based on PAA and either the hydrophobic Pluronic L92 (average composition, EO8PO52EO8; PPO content, 80%) or the hydrophilic Pluronic F127 (average composition, EO99PO67EO99; PPO content, 30%) was studied and compared to that in the solutions of the parent Pluronic. The neutron scattering results indicate the formation of micelle-like aggregates within the F127-based microgel particles, while the L92-based microgels formed fractal structures of dense nanoparticles. The microgels exhibit thermodynamically favorable volume phase transitions within certain temperature ranges due to reversible aggregation of the PPO chains, which occurs because of hydrophobic associations. The values of the apparent standard enthalpy of aggregation in the microgel suspensions indicate aggregation of hydrophobic clusters that are more hydrophobic than the un-cross-linked PPO chains in the Pluronic. Differences in the PPO content in Pluronics L92 and F127 result in a higher hydrophobicity of the resulting L92-PAA-EGDMA microgels and a larger presence of hydrophobic, densely cross-linked clusters that aggregate into supramolecular structures rather than micelle-like aggregates such as those formed in the F127-PAA-EGDMA microgels.