Stimuli-responsive microgels are colloidal particles and promising candidates for applications such as targeted drug delivery, matrices for catalysts, nanoactuators and smart surface coatings. To tailor the response, the architecture of microgels is of paramount importance with respect to these applications. Statistical copolymer microgels based on N-isopropylmethacrylamide (NiPMAM) and N-n-propylacrylamide (NnPAM) show a cooperative phase transition leading to a collapse at a specific temperature. Interestingly, some core-shell microgel particles reveal a linear response of the hydrodynamic radius with temperature. Such observations were made by photon correlation spectroscopy (PCS), which is limited to the diffusion properties dominated by the particle shell. In this work we investigate the molecular hydration within the network of microgels in H2O by temperature-dependent FTIR spectroscopy. The phase transition temperature was determined by the shift in frequency of the NH bending vibration in homopolymer and statistical copolymer microgels and the results are in accordance with those from PCS. In contrast, experiments on core-shell particles show a broadening and shift of the respective phase transition temperatures of core and shell indicating an interaction of core and shell polymers on a molecular level that extends far into the core. In conclusion, temperature-dependent FTIR spectroscopy is a convenient approach to elucidate the internal architecture of complex microgel particles in H2O.