Poly(N-isopropylacrylamide) (PNIPAM) microgels and PNIPAM colloidal shells attract continuous strong interest due to their thermoresponsive behavior, as their size and properties can be tuned by temperature. The direct single particle observation and characterization of pure, unlabeled PNIPAM microgels in their native aqueous environment relies on imaging techniques that operate either at interfaces or in cryogenic conditions, thus limiting the observation of their dynamic nature. Liquid Cell (Scanning) Transmission Electron Microscopy (LC-(S) TEM) imaging allows the characterization of materials and dynamic processes such as nanoparticle growth, etching, and diffusion, at nanometric resolution in liquids. Here we show that via a facile post-synthetic in situ polymer labelling step with high-contrast marker core–shell Au@SiO2 nanoparticles (NPs) it is possible to determine the full volume of PNIPAM microgels in water. The labelling allowed for the successful characterization of the thermoresponsive behavior of PNIPAM microgels and core shell silica@PNIPAM hybrid microgels, as well as the co-nonsolvency of PNIPAM in aqueous alcoholic solutions. The interplay between electron beam irradiation and PNIPAM systems in water resulted in irreversible shrinkage due to beam induced water radiolysis products, which in turn also affected the thermoresponsive behavior of PNIPAM. The addition of 2-propanol as radical scavenger improved PNIPAM stability in water under electron beam irradiation.