The ability to examine the vibrational spectra of liquids with nanometer spatial resolution will greatly expand the potential to study liquids and liquid interfaces. In fact, the fundamental properties of water, including complexities in its phase diagram, electrochemistry, and bonding due to nanoscale confinement are current research topics. For any liquid, direct investigation of ordered liquid structures, interfacial double layers, and adsorbed species at liquid–solid interfaces are of interest. Here, a novel way of characterizing the vibrational properties of liquid water with high spatial resolution using transmission electron microscopy is reported. By encapsulating water between two sheets of boron nitride, the ability to capture vibrational spectra to quantify the structure of the liquid, its interaction with the liquid‐cell surfaces, and the ability to identify isotopes including H2O and D2O using electron energy‐loss spectroscopy is demonstrated. The electron microscope used here, equipped with a high‐energy‐resolution monochromator, is able to record vibrational spectra of liquids and molecules and is sensitive to surface and bulk morphological properties both at the nano‐ and micrometer scales. These results represent an important milestone for liquid and isotope‐labeled materials characterization with high spatial resolution, combining nanoscale imaging with vibrational spectroscopy.