Water is a critical volatile component in planetary bodies and plays a key role in the Earth’s dynamic evolution. Traditional methods to analyze water in either mineral or glass phases are usually limited to areas larger than 10 microns. The advent of secondary ion mass spectrometry (SIMS), especially nanoscale SIMS (NanoSIMS), has enabled in situ analysis at micron- to submicron scales. However, there is an increasing demand to quantify water content at much finer scales, including those recovered from high-pressure experiments or nanoscale planetary materials. This study demonstrates the ability of atom probe tomography (APT) to investigate the distribution of hydroxyl water in glass at sub-nanoscale resolution. Five glass working standards with trace amounts of water were analyzed to demonstrate that the OH+ mass spectrum obtained by APT could potentially represent the hydroxyl content of the glass. The detection limit of the APT was determined to be better than 0.02 atomic %. The heterogeneity of APT OH+ in the form of nanoclusters in glass was readily discerned, and its concentration in the nanoclusters increased proportionally to the water content in the studied samples. These findings provide valuable insights into the sub-nanoscale distribution of hydroxyl water in glasses and establish APT as a promising tool for characterizing water at an ultra-high spatial resolution.