Controlling the structure of colloidal nanocrystals (NCs) is key to the generation of their complex functionality. This requires an understanding of the NC surface at the atomic level. The structure of colloidal PbS NCs passivated with oleic acid has been studied theoretically and experimentally. We show the existence of surface OH-groups, which play a key role in stabilizing the PbS(111) facets, consistent with x-ray photoelectron spectroscopy as well as other spectroscopic and chemical experiments. The role of water in the synthesis process is also revealed. Our model, along with existing observations of NC surface termination and passivation by ligands, helps to explain and predict the properties of NCs and their assemblies.