Nanocrystalline diamond (NCD) films are of great importance for many applications. They can be implemented as transparent protective coatings or for the use in electronic devices, sensor systems, and bioelectronic systems. In many applications the surface properties dictate the eventual performance of the device and, therefore, need to be thoroughly understood. This paper is devoted to investigating the changes occurring in the vibrational structure and surface chemical composition of hydrogen-containing NCD films as a function of annealing treatments as well as exposure to atomic hydrogen. High resolution electron energy loss spectroscopy (HREELS) as a surface sensitive method was utilized to analyze the temperature-correlated desorption of hydrogen and graphitization of the surface. These measurements were correlated with X-ray-induced photoelectron spectroscopy (XPS) measurements to study the chemical composition. Results indicate that water and graphitic-like contaminations are removed from the sample surface after annealing up to about 350 °C. Annealing the sample up to 950 °C decreases the hydrogen content drastically. At temperatures up to 1050 °C the CH stretching and bending modes are not detectable, indicating that the hydrogen is totally removed from the surface. Analysis of the C 1s XPS spectra revealed that a graphitic-like phase is formed. An atomic hydrogen treatment was applied to get further information about the surface composition. Additionally, from our HREELS and XPS data we are able to determine the sp2/sp3 ratio for the different surface treatments.