The present work studies the incorporation of hydrogen and its bonding configuration in diamond films composed of diamond grains of varying size which were deposited by three different methods: hot filament (HF), microwave (MW), and direct current glow discharge (dc GD) chemical vapor deposition (CVD). The size of diamond grains which constitute the films varies in the following way: hundreds of nanometers in the case of HF CVD (“submicron size,” ∼300 nm), tens of nanometers in the case of MW CVD (3–30 nm), and a few nanometers in the case of dc GD CVD (“ultrananocrystalline diamond,” ∼5 nm). Raman spectroscopy, secondary ion mass spectroscopy, and high resolution electron energy loss spectroscopy (HR-EELS) were applied to investigate the hydrogen trapping in the films. The hydrogen retention of the diamond films increases with decreasing grain size, indicating that most likely, hydrogen is bonded and trapped in grain boundaries as well as on the internal grain surfaces. Raman and HR-EELS analyses show that at least part of this hydrogen is bonded to sp2- and sp3-hybridized carbon, thus giving rise to typical CH vibration modes. Both vibrational spectroscopies show the increase of (sp2)-CH mode intensity in transition from submicron to ultrananocrystalline grain size. The impact of diamond grain size on the shape of the Raman and HR-EELS hydrogenated diamond spectra is reported and discussed.