Near-infrared (NIR) and mid-infrared (MIR) spectroscopy are irreplaceable methods for characterization of bentonites. The paper presents work on bentonites modified with inorganic Na+ and organic HDTMA+ (hexadecyltrimethylammonium) cations and treated by 1.5, 3, 4.5 and 6 M H2SO4. The characterization was based on the assignment of the stretching (ν) and bending (δ) vibrations observed in the MIR region and the first overtone [2ν(R–H)] and combination [ν(R–H) + δ(R–H)] modes of R–H groups (R = O, C) in the NIR region. NIR spectrum shows the characteristic OH and CH bonds for organomontmorillonite. The effect of larger alkylammonium cations on the vibrations of Si–O and OH bonds in montmorillonite layers is observed. A few key-bands in the NIR region show the change of water in the interlayer montmorillonite. The intensities of the overtone (7080 and 6840 cm−1) and combination (5242 cm−1) bands of H2O have considerably decreased as a result of hydrophobic character of the NaOM. Spectra of acid-treated samples show a gradual decrease in the intensities of the OH overtone (near 7100–7000 cm−1) and combination bands (4600–4300 cm−1) reflecting a fewer number of octahedral atoms. This paper also points out that ATR technique and the 2nd derivative spectrum enables much precise band assignment.