This study focused on the structure and physical properties of acid-treated bentonite L45 from the Lieskovec deposit (Slovakia). New applications of near infrared and visible spectroscopies were used to follow Fe-montmorillonite dissolution and layer-charge reduction. Progressive dissolution of L45 results in the formation of a protonated amorphous silica phase. The OH overtone at 7312 cm−1 revealed the creation of Si–OH groups in the mildly treated samples. The area of the Si–O–Moct band, as obtained by a peak-fitting procedure, is a sensitive indicator of the changes in the octahedral sheets. Ultraviolet-visible (UV-VIS) spectroscopy of the smectite dispersions with methylene blue (MB) is an efficient method for controlling the acid activation process of bentonites. The results reveal that acid treatment causes a substantial layer-charge reduction, probably due to prevailing dissolution of MgO4(OH)2 polyhedra in the octahedral sheets. The layer-charge reduction is proportional to the structural changes and to the extent of mineral decomposition upon acid treatment.