In-situ FTIR spectroscopy was used to investigate the dehydration mechanism of naturally occurring scolecite from the Deccan traps. The dehydration and rehydration processes were studied by monitoring the thermally induced variations of fundamental bending (v2) and stretching (v3 and v1) modes of the water molecules in the range 1550–1800 cm−1 and 3000–3600 cm−1, as well as the corresponding second-order modes in the wavenumber region 4000–8000 cm−1. Completely reversible spectral variations of the fundamental modes indicate that the transformation of scolecite to meta-scolecite at 495 K is reversible. Two-step dehydration behaviour is clearly observed in the thermally induced variations of the second-order modes. A combination mode in scolecite, due to Al-OH bonding around 4609 cm−1, is seen to disappear in the meta-scolecite phase. Growth of a new mode around 4485 cm−1 is observed in the temperature range 630–675 K, indicating the presence of hydroxyl groups in the amorphous phase, created by the breaking of T-O-T bonds.