Archaeal rhodopsins possess retinal molecule as their chromophores, and their light-energy and light-signal conversions are triggered by all-trans to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of protein then leads to functional processes, light-driven ion pump or transducer activation. Internal water molecules were considered to play an important role in the functional processes of archaeal rhodopsins, although limited information has been obtained about the structure and function of internal water molecules. Recent progress in Fourier-transform infrared (FTIR) spectroscopy and X-ray crystallography provided new information of water molecules inside archaeal rhodopsins. This article reviews studies on internal water molecules of archaeal rhodopsins by means of low-temperature FTIR spectroscopy.