This study investigated and compared the thermodynamic stability, kinetic behaviour, and effectiveness of a water purification process using pentafluoroethane (HFC125a) and 1,1,1,2-tetrafluoroethane (HFC134a) as guest molecules. The hydrate phase equilibria of each fluorinated gas (F-gas) in pure water and NaCl solution were predicted using the Hu-Lee-Sum correlation, which agreed well with the experimental results from our previous studies. Under the same subcooling temperature of 3 K (at 0.3 MPa), the rate of hydrate growth with HFC134a was faster than that of HFC125a in the absence or presence of NaCl. In situ Raman spectroscopy confirmed that the HFC134a and HFC125a molecules occupy only a large cage of structure II hydrate. The Raman shifts of C H and C C bands in all phases (gas, liquid, and hydrate phases) of HFC125a shifted to higher wavelengths than those of HFC134a due to the increase in the number of fluorine atoms. The change in the salinity was studied to evaluate the effectiveness of an F-gas hydrate-based water purification process. In addition, the desalination efficiency of the HFC134a and HFC125a hydrates was compared by separating hydrate crystals from the slurries. The results showed that the desalination efficiency (or total dissolved solids removal efficiency) of HFC134a hydrate was higher than that of HFC125a hydrate. This study proves the importance of the water purification process using hydrates.