The ceramic artefacts, excavated from ancient shipwrecks, are generally saturated with soluble salts, mainly NaCl, within the porous structure of ceramics. The salinity contents typically exhibit ionic and osmotic pressures to the ceramic microstructures, thus causing significant damages to the integrity of ceramic artefacts. While the utilisation of aqueous soaking methods is commonly accepted for effective desalination processes of ceramics, the relationships between the structural characteristics of ceramics and the desalination efficiency have not been demonstrated. In this study, we examined the desalination processes of various ceramics excavated from the Taean shipwrecks in South Korea to identify major controlling factors for the desalination processes. Our results indicated that the physical properties of ceramics including the water absorption and the pore size distribution greatly influence on the desalination process time and efficiency. It is also found that the surface condition of ceramic samples such as microstructural cracks on the glaze layer is a crucial component of the desalination characteristics. Nevertheless, the small residue of salts such as NaCl crystals were found in the microstructures of some ceramics after prolonged desalination periods. Therefore, it is important to control the humidity and temperature in the conservation environment for desalinated ceramic artefacts even after desalination.