Various kinds of heritages, such as architectures, statues, grave posts and towers, are made by stone, and they are facing the crisis of weathering. Therefore, it is necessary to give appropriate treatments to keep them in good conditions. Kyushu Research Institute for Cultural Properties Inc. and Kumamoto University introduced a new method, Aquo-Siloxane Method, in order to protect the stone heritages. In this study, preservation effect by AquoSiloxane method towards water permeation and material diffusion was verified. Here one-dimensional permeation and diffusion tests were conducted, and the intrinsic permeability and diffusion coefficient of rock samples with and without Aquo-Siloxane treatments were evaluated. As rock samples, 3 types of sandstones and concrete were applied. It was found that the permeability decreased to less than 1/10 to 1/100 of without Aquo-Siloxane treatment, and that the effect gradually developed during more than one year. One-dimensional diffusion tests were also conducted, and the diffusion process in rock samples are visualized by X-ray CT scanner system. It was confirmed internal structures of samples are clearly visualized, and that the diffusion process was also visualized as X-ray CT images. In order to extract the necessary information due to diffusion, image subtraction method was applied to image data. Then, by comparing obtained CT image data and numerical solutions, diffusion coefficients of rock samples with and without Aquo-Siloxane treatments were evaluated. As a result, diffusion coefficients also became smaller by applying Aquo-Siloxane treatments. It is revealed that material movement due to diffusion was also efficiently suppressed by applying Aquo-Siloxane method. Finally, Aquo-Siloxane method was applied to a stone heritage. It was found that no more chippings and cracks were observed and that the heritage has been kept in good condition for at least four years.