The application of penetrating water repellent sometimes accelerates degradation of building materials, especially when there are water sources inside such as ground water. A series of experiments using the gamma-ray attenuation method and numerical analysis corresponding to the experiments were performed to reveal the moisture behavior in building materials treated with silane water repellent and to develop a proper numerical model for the repellent layer. The experimental and calculation results show a large difference in water content between the repellent layer and the substrate, which may cause the abovementioned problems.