Waterproofing treatment is important for the preservation of smectite-rich rocks because of their shrinking and swelling properties. The effects of water repellents on the smectite structure and the water sorption of untreated and treated smectites were studied using X-ray diffraction. The hydrophobic Wacker BS 290 (around 100% silane/siloxane) does not prevent water from sorbing on the interlayer surface of smectite because the hydrophobic silane/siloxane is not intercalated into the interlayer space, but adsorbed onto the external surface of smectite. However, the hydrophilic Wacker BS 1001 (water-soluble emulsified silane/siloxane) prevents water from sorbing onto the interlayer surface beyond 33.3 wt.% because the hydrophobic part of the intercalated surfactant has a poor affinity for water. These results imply that water repellent containing a surfactant is suitable for smectite-rich rocks, but the expansion of smectite by intercalation of the surfactant is likely to influence volume change in smectite-rich rocks. This study notes that smectite within a rock can be one of the most important factors influencing the effectiveness of waterproof treatment. This study proposes that an intensive preliminary examination should be performed before applying water repellents to rocks, and furthermore, encourages development of new chemical reagents suitable for protecting smectite-rich rocks from moisture.