Interface phenomena are the starting point for every corrosion reaction. In this work, the corrosion of calcium–silicate–hydrate (C–S–H) phases by water is investigated by implementing silicon wafers as substrates. The carbonation of these phases was avoided by synthesizing the samples in a controlled atmosphere. The passivation of these mineral surfaces is a significant step for materials sustainability. The coating of the surfaces with four different molecules is presented here: carbonation, sodium silicate layers, tetraethyl orthosilicates (TEOS), and octadecylphosphonic acid (ODPA) monolayers. The performance of every technique against corrosion by water is evaluated by infrared spectroscopy, inductively coupled plasma optical emission spectroscopy, water contact angle, and pH measurements. Since the concentration of protons in water is the relevant parameter in this corrosion process, three different values were analyzed at the experiments. After comparing the passivation techniques, the results obtained by coating with ODPA are the most promising ones, and it is, therefore, applied to a more realistic model: hydrated cement. The passivation by ODPA is then analyzed to unravel the mechanism of hydrophobization, finding its dependence with the Ca/Si ratio of the surfaces, supported by first-principles calculations. The passivation by applying this kind of molecule is very promising because of its efficiency against water corrosion and due to the easiness of preparation of the surface before its application.