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Interfacial water participates in a wide range of phenomena involving graphite, graphite-like and 2D material interfaces. Recently, several high-spatial resolution experiments have questioned the existence of hydration layers on graphite, graphite-like and 2D material surfaces. Here, 3D AFM was applied to follow in real-time and with atomic-scale depth resolution the evolution of graphite–water interfaces. Pristine graphite surfaces upon immersion in water showed the presence of several hydration layers separated by a distance of 0.3 nm. Those layers were short-lived. After several minutes, the interlayer distance increased to 0.45 nm. At longer immersion times (∼50 min) we observed the formation of a third layer. An interlayer distance of 0.45 nm characterizes the layering of predominantly alkane-like hydrocarbons. Molecular dynamics calculations supported the experimental observations. The replacement of water molecules by hydrocarbons on graphite is spontaneous. It happens whenever the graphite–water volume is exposed to air.