The demand for oil is increasing, but many reservoirs are reaching the end of their productive lifetime. A clearer understanding of the fundamental chemical and physical controls on the wetting behavior of reservoir pore surfaces would provide clues for developing methods to improve, or enhance, recovery of the currently inaccessible oil (improved/enhanced oil recovery, IOR/EOR). In this work, the surfaces of chalk were investigated to understand hydrophobicity at nanometer scale spatial resolution. Chalk samples from the gas and water zones of the Danish sector in the North Sea Basin were used. With inverse gas chromatography (IGC), the surface characteristics were compared. Chalk from the gas zone has a lower surface energy, dispersive as well as specific, than chalk from the water zone, clearly indicating that the gas zone pore surfaces are more hydrophobic. X-ray photoelectron spectroscopy shows that the concentration of hydrocarbons is higher in gas zone chalk than in water zone chalk, which is consistent with IGC measurements. With combined atomic force microscopy and chemical force mapping, we demonstrated that the hydrophobicity of chalk is not correlated spatially with the calcite of the coccolith elements, but rather with nanometer-sized authigenic clay crystals that decorate the surfaces of the coccoliths. Our results suggest that clay and adsorbed organic material, not calcite, are responsible for wettability alterations in chalk during the introduction of hydrocarbons. Furthermore, we show that surface hydrophobicity is heterogeneous, even within single-clay laths.