We report the intrinsic water contact angle (WCA) of multilayer graphene, explore different methods of cleaning multilayer graphene, and evaluate the efficiency of those methods on the basis of spectroscopic analysis. Highly ordered pyrolytic graphite (HOPG) was used as a model material system to study the wettability of the multilayer graphene surface by WCA measurements. A WCA value of 45° ± 3° was measured for a clean HOPG surface, which can serve as the intrinsic WCA for multilayer graphene. A 1 min plasma treatment (100 W) decreased the WCA to 6°, owing to the creation of surface defects and functionalization by oxygen-containing groups. Molecular dynamics simulations of water droplets on the HOPG surface with or without the oxygen-containing defect sites confirmed the experimental results. Heat treatment at near atmospheric pressure and wet chemical cleaning methods using hydrofluoric acid and chloroform did not change the WCA significantly. Low-pressure, high-temperature annealing under argon and hydrogen reduced the WCA to 54°, close to the intrinsic WCA of HOPG. Raman spectroscopy and atomic force microscopy did not show any significant change for the HOPG surface after this treatment, confirming low-pressure, high-temperature annealing as an effective technique to clean multilayer graphene without damaging the surface. Time-of-flight secondary ion mass spectrometry indicated the existence of hydrocarbon species on the surface of the HOPG sample that was exposed to air for <5 min and the absence of these impurities in the bulk. X-ray photoelectron spectroscopy analyses of the sample surfaces after the different cleaning techniques were performed to correlate the WCA to the surface chemistry. X-ray photoelectron spectroscopy results revealed that the WCA value changed drastically, depending on the amounts of oxygen-containing and hydrocarbon-containing groups on the surface.