A study of the differences among the capacitances of freshly exfoliated highly ordered pyrolytic graphite (HOPG, sample denoted FEG), HOPG aged in air (denoted AAG), and HOPG aged in an inert atmosphere (hereafter IAG) is presented in this work. The FEG is found to be more hydrophilic than AAG and IAG because the aqueous electrolyte contact angle (CA) increases from 61.7° to 72.5° and 81.8° after aging in Ar and air, respectively. Electrochemical impedance spectroscopy shows the FEG has an intrinsic capacitance (6.0 μF cm–2 at the potential of minimum capacitance) higher than those of AAG (4.3 μF cm–2) and IAG (4.7 μF cm–2). The observed changes in the electrochemical response are correlated with spectroscopic characterization (Raman spectroscopy and X-ray photoelectron spectroscopy), which show that the surface of HOPG was doped or contaminated after exposure to air. Taken together, these changes upon atmospheric exposure are attributed to oxygen molecule, moisture, and airborne organic contaminations: high-vacuum annealing was applied for the removal of the adsorbed contaminants. It was found that annealing the aged sample at 500 °C leads to partial removal of the contaminants, as gauged by the recovery of the measured capacitance. To the best of our knowledge, this is first study of the effect of the airborne contaminants on the capacitance of carbon-based materials.