In situ calibration of a sample's mechanical properties in different mediums is of vital importance for engineering and biomedical applications. In this paper, we describe the nanomechanical calibration of two copper specimens with different roughness in dry nitrogen and deionized water. The hardness (H), reduced elastic modulus (Er), and creep properties of the copper specimen were accurately measured by a nanoindenter. Indentations on the two specimens were performed in both mediums by a spherical fluid cell probe (FCP). It is found that there is no apparent difference in both media for a smooth surface, and this demonstrates the validation of the FCP and the apparatus. Meanwhile, for rough surfaces, the maximum depth measured in a liquid at a given load is larger than that in nitrogen, thus the measured mechanical properties decrease, especially for rough surfaces. A molecular dynamics (MD) model is employed for further investigation of the indentation behaviours and the interaction mechanism at the liquid-solid interface. Our simulation results show that the liquid molecules confined in the narrow surface roughness valleys enlarge the maximum indention depth of the probe tip in a wetting environment, and this results in the corresponding change in the measured mechanical properties.